review article the roles of snf2/swi2 nucleosome ...jbp2 drd1 rad54 lodestar rad5/16 ris1 shprh adp...

Review ArticleThe Roles of SNF2SWI2 Nucleosome Remodeling Enzymes inBlood Cell Differentiation and Leukemia

Punit Prasad Andreas Lennartsson and Karl Ekwall

Department of Biosciences and Nutrition Karolinska Institute 141 57 Huddinge Sweden

Correspondence should be addressed to Punit Prasad punitprasadkise and Karl Ekwall karlekwallkise

Received 23 November 2014 Accepted 27 January 2015

Academic Editor Andre Van Wijnen

Copyright copy 2015 Punit Prasad et al This is an open access article distributed under the Creative Commons Attribution Licensewhich permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited

Here we review the role of sucrose nonfermenting (SNF2) family enzymes in blood cell development The SNF2 familycomprises helicase-like ATPases originally discovered in yeast that can remodel chromatin by changing chromatin structureand composition The human genome encodes 30 different SNF2 enzymes SNF2 family enzymes are often part of multisubunitchromatin remodeling complexes (CRCs) which consist of noncatalyticauxiliary subunit alongwith theATPase subunit Howeverblood cells express a limited set of SNF2 ATPases that are necessary to maintain the pool of hematopoietic stem cells (HSCs) anddrive normal blood cell development and differentiation The composition of CRCs can be altered by the association of specificauxiliary subunits Several auxiliary CRC subunits have specific functions in hematopoiesis Aberrant expressions of SNF2 ATPasesandor auxiliary CRC subunit(s) are often observed in hematological malignancies Using large-scale data from the InternationalCancer Genome Consortium (ICGC) we observed frequent mutations in genes encoding SNF2 helicase-like enzymes and auxiliaryCRC subunits in leukemia Hence orderly function of SNF2 family enzymes is crucial for the execution of normal blood celldevelopmental program and defects in chromatin remodeling caused by mutations or aberrant expression of these proteins maycontribute to leukemogenesis

1 Introduction

The gene encoding the first SNF2SWI2 enzyme was dis-covered by the yeast geneticists Ira Herskowitz and MarianCarlson in the 1980s These researchers named the gene twodifferent names depending on the genetic screen used fortheir identification [1 2] sucrose nonfermenting mutant(SNF2) and mating-type switching mutant (SWI2) Analysisof chromatin from these mutants in vivo suggested thatthe gene products affected chromatin structure [3] Approxi-mately 10 years after their genetic discovery the yeast SWISNFprotein complex was purified It was demonstrated toremodel nucleosomes in vitro and to affect the binding ofthe transcription factor GAL4 [4]The yeast community nowuses the SNF2 gene name (httpwwwyeastgenomeorg)and we use this nomenclature in this review article

A SNF2 protein is an enzyme that belongs to the SF2helicase-like superfamily and it is the founding member of asubfamily of enzymes called SNF2-like helicases which allharbor a conserved helicase-related motifs similar to SNF2

[5] The SNF2 family proteins have multiple members whichare approximately 30 different enzymes in human cells (53different enzymes including all the splice variants) and 17different enzymes in budding yeast SNF2 enzymes can befurther classified into six groups based on the structureof the helicase domain These groups are Swi2Snf2-likeSwr1-like SS01653-like Rad54-like Rad56-like and distant(SMARCAL1) enzymes (Figure 1(a)) [5] Many of the SNF2enzymes have been shown to remodel chromatin in vitro in anATP-dependent manner and several enzymes remain to betested

Because SNF2 enzymes regulate DNA accessibility inchromatin fibers they are important regulators of geneexpression and genome stability SNF2 enzymes are key play-ers in epigenetic control They affect several epigenetic mod-ification processes including DNA methylation histonemodification histone variant exchange noncoding RNA andhigher order chromatin structure [6] SNF2 enzymes alsofunction downstream of epigenetic modifications targeted toacetylated chromatin via a special domains to remodel

Hindawi Publishing CorporationBioMed Research InternationalVolume 2015 Article ID 347571 17 pageshttpdxdoiorg1011552015347571

2 BioMed Research International

Helicase-like superfamily 2 (SF2)

ATP

Nucleosome sliding

Nuclesome spacing Nucleosome assembly

Histone dimer exchange

DNA accessibility

ncRNA expression

Transcription regulation

Histone eviction

Histone turnover

Outcome of chromatin remodeling

DEAD boxhelicases

RecGhelicases

Snf2 Type IIIIrestrictionenzymes

DEAHDExHhelicases

Snf2-like Swr1-like SSO1653-like Rad54-like Rad516-like SMARCAL1ALC1IswiCHD7Chd1Mi-2LshSnf2

EP400Swr1Ino80Etl1

ERCC6SSO1653Mot1

ATRXArip4JBP2DRD1Rad54

LodestarRad516Ris1SHPRH

ADP + Pi

(a)

B-cell

Monocytemacrophage

Neutrophil

Eosinophil

NK cell

Basophil

Mast cells

RBC

Megakaryocytes

HSC

CLP

CMP

GMP

MEP

CD4+ T-cell

CD8+ T-cell

(b)Figure 1 Classification of SNF2 enzymes and schema of mammalian hematopoiesis SNF2-like chromatin remodelers belong to SF2superfamily and are classified based on conserved structure of the ATPase domain as discussed in Flaus et al [5] (a) Overview of mammalianhematopoietic cell development and differentiation Dashed arrows show intermediate stages of hematopoietic development which is notshown in the figure for simplicity purpose (b)

chromatin For example the SNF2 enzyme SMARCA4Brg1is targeted via a Bromodomain [6 7]

Numerous in vivo and biochemical studies have beenemployed using different model organisms to address thedetailed effects of SNF2 enzymes on chromatin The chro-matin remodeling reaction can lead to nucleosome slidinghistone exchange histone eviction (disassembly) and nucle-osome spacing to form regular arrays or nucleosome assem-bly depending on both which SNF2 enzyme is used andwhether other cofactors such as histone chaperones areadded to the experiments (recently reviewed in [6]) Thedisassembly function is particularly important in gene regu-lation to ensure that promoter and enhancer DNA sequencesare accessible for transcription factors epigenetic modifiersand RNA polymerase II SNF2 enzymes are often part ofmultisubunit chromatin remodeling complexes (CRC) con-taining several auxiliary subunits

2 Chromatin Reorganizationduring Hematopoiesis

The hematopoietic system consists of two main cell lineagesthe myeloid and the lymphoid which both originate from

hematopoietic stem cells (HSCs) (Figure 1(b)) BrieflymultipotentHSCs differentiate to give rise to commonmyeloidprogenitors (CMPs) and common lymphoid progenitors(CLPs) Further differentiation ofCMPs yieldsmegakaryocyteerythroid progenitor (MEP) and granulocyte-monocyteprogenitor (GMP) The MEP differentiates and matures intoerythrocytes and megakaryocytes whereas the GMP dif-ferentiates into monocytes and granulocytes (neutrophilseosinophils and basophils) which are the first line of defenseagainst infections [8] CLPs give rise to T-cells B-cells andNatural Killer (NK) cells The lymphoid subtypes ofhematopoietic cells are crucial for adaptive immunity FinalB- T- and NK-cell maturation occur in the peripherallymphoid tissue where antigen selection takes place

Lineage choice and blood cell differentiation are tightlyregulated at several levels Different transcription factors (TFs)have been identified that together form a regulatory networkfor hematopoiesis (reviewed in [9]) Several TFs have beenshown to interact with epigenetic regulators including CRCssuch as theNucleosomeRemodeling anddeacetylase (NuRD)complex (reviewed in [8]) The importance of chromatinremodelers in hematopoiesis was recently suggested by two

BioMed Research International 3

studies which demonstrated a massive chromatin reorgani-zation during blood cell differentiation [10 11] Both studieselegantly showed how chromatin compaction is modified inenhancer regions during hematopoiesis in a lineage-specificmanner [10 12] H3K4 monomethylation and chromatindecompaction were demonstrated to precede H3K27 acetyla-tion and enhancer activation [10] Thus nucleosome reorga-nization is highly regulated in a stepwise manner that likelyincludes both transcription factors and CRCs Additionallyhuman nucleosome organization differs between mature celltypes frommyeloid and lymphoid lineages [11] Detailed anal-ysis of nucleosome positioning with micrococcal nuclease(MNase) combined with parallel sequencing clearly showedsignificant cell type-specific differences in nucleosome orga-nization between granulocytes and T-cells [11] The linkerlength between nucleosomes in granulocytes is 46 base pairsbut 56 base pairs in T-cells [11] Differences in chromatinorganization are not surprising given the polylobular nuclearshape in granulocytes that differs dramatically from that ofthe small round nuclei in T-cells Because all blood cell typesstem from a common HSC a major nucleosome reorga-nization must occur during hematopoiesis to yield all thevarious blood cell types Thus SNF2 family enzymes andassociated auxiliary subunits play important roles in bloodcell differentiation

3 Specific Roles for SNF2 Family Enzymes inHematopoietic Cell Differentiation

How alterations in chromatin structure allow for temporalcontrol of gene expression to orchestrate the different devel-opmental programs is just now beginning to unfold A recentstudy in Zebrafish by Huang et al found several chromatinmodulators including CRCs such as BAF ISWI and NuRDto be key regulators of hematopoiesis [13] Here we reviewhow the various hematopoietic lineages are regulated by anetwork of TFs and associated ATP-dependent chromatinremodeling factors

31 SWISNF The SWISNF complex has been extensivelystudied in model organisms where it both activates andrepresses gene expression [14] In mammals the approxi-mately 2MDa-sized SWISNF complex exists with two dis-tinct catalytic cores either Brahma (BRM)SMARCA2 or theproduct of the Brm related gene1 (BRG1)SMARCA4 TheBRGBRM complexes contain both common and distinctauxiliary factors and have therefore been named BAF com-plexes (containing BRGBRM associated factors) [15] Mousegenetics has been instrumental to elucidating SWISNFfunctions in development Another subcomplex of BAFcalled PBAF (polybromo associated factors) consists of aSMARCA4 catalytic core along with BAF200ARID2 andBAF180PBRM1 auxiliary factors Biochemically both BAFand PBAF complex have similar nucleosome remodelingactivity [16]Brg1--mouse embryos die at the preimplantationstage whereasBrm--mice developnormally [17] This pioneer-ing study by Reyes et al also demonstrated that SMARCA4

expression is enhanced in the absence of SMARCA2 sug-gesting that SMARCA2 is dispensable and that SMARCA4has a role that is essential for early embryonic developmentSince their study further research has revealed the precisefunctions of BAF complexes in mouse embryogenesisorganogenesis and tissue formation [18 19]

BAF complexes are implicated in HSC maintenance [20]and regulation of erythroid [21] lymphoid [22] and myeloidlineages [23] The SMARCA4 complex contains several BAFsubunits These subunits play essential roles in maintainingthe integrity of the complex and support the function of thecomplex [24] For example mice bearing the Baf155-- muta-tion die at the preimplantation stage similar to Brg1-- nullmutation [25] Mice heterozygous for a mutation in Baf155-+

show defects in brain organization [25] whereas Baf155--homozygous mutant mice harboring a transgene expressingBAF155SMARCC1 show a defect in blood vessel formation[26] These findings show an important function for the aux-iliary subunit SMARCC1 in neurogenesis and illustrate theimportance of having a correct gene dosage for hematopoi-etic physiology A mutation in SMARCB1 another integralcomponent of the BAF complex results in bone marrowfailure and T-cell lymphoma [27] We recently showed thatACTL6A displays hematopoietic progenitor-specific expres-sion (Figure 2(b)) [28] Krasteva et al recently demonstratedwith functions in HSC maintenance and proliferation [20]

In the erythroid lineage a SMARCA4-containing BAFcomplex is essential for both primitive and definitive ery-thropoiesis [29 30] Erythropoiesis depends on the efficientrecruitment and chromatin remodeling by SMARCA4 toenable the transcription of the embryonic and adult 120573-globingenes This mechanism was discovered by Bultman et alusing a hypomorph point mutation (E1083G) located in theATPase domain of SMARCA4This mutation does not affectBAF complex integrity ATP hydrolysis or recruitment of thecomplex to the adult 120573-globin genes However this muta-tion does compromise the chromatin remodeling activity ofSMARCA4 and leads to a closed chromatin confirmationthereby inhibiting the transcription of 120573-globin genes fordefinitive erythropoiesis [29] However a Brg1-- conditionalnullmutation affects the expression of the120572-globin locus andhence primitive erythropoiesis [30] This finding suggeststhat the E1083G mutation may have a locus-specific chro-matin remodeling activity that is critical only for 120573-globingene expression

TheT-cells thatmigrate to thymocytes frombonemarrowdo not possess CD4 or CD8 antigen coreceptors and are thusdescribed as double negative (DN) cells During subsequentstages of T-cell differentiation in the thymus the CD8 recep-tor is activated followed by depression of the CD4 marker orvice versa Once the T-cells become CD4+ or CD8+ theyundergo a final maturation [31] The BRG1 complex iscrucial for T-cell development CD4+ CD8minus (helper T-cells)CD4minus CD8+ (cytotoxic T-cells) lineage choice and T-cell activation [22 31 32] One of the earliest studies by Zhaoet al demonstrated that BRG1 and its associated auxiliarycofactor BAF53 are required for the dynamic chromatindecompaction of chromatin that occurs during lymphocyte


RAD54L

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CHD8

SRCAP

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ERCC6

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SMARCA4

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BTAF1

CHD1

SMARCA2

CHD4

CHD2

TTF2

HELLS

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000

0

093

8

113

2

133

3

149

4

163

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170

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193

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Figure 2 Expression of human CRCs and their cofactors in normal hematopoietic cellsThe CAGE expression data were extracted from [28]and tags per million values were increased by a unit and converted to log10 values The hierarchal clustering and heatmaps were constructedusing one matrix clustered image maps (CIMminer) using the Euclidean distance method (httpdiscoverncinihgovcimminerhomedo)for the CRC ATPase subunit (a) and associated auxiliary cofactors (b)


activation in response to phosphoinositol [33] A few yearslater Chi et al performed a systematic study of the function ofSMARCA4 at different stages of T lymphocyte differentiationand maturation into CD4+ and CD8+ populations Theyfound that Wnt and pre-T-cell-receptor signaling along withSMARCA4 are essential at successive stages of T-cell differ-entiation to change the chromatin landscape of the cells [31]A conditional mutation in Brg1 blocks T-cell differentiation[22 31] and ablation of SMARCA4 results predominantly ina double negative (DN) (CD8minus and CD4minus) T-cell populationHowever a small number of cells become CD4+ but fail toundergo maturation resulting in a loss of T-cells [22 31]Mechanistically SMARCA4 was demonstrated to bind tosilencer elements and repress CD4 receptor expression in DNT-cells and to promote the activation of CD8 expression [34]Interestingly an N-terminal truncation of the HMG domainin SMARCE1 silences the CD4 receptor but not the expres-sion of CD8 indicating that it functions in lineage choice[35] In a recent study byWan et al the SMARCE1-containingSMARCA4 complex was shown to be required for remod-eling chromatin at CD4 silencer regions and this remod-eling is crucial for the binding of the RUNX1 transcriptionrepressor to the silencer DNA elements [36] Holloway et alprovided direct evidence for chromatin remodeling by theBAF complex at the GM-CSF (granulocytemacrophagecolony stimulating factor) gene promoter in T-cells Theydemonstrated a NF-120581B-dependent remodeling of a singlenucleosome in the GM-CSF promoter upon T-cell activation[37]

Only a few studies have explored the role of BAF com-plexes in B-cell development Mice deficient in Baf155 andBrg1 show defects in early B-cell development FurthermoreBaf155 deficiency results in low levels of B-cell-specific geneexpression loss of IL-7 signaling lack of V(D)J rearrange-ments and lack of activation of the TF EBF1 [38] Our recentfinding using CAGE expression profiling of epigenetic factorsshowed a B-cell-specific expression of DPF3 compared tohematopoietic progenitors and other mature cells suggestingthat this BAF subunit exhibits B-cell-specific function [28]However further studies are required to verify the biologicalfunction of DPF3 in B-cells

Several TFs have been implicated in myeloid develop-ment andmaturationTheCCAATenhancer binding protein(CEBP) family of proteins participate in cell proliferationand terminal differentiation [39] CEBP and its TF isoformsare expressed at different stages of the myeloid branch [40]One of the isoforms CEBP120573 interacts with the BAF complexvia its N-terminal activating domain to activate myeloidspecific genes [41] Vradii et al further demonstrated thatSMARCA4 is essential for the differentiation of myeloidprogenitors to metamyelocytes when stimulated with G-CSF[23]

32 Imitation Switch (ISWI) Complexes The ISWI subfamilyof CRCs has a highly conserved ATPase catalytic core alongwith 1ndash3 auxiliary cofactors In mammals as many as sevendifferent ISWI complexes have been described includingACF (ATP-utilizing chromatin assembly and remodeling

factor) CHRAC (chromatin remodeling and assembly com-plex) RSF (remodeling and spacing factor) WICH (WSTF-ISWI chromatin remodeling complex) NoRC (nucleolarremodeling complex) CERF (CECR2-containing remod-eling factor) and NURF (nucleosome remodeling factor)[42 43] ACF CHRAC RSF WICH and NoRC con-tain SNF2HSMARCA5 whereas CERF and NURF containSNF2LSMARCA1 as their catalytic SNF2 subunit ISWIcomplexes are recruited to their nucleosomal substratesthrough their interactions with DNA-binding domains withthe extranucleosomal DNA andor by recognizing histonemodifications to modulate chromatin structure [43 44]SMARCA5 is essential for early embryonic development andfor hematopoietic progenitor cell proliferation CD34+ pro-genitor cells lacking SMARCA5 are significantly stunted intheir proliferative capacity and fail to respond to cytokines toinduce differentiation [45]

Unlike the BAF complex which is essential for T-celldevelopment the ISWI complex NURF is required for T-cell maturation only after the CD4+CD8+ selection stage[46] Landry et al observed that mice carrying a conditionalmutation of Bptf the largest subunit of the NURF complexdisplayed a significant reduction in single positive CD4+ andCD8+ T-cells Furthermore they observed that this defect inT-cell maturation was due to a change in the chromatin land-scape as measured by DNase I hypersensitivity [46] Thusthese studies indicate that different mammalian ISWI com-plexes are important for hematopoiesis and warrant furthercharacterization to precisely understand the mechanisticdetails

33 Chromodomain Helicase DNA Binding (CHD) ProteinsMammals harbor nine different CHD proteins which arecharacterized by the presence of tandemchromodomains anda SNF2 helicase domain CHDs are further classified intothree subfamilies depending on the presence of additionaldomains CHD1-2 has an additional DNA-binding domainCHD3ndash5 has a dual PHD domain and CHD6ndash9 has a BRKdomain They are classified into subfamilies I II and IIIrespectively [47] The signature motifs of CHDs chromod-omains interact with DNA RNA and methylated histonetails but these domains have variable affinities towards his-tone methylation [48 49] These enzymes act on chromatinsubstrates as a monomer in conjunction with other cofactorsand with other remodeling complex [50 51] They have beenimplicated in diverse roles such as orchestrating chromatinstructure transcription activationrepression and histoneturnover [52 53] CHD1 has been shown to be essential inmaintaining open chromatin confirmation and the pluripo-tency of embryonic stem cells [54] The yeast homolog ofCHD1 is crucial for uniformly spacing nucleosomal arraysboth in vivo and in vitro [55 56] Although much work hasbeen performed both biochemically and in vivo to studythe biological role of CHD1 its function in hematopoiesisremains elusive However a study by Chen et al hints at apotential role for CHD1 in bone marrow hematopoiesis andmyeloid transformation through its function at Hox genes[57] Nagarajan et al showed that homozygous null Chd2


mice have a defect in HSC differentiation into the erythroidlineage and that heterozygous mutant mice develop T-celllymphomas [58]

The nucleosome remodeling and deacetylase (NuRD)complex consists of Mi-2120572CHD3 and Mi-2120573CHD4 asSNF2 ATPase subunits and two histone deacetylases HDAC1and HDAC2 and several auxiliary subunits [59] TheNuRD complex is diverse in its subunit compositionwhich dictates its specialized functions as a transcrip-tional corepressor The variable subunits of the NuRDcomplex include the methyl-CpG binding domain pro-teins 2 and 3 (MBD23) the metastasis-associated proteins(MTA123) the retinoblastoma-associated binding proteins(RbAP4648) a lysine-specific demethylase (LSD1KRDM1)GATAD2A (p66120572) and GATAD2B (p66120573) [59 60] TheChd4NuRD complex is important for both the self-renewalcapacity of HSCs and lineage choice HSCs deficient in Chd4enter the cell cycle and differentiate into the erythroid lineagebut not into other myeloid lineages or into lymphocytes [61]which exhausts HSCs and progenitors Moreover NuRDinteracts with specific TFs such as Ikaros and Helios whichare zinc-finger DNA-binding proteins that are critical for thy-mocyte development [62] Furthermore the Ikaros-NuRDinteraction which is primarily through CHD4 ATPase isessential not only for thymocyte development but also forHSCs and B-cells [60] This interaction guides the NuRDcomplex to specific gene targets through the DNA-bindingactivity of Ikaros [63]

The B-cellsCd79a gene encodes Ig120572 which is essential forimmunoglobulin assembly and intracellular signaling whenthe B-cell receptor interacts with an antigenThe activation ofthe gene encoding Cd79a is regulated not only by several TFsbut also via different epigenetic mechanisms [64]The CHD4component of NuRD complex was found to be essential forrepressing the transcription of Cd79120572 as the knock-downof CHD4 increases transcription accessibility of chromatinandDNAdemethylation [65] Interestingly the BAF complexactivates the Cd79a promoter element in the presence ofEBF and Pax5 TFs by binding to it and the knock-down ofSMARCA4SMARCA2 reduces chromatin accessibility Theopposing function of NuRD and BAF complexes defines adelicate Cd79a expression balance [65] Similar opposingfunctions for BAF and NuRD complexes have been observedfor inflammatory response genes when macrophages werestimulated with lipopolysaccharide [66]

The differentiation and maturation of DN to DP T-cellsare also regulated by the NuRD complex predominantlythrough its interaction with CHD4 ATPase Conditionalinactivation of CHD4 abrogates the expression of CD4 andreduces single positive CD4+ T-cells [67] FurthermoreCHD4 binds to the enhancer element of CD4 and recruitshistone acetyl-transferase p300 and the TFHEB thereby sup-porting the transcription of CD4 InterestinglyWilliams et aldid not find an association with HDAC2 in their coimmuno-precipitation assays suggesting that CHD4may act indepen-dently of the NuRD complex and may activate rather thanrepress genes [67] In a separate study theNuRDcomplexwasshown to be associated with BCL11B (B-cell chronic lympho-cytic leukemialymphoma 11B) through theMTA-1 subunit in

CD4+ T-cells to promote transcriptional repression in targetpromoters [68]

34 Other CRCs We also surveyed the existing evidence forroles of other SNF2 ATPases in hematopoiesis as follows (1)The helicase lymphoid-specific enzyme (HELLS) also knownas the lymphoid-specific helicase (LSH) is a member of theSNF2 helicase family Loss ofHELLS inmice results in amod-est reduction in the transition of T-cells from the DN stageCD4minusCD8minus to the DP stage CD4+CD8+ [69] (2) EP400belongs to the SWR1 subfamily of SNF2 enzymes An internaldeletion within the catalytic core of EP400 yields defects inembryonic development and primitive hematopoiesis inmice[70] EP400 conditional knockout mice exhibit embryoniclethality within two weeks with acute loss of bone marrowHSCs and impaired cell cycle progression [71]

4 SNF2 Expression Patterns inHuman Blood Cells

Genome-wide methodologies to study gene expression pro-vide a holistic picture of promoter usage levels of mRNAand proteins within cellstissues To construct a comprehen-sive picture of the levels of expression of genes encodingepigenetic factors in various blood cells we exploited the CapAnalysis of Gene Expression (CAGE) technique as a part ofthe Fantom 5 collaborative project (httpfantomgscrikenjp) [28] To better assess the gene expression levels we ana-lyzed themRNA expression of genes encoding SNF2ATPasesseparately from the genes encoding the CRC auxiliary sub-units (Figures 2(a) and 2(b)) Interestingly we observed thatseveral of these genes were expressed at different levels Addi-tionally some genes were abundantly expressed includinggenes encoding SNF2 ATPases and CRC auxiliary subunitssuch as CHD2 CHD4 BTAF1 SMARCA5 and BAZ1A EPC1and MORF4L2 respectively (Figures 2(a) and 2(b)) How-ever CHD5 and SMARCA1 were not expressed in any ofthe blood cells tested (Figure 2(a)) consistent with the factthat they are highly expressed in neuronal tissue [72 73]Thissuggests a broad function for some of the SNF2 genesin hematopoietic cells physiology Moreover we foundprogenitor-specific expression for some genes such asHELLSand HLTF suggesting that these factors may play importantroles in maintaining HSCs (Figure 2(a)) Furthermore somegenes had lineage-specific expression patterns for exampleCHD3 displayed higher transcript levels in the lymphoid lin-eage compared with the myeloid lineage [28] Thus genome-wide CAGE transcriptome profiling in hematopoietic cellshas given overview of expression patterns of not only SNF2ATPases but also auxiliary subunits important to understandcombinatorial assembly of CRCs (discussed in the followingsection)

We also included several leukemic cell lines in our epige-netic transcriptome analysis and found that the leukemic celllines clustered together with progenitor cells based on theirexpression profiles [28]This finding suggests that they prob-ably share epigenetic mechanisms required for self-renewalConversely we also observed significant differences in the


expression levels of several genes encoding SNF2 enzymesand CRC subunits compared with normal hematopoieticcells suggesting a putative role in promoting the leukemicphenotype Systematic studies of both normal hematopoieticcells and leukemic cell lines provide a broader perspective ofSNF2 family enzymes expression however detailed investi-gations are required to understand their molecular functionsin normal and malignant hematopoiesis

5 CRC Isoforms in Hematopoiesis

CRCs are often multisubunit complexes containing one ortwo SNF2 ATPase subunits that are capable of hydrolyzingATP along with several auxiliary subunits Subsequentlythey can convert energy released from ATP hydrolysis tomechanical energy for changing chromatin confirmationsHowever suchmechanical actions are not only performed bythe ATPase subunit but also require the participation of theentire complex [44] Although auxiliary subunits do not indi-vidually catalyze ATP hydrolysis or chromatin remodelingthey do dictate the specific functions of a CRC [53] Bothbiochemical and in vivo functional data are now availablewhich explains the specific roles of different CRC subunits inprogramming the development and differentiation of cells[18 44] This mechanism of action was recently highlightedin neuronal development [74] heart andmuscle development[75 76] and in controlling the development of blood celllineages [13 20] In our recent CAGE expression studywe identified several potential auxiliary subunits that wereeither hematopoietic cell- or lineage-specific For exampleBAF45CDPF3 BAF53AACTL6A andBAF60CSMARCD3transcripts were enriched in B-cells hematopoietic progeni-tor and monocytic cells respectively (Figure 2(b)) [28] Pre-viously Lickert et al showed that tissue-specific SMARCD3containing BAF complex is essential in heart morphogenesisand knockdown of SMARCD3 results in defect in heartdevelopment [76] Similarly DPF3-BAF complex is essen-tial for both heart and muscle development [75] RecentlyKrasteva et al highlighted the role of ACTL6A-BAF complexin proliferation of HSCs and adult hematopoiesis [20] Muchwork is required to investigate the combinatorial associationof auxiliary subunits of SNF2 ATPases in hematopoiesis

The ATPase motors in the BAF complex with eitherSMARCA4Brg1 or SMARCA2Brm share significant iden-tity in their amino acid composition and biochemical chro-matin remodeling activities However notably SMARCA4is essential whereas SMARCA2 is dispensable [30] Suchdistinct biological activities have been attributed to thenonconserved N-terminal regions of the ATPases which arepotential targets for different TFs and signaling moleculesand therefore regulate distinct cellular processes [77] Morerecently the PBAF complex with SMARCA4 as the catalyticcore was demonstrated to interact with CHD7 to cooccupythe distal enhancer element of Sox9 and activate neural crestformation [51] Phelan et al demonstrated that SMARCA4BAF45 BAF155SMARCC1 and BAF170SMARCC2 sub-units can form a functional SMARCA4 complex that is capa-ble of remodeling nucleosomes [78] What then is the func-tion of the other subunits associated with the BAF complex

The answer lies in understanding the diverse and dynamicfunctions of the BAF complex through its association withspecific auxiliary cofactors in celltissue-specificmanner [18]The underlying mechanism for the existence of diverse BAFcomplexes lies in the presence of different domains withinspecific auxiliary subunits which can read posttranslationalhistone modification in context of chromatin in a tissuespecificmanner For example DPF3 contains two PHD (planthomeodomain) fingers which recognize bothmethylated andacetylated histone residues and direct BAF complex to spe-cific genomic targets [75] We cannot rule out the existenceof similar mechanisms in hematopoietic development whichthus warrants further investigationThese studies thus reflectthe dynamic mechanisms of action of BAF complexes atdifferent levels in promoting normal tissue development

CRCs can also form subcomplexes with transcriptionfactors to target specific genes For example the transcrip-tion factor EKLF (erythroid Kruppel-like factor) binds tothe 120573-globin gene promoter and activates its transcrip-tion [79] Biochemical characterization revealed interactionsbetween EKLF and SMARCA4 SMARCC1 SMARCC2BAF47SMARCB1hSNF5 and BAF57SMARCE1 in a sub-complex called E-RC1 (EKLF coactivator remodeling com-plex 1)This complex can remodel chromatin and facilitate thetranscription of chromatinized templates of the120573-globin genepromoter in vitro [21] Interestingly the BAF complex cannotsubstitute for E-RC1 in 120573-globin gene expression indicatingthat E-RC1 has a specialized function [80]

The composition of the NuRD complex is dynamic andchanges with its distinct roles in cell survival differentiationdevelopment and homeostasis in various organisms [81] Forexample the MTA3-NuRD complex is essential for primitivehematopoiesis in the Zebrafish [82] and for B-cell-specifictranscriptional programming with the Bcl6 transcriptionalrepressor [83] MBD2 can replace MBD3 in NuRD to forma distinct complex with nonoverlapping functions [84]Intriguingly MBD3-deficient mice are embryonic lethalwhereasMBD2 deficientmice develop normally [85] Furtherstudies by Kaji et al showed that the MBD3-NuRD complexis essential for the pluripotency of embryonic stem cells [86]An LSD1 containing NuRD complex was identified in breastcancer cells where it demethylates histone H3 at amino acidslysine 4 and lysine 9 [87] Although LSD1 participates inseveral stages of HSC maintenance and differentiation itsfunction in complex with NuRD in hematopoiesis remainselusive [88]

Thus we can conclude that CRC composition is diversein blood cells and that several different CRC isoforms existfor specialized function

6 Aberrant Expression of SNF2 ATPases andCRC Auxiliary Subunits in Leukemia

Dysfunctional expression of CRC subunits has been asso-ciated with leukemia Downregulation of the BAF complexsubunits SMARCA4 ARID1A and SMARCB1 has beenassociated with glucocorticoid-resistance in acute lymphoidleukemia (ALL) [89]


Acute myeloid leukemia (AML) is a heterogeneous dis-ease that consists of several subtypes based on cytogeneticand genetic alterations which form the basis for classificationand prognosis AML is characterized by disturbed transcrip-tional regulation which leads to a differentiation block andincreased proliferation Several chromosomal translocationsor mutations in AML involve epigenetic regulators (egDNMT3a MLL and TET2) or transcription factors (egCEBP120572 and AML1) (reviewed in [90]) Transcription factorsthat regulate hematopoiesis are also targets for the aberrantepigenetic regulation that modulate their expression levelswhich affect cell differentiation For example patients witha mutated DNMT3A gene have genomes enriched for DNAdemethylation at genes that encode for TFs [91] Although theexpression patterns of CRCs are in most cases similar to theexpression patterns of normal myeloid progenitor cells andare not deregulated in AML some genes encoding for SNF2enzymes and CRC subunits are aberrantly expressed in AMLcompared with their normal counterparts (Table 1) Ouranalysis of SNF2 family enzymes and CRC auxiliary subunitsin different AML subtypes using the AML cohort from TheCancer Genome Atlas (TCGA) revealed that the expressionpatterns are not sufficiently specific to cluster the patientsbased on prognosis [92] (Figure 3) However some of thegenes display large variations in expression between patients(Figure 3) For example the expression levels for HELLSRUVBL1 and EP400 differ by 17- 12- and 5-fold respec-tively between the three patients with the highest or lowestexpression RUVBL1 is located on a chromosomal regionthat is frequently rearranged in leukemia and solid tumorswhich further suggests a role for RUVBL1 in leukemogenesis[93 94] The AML blast cells highly express SMARCA5 andits expression goes down upon treatment [95] We observedhigh levels of SMARCA5 transcripts from the patient dataextracted from TCGA (Figure 3) This may contribute toincreased proliferation of leukemic cells because SMARCA5has a role in promoting the proliferation of hematopoieticprogenitor cells (asmentioned above) CTCF andPU1 are keyTFs that regulate the growth and differentiation of myeloidcells [96 97] CTCF and SMARCA5 cooperatively interactwith the DNA regulatory elements of PU1 Consequentlythe SMARCA5 interaction increases the expression of PU1which supports myeloid differentiation Interestingly thesuccess of this interaction depends on the DNA methylationstatus of the PU1 regulatory elements Azacytidine treatmentof AML blast cells demethylates DNA and restores PU1expression thereby enabling myeloid differentiation [98]These studies reflect upon the mode of action of SMARCA5and regulation of PU1 expression in patients suffering fromAML

Aperturbed regulatory balance can contribute to carcino-genesis depending on the cellular context The SNF2 ATPaseCHD1 has a dual role in cancer The CHD1 gene is overex-pressed in AML cells possibly indicating an oncogenic rolein leukemia (Table 1) However prostate cancer patientsfrequently harbor Chd1 gene deletions indicating that Chd1may act as a tumor suppressor in the prostate [99 100]The downregulation of HELLS in AML patients (Table 1) isinteresting because HELLS has been demonstrated to have

Table 1 Aberrant expression of SNF2 enzymes and CRC subunitsin AML

Upregulated in AML Downregulated inAML

SNF2 enzymes

CHD1FC 19CHD2FC 49

HELLSFC 069

SMARCAD1Etl1FC 048TTF2FC 054HLTFFC 06

SWISNF complexsubunits

ARID1ABAF250aFC 21

SMARCD1BAF60AFC 17

SMARCC2BAF170FC 25

ARID1BBAF250bFC 06

ACTL6ABAF53AFC 04

SMARCE1BAF57FC 07

INO80 complex INO80DFLJ20309FC 15

The table shows CRC with significantly changed expression (119875 lt 00001) inAML compared to its closest normal counterpart atHemaExplorer [115]TheAML cohort consist of 144 patients with the following subtypes 39 patientswith t(821) 38 patients with t(1517) 29 patients with inv(16)t(1616) and 38patients with t(11q23)MLL FC = fold change

a role in DNA repair The phosphorylation of H2AX atdouble strand breaks is dependent on the ability of HELLSto hydrolyze ATP and is required for successful DNA repair[101] Deregulated DNA methylation is a hallmark of AMLand HELLS represses transcription via interacting with theDNA methyltransferase DNMT1 [102 103] HELLS regulatesHOX gene expression during normal development [104]The downregulation of HELLS in AML may dysregulate theexpression of HOX genes that is associated with both AMLandALL (reviewed in [105]) AML cells display a shift in theirSWISNF complex subunits with ARID1A being overex-pressed while the expression of ARID1B is reduced comparedwith normal counterparts (Table 1) The role of ARID1A inadult hematopoiesis is not clear but ARID1A activity instroma cells has been demonstrated to control the size of thefetal HSC pool [106] The role of ARID1B in hematopoiesisand leukemia is less clear but loss of function of ARID1B hasbeen proposed to have tumor suppressor function in lung andpancreatic cancer [107 108] The downregulation in AMLsuggests a similar tumor suppressor function for ARID1B inbloodThe expression of another SWISNF complex subunitACTL6A is also repressed inAMLACTL6Ahas been shown


ACTL

6BM

TA2

CHD

5SM

ARC

A1

DPF

3D

PF1

ACTB

MO

RF4L

2M

ORF

4L1

CHD

2BP

TFEP

C1BA

Z1A

RBBP

4SM

ARC

E1RU

VBL

2A

RID

1ARB

BP7

CHD

1LCH

D9

CHD

1SM

ARC

A2

SMA

RCC1

SMA

RCA

5BR

D8

PHF1

0SM

ARC

A4

POLE

3H

LTF

MTA

1A

RID

2IN

G3

INO

80D

ACTL

6ABR

D7

MEA

F6BT

AF1

ATRX

PBRM

1A

RID

1B

GAT

AD

2AIN

O80

CHD

4

CHD

8SM

ARC

B1M

BD3

GAT

AD

2BSM

ARC

D2

EP40

0RU

VBL

1D

PF2

KAT5

CHD

3TT

F2BR

D9

HEL

LSAT

AD

2IN

O80

CU

CHL5

VPS

72TR

RAP

ACTR

6SH

RPH

CHRA

C1AC

TR8

SMA

RCD

1M

CRS1

INO

80E

NFR

KBCH

D6

YEAT

S4D

AM

P1AC

TR5

TFPT

ZRA

NB3

SMA

RCD

3RA

D54

L2M

TA3

ERCC

6IN

O80

BRA

D54

LRA

D54

B

Prognosis poor favorable and intermediatenormal

100 293 325 344 360 374 390 408 555

Figure 3 Expression of CRCs in subtypes of AML patients The gene expression data from 194 AML patients were mined for CRC subunitsfrom the TCGA (The Cancer Genome Atlas) data portal (httpstcga-datancinihgovtcga) The expression values were log10 transformedand hierarchal clustering and the heatmap were constructed using CIMminer The colored bar on the right side of the heatmap indicatespatients with a poor (blue) favorable (black) and intermediatenormal (pink) prognosis

to be essential for adult hematopoiesis andHSCmaintenance[20] However its role in AML remains to be elucidated

The BAF complex has been suggested to have differentcompositions in HSC and leukemic cells [109] The BAFcomplex in leukemic cells (leukBAF complex) contains thecatalytic subunit SMARCA4 which is dispensable for main-tenance of LT-HSC but is required for proliferation and mul-tipotency [109] Leukemic cells lacking SMARCA4 undergocell cycle arrest and apoptosis The expression pattern ofcatalytic and complex subunits in long-term quiescenceHSC (LT-HSC) suggest that LT-HSC has a BAF complexcontaining SMARCA2 as the catalytic subunit dominantAccordingly Buscarlet et al proposed that the BAF complexcomposition switch between HSC and leukemic cells con-tributes to leukemogenesis [109] Mechanistically Shi et alshowed that SMARCA4 interacts with Myc enhancer ele-ments remodel chromatin to promote TF occupancy andlong range interaction with the Myc promoter to maintainleukemogenesis [110] Such mechanisms give insight as tohow leukemic cells manipulate the function of CRCs tomaintain cancerous nature

7 SNF2 and CRC Mutations in Leukemia

In recent years large-scale genomics efforts based on newparallel sequencing techniques such as the InternationalCancer Genome Consortium (ICGC) and the CancerGenome Atlas (TCGA) have provided large datasets that

enable systematic studies of mutations in epigenetic machin-ery in cancer Genes encoding enzymes involved in basic epi-geneticmechanisms such as histonemodification chromatinremodeling and DNA methylation are frequently mutatedin cancer including a range of tissue types such as breastbrain lung ovarian blood kidney colon uterus liver andpancreas (reviewed in [90]) Mutations in genes encodingSNF2 enzymes and CRC subunits have been identified indifferent blood cancers For example the gene for HELLS isfrequently truncated by 75 base pairs in AML (567) andALL (37) patients [111] Another example is a mutation inthe SMARCB1 subunit of BAF complex which was reportedto cause a loss of function in 24of chronicmyeloid leukemiapatients [112] Here we focus on the occurrence of mutationsof chromatin remodelers in blood cancers The ICGC dataportal was queriedwith all 30 human SNF2helicase genes and67 genes encoding CRC auxiliary subunits (October 2014)Frequent mutations in SNF2 genes were found in malignantlymphoma patients in a German cohort of 44 patients andin a cohort 75 of acute myeloid leukemia (AML) patientsfrom South Korea The SNF2 genes SMARCA4 (34)ZRANB3 (32) and CHD9 (20) were the three mostfrequently mutated genes in patients with malignant lym-phomawhereasCHD3was themost frequentlymutated geneinAML (Table 2)There are also relatively frequentmutationsin genes encoding some SNF2 enzymes that is the CHD2enzyme (46) in a Spanish cohort of 109 Chronic Lympho-cytic Lymphoma (CLL) patients Thus mutations in SNF2genes appear to be quite common in blood cancers


Table 2 ICGC data for the SNF2 enzymes

SNF2 enzyme Mutations in malignant lymphoma Mutations in AML Mutations in CLLSMARCA4Brg1 1544 (34) 275 (27) mdashSMARCA2Brm 844 (18) 375 (40) 1109 (092)SMARCA5SNF2H 144 (23) mdash mdashSMARCA1SNF2L 544 (11) mdash mdashCHD1 244 (45) 275 (27) mdashCHD2 544 (11) 475 (53) 5109 (46)CHD3 mdash 475 (53) mdashCHD4 544 (11) 375 (40) mdashCHD5 144 (23) 375 (40) mdashCHD6 644 (14) 475 (53) mdashCHD7 844 (18) 175 (13) mdashCHD8 344 (68) 375 (40) mdashCHD9 944 (20) 375 (40) mdashHELLS 444 (91) 375 (40) mdashCHD1L 344 (68) 175 (13) mdashSRCAP 244 (45) 175 (13)EP400 344 (68) 275 (27) mdashINO80 744 (16) 175 (13) mdashSMARCAD1Etl1 344 (68) 175 (13)RAD54B 244 (45) 375 (40) mdashRAD54L 444 (91) 175 (13) mdashATRX mdash 275 (27) mdashArip4 ND ND NDSMARCA3 344 (68) 275 (27) mdashTTF2 244 (45) 175 (12) mdashSHPRH 844 (18) 375 (40) 1109 (092)BTAF1 744 (16) 275 (27) mdashERCC6 244 (45) 275 (27) mdashSMARCAL1 244 (45) mdash mdashZRANB3 1444 (32) 375 (40) mdashThe ICGC data portal (httpsdccicgcorg) was queried with all 30 human SNF2 helicase genes (October 2014) The frequency and percent of mutations inthe patients are indicated for each gene ND = not determined

SMARCA4 is one of the catalytic subunits of the BAFcomplex Subunits of BAF complex are mutated in a varietyof cancers loss of function of the auxiliary subunit SMARCB1was detected in 98 of rhabdoid tumors and in 30ndash40 offamilial Schwannomatosis the subunit PBRM1 was mutatedin 41 of renal carcinoma the subunit ARID1A was mutatedin 50 of ovarian clear cell carcinoma and in 35 ofendometrial carcinoma and SMARCA4 itself wasmutated in35 of nonsmall cell lung cancers [113] We used the ICGCdata portal to assess whether these and other CRC subunitsaremutated in hematologicalmalignanciesWe observed thatmutations were frequent in malignant lymphoma (Germi-nal center B-cell derived lymphomas) for the BAF ATPaseSMARCA2 (18) and auxiliary subunits ARID1A (18)ARIDB (32) ARID2 (18) and DPF3 (23) and othersubunits were also mutated at lower frequencies (Table 3)These frequencies are higher than a report of mutations in acohort of 68 Diffuse large B-cell lymphoma patients whoharbored 162 of mutations in any gene encoding BAF

subunits and 29 for ARID1A and 59 for ARID1B [114]Interestingly the ICGC portal showed that some BAF sub-units were frequently mutated in the South Korean cohortof AML patients that is PBRM1 (67) SMARCC1 (67)and DPF3 (67) However significantly lower frequenciesof SWISNF mutations were identified in the Spanish CLLcohort (4 mutations in 109 patients) which agrees with thestudy by Shain and Pollack [114] who identified 8 mutationsin any BAF subunit gene in a cohort of 196 CLL patients

The subunits of the other CRC complexes were alsomutated in patients with lymphoma though at frequenciessomewhat lower compared with SWISNF For examplemutations in the NuRD complex subunits MTA3 (18)and p66betaGATAD28 (16) were observed The MRG15subunit of the EP400 complex wasmutated in 16 of patientswithmalignant lymphoma and in 53 ofAMLpatients CRCmutations were rare in the CLL cohort Thus in agreementwith the central role for SNF2 enzymes and their CRCcomplexes in blood cell differentiation mutations are often


Table 3 ICGC data for the noncatalytic CRC subunits

CRC complex subunits Mutations inmalignant lymphoma Mutations in AML Mutations in CLL

SWISNF complexSMARCA4Brg1 1544 (34) 275 (27) mdashSMARCA2Brm 844 (18) 375 (40) 1109 (092)ARID1ABAF250a 844 (18) 275 (27) 2109 (18)ARID1BBAF250b 1444 (32) 175 (13) mdashARID2BAF200 844 (18) mdash mdashBAF180PBRM1 mdash 575 (67) mdashSMARCC1BAF155 544 (11) 575 (67) mdashSMARCC2BAF170 mdash mdash mdashSMARCD1BAF60A mdash mdash mdashSMARCD2BAF60B 244 (45) 175 (13) mdashSMARCD3BAF60C 444 (91) mdash mdashACTL6ABAF53Alowast 544 (11) mdash mdashACTL6BBAF53B 144 (23) mdash mdashSMARCB1BAF47hSNF5 244 (45) 275 (27) mdashBAF45APHF10 344 (68) mdash mdashDPF1BAF45B mdash 175 (13) mdashDPF3BAF45C 1044 (23) 575 (67) mdashDPF2BAF45D mdash 175 (13) 1109 (092)SMARCE1BAF57 344 (68) mdash mdashBRD7 244 (45) mdash mdashBRD9 mdash 175 (13) mdash120573-actinACTB 544 (11) mdash mdashINO80 complexINO80 744 (16) 175 (13) mdash120573-actinACTBlowast 544 (11) mdash mdashACTL6ABAF53Alowast 144 (23) mdash mdashArp5ACTR5 144 (23) 175 (13) mdashArp8ACTR8 144 (23) 375 (40) mdashRUVBL1TIP49Alowast 344 (68) 275 (27) mdashRUVBL2TIP49Blowast 344 (68) 275 (27) mdashIES2INO80BPAPA-1 144 (23) 275 (27) 1109 (092)IES6INO80Cc18orf37 344 (68) 375 (40) mdashYY1 444 (91) mdash mdashUCH37UCHL5 344 (68) mdash mdashNFRKBINO80G mdash 375 (40) mdashMCRS1MCRS2MSP58INO80Q 244 (45) mdash mdashTFPTAmidaINO80F ND ND NDINO80DFLJ20309 444 (91) 175 (13) mdashINO80ECCDC95FLJ90652 244 (45) 175 (13) mdashEP400 complex See shared subunitslowast and additional subunits belowEP400 344 (68) 275 (27) mdashBRD8 244 (45) 275 (27) mdashTRRAP 644 (14) 375 (40) mdashTip60KAT5 244 (45) mdash mdashMRG15 744 (16) 475 (53) mdashMRGX mdash 275 (27) mdash


Table 3 Continued


FLJ11730 144 (23) 175 (13) mdashMRGBP 244 (45) 275 (27) mdashEPC1 644 (14) 175 (13) mdashING3 344 (68) 175 (13) mdashSRCAP complexSRCAP 244 (45) 175 (13) mdashRUVBL1TIP49Alowast 344 (68) 275 (27) mdashRUVBL2TIP49Blowast 344 (68) 275 (27)ACTL6ABAF53Alowast 544 (11) mdash mdashACTR6 ND ND NDGAS41lowast 244 (45) 175 (13) mdashDMAP1lowast 144 (23) 275 (27) mdashYL-1lowast 244 (45) 175 (13) mdashNuRD complex (Mi-2)CHD4 544 (11) 375 (40) mdashCHD3 mdash 475 (53) mdashMBD3 mdash mdash mdashMTA1 344 (68) 275 (27) 1109 (092)MTA2 144 (23) 175 (13)MTA3 844 (18) mdash mdashHDAC1 344 (68) mdash mdashHDAC2 444 (91) 375 (40) mdashRBBP7RbAp46 144 (23) 175 (13) mdashRBBP4RbAp48 mdash 275 (27) mdashp66-120572GATAD2A 544 (11) 175 (13) mdashp66-120573GATAD2B 744 (16) 175 (13) mdashNURF complexSMARCA1 (SNF2L) 544 (11) mdash mdashBPTF 344 (68) 175 (13) mdashRBBP7RbAp46 144 (23) 175 (13) mdashRBBP4RbAp48 mdash 275 (27) mdashCHRAC complexSMARCA5 (SNF2H) 144 (23) mdash mdashhACF1WCRF180 444 (91) mdash mdashhCHRAC17POLE3 144 (23) mdash mdashhCHRAC 15 mdash mdash mdashThe ICGC data portal (httpsdccicgcorg) was queried with 67 genes encoding CRC subunits (October 2014) The frequency and percentage of mutations inthe patients are indicated for each gene Shared CRC subunits are marked with an asterisk (lowast) ND = not determined

observed in patients with malignant lymphoma and AMLsuggesting that disruptions in the function of these enzymesand complexes could contribute to these blood cancer phe-notypes

8 Conclusions

SNF2 family enzymes are key players in the epigenetic controlof celltissue development differentiation and maturationThe question is how and by what mechanisms SNF2 enzymesand CRCs regulate epigenetic switches Decades of research

by several groups have shown that these enzymes changethe accessibility of DNA by multiple chromatin remodelingmechanisms Such mechanisms are critical for maintenanceof genome integrity regulation of transcription and organi-zation of chromatin into higher-order structures Biochemi-cal experiments to assess the functions of CRCs in a homoge-neous in vitro assembled chromatin system revealed that allCRCs tested so far translocate on the nucleosomal DNA [7]This DNA translocase activity results in different chromatinremodeling outcomes For example yeast SWISNF can slideas well as evict nucleosomes while ISW2 mostly slides nucle-osomes [7 43 44] This shows that different SNF2 family


enzymes remodel chromatin by both redundant and nonre-dundant mechanisms However access to the target chro-matic loci and remodeling byCRCs in vivo aremore complexSince CRCs lackmotifs to recognize specific DNA sequencesother factors are required to recruit CRCs to their genomictargets The interactions of CRCs with transcription factorsand posttranslational histone modifications perform thisfunction in celltissue specific manner

Recent studies have shown that the auxiliary subunitcomposition of CRCs is dynamic and variable during cellulardevelopment Such diversification adds to another level ofcomplexity to the current understanding of gene regulationby CRCs in heart muscle and neuronal development asdiscussed above More recently studies have shown that themultilineage hematopoietic system possesses a similar modeof regulation where subunit composition of CRCs suchas BAF and NuRD changes during hematopoietic lineagechoices Our genome-wide expression data revealed severalsuch differentially expressed CRC components [28] In anelegant study by the Lessard group the necessity of ACTL6Afor maintaining the HSC pool and that the SMARCA4 con-taining BAF to be critical for promoting leukemogenesis wasdemonstrated [20 109] The Vakoc group recently providedinsights into the mechanism of leukemogenesis where theSMARCA4 containing BAF complex interacts with the Mycenhancer element and via chromatin looping to the Mycpromoter to stimulate its oncogenic transcription [110] Inheart andmuscle development the key auxiliary CRC subunitDPF3 targets chromatin through its PHD domains whichinteract with acetylated and methylated chromatin regions[75 76] We show that DPF3 is specifically expressed in Blymphocytes however its biological relevance in blood cellsstill needs to be established [28]

Defects in chromatin remodeling caused by mutationsin the genes encoding SNF2 ATPases and CRC auxiliarysubunits are common in leukemia Data mining from ICGCconsortium shows that these mutations are common in genesencoding SNF2 family enzymes We also observed aberrantexpression of genes encoding SNF2 family enzymes and CRCsubunits in acute myeloid leukemia (AML) using data fromthe Cancer Genome Atlas (TCGA) Mechanistic studies willclearly be important to understand the contribution of thesemutations and expression changes to leukemogenesis andpossibly to allow for the development of personalized ther-apies based on specific SNF2 or CRC targets In this reviewwe have attempted to summarize the current knowledge ofSNF2 and CRC functions in hematopoiesis and leukemiaFurther studies are required to unfold multiple mechanismsof chromatin remodeling complexes by which hematopoieticcells can follow normal or malignant hematopoiesis

Conflict of Interests

The authors declare that there is no conflict of interestsregarding the publication of this paper

Acknowledgments

Karl Ekwall acknowledges funding from the Swedish CancerSociety (Grant no CAN 2012238) the Swedish Research

Council (Grant nos VR-M 2579 and VR-NT 4448) and theKnut and Alice Wallenberg Foundation (a grant to studyClinical epigenetics of AML) Punit Prasad received financialsupport from the Ake Olsson Foundation for HematologicalResearch and the Alex and Eva Wallstrom Foundation at KIAndreas Lennartsson is funded by the Ake Olsson Founda-tion for Hematological ResearchThe authors thank Ying Qufor his help in analyzing the TCGA data and Indranil Sinhafor his help with data analysis

References

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[2] M Stern R Jensen and I Herskowitz ldquoFive SWI genes arerequired for expression of the HO gene in yeastrdquo Journal ofMolecular Biology vol 178 no 4 pp 853ndash868 1984

[3] J N Hirschhorn S A Brown C D Clark and F WinstonldquoEvidence that SNF2SWI2 and SNF5 activate transcription inyeast by altering chromatin structurerdquo Genes and Developmentvol 6 no 12 pp 2288ndash2298 1992

[4] J Cote J Quinn J L Workman and C L Peterson ldquoStimu-lation of GAL4 derivative binding to nucleosomal DNA by theyeast SWISNF complexrdquo Science vol 265 no 5168 pp 53ndash601994

[5] A Flaus D M A Martin G J Barton and T Owen-HughesldquoIdentification of multiple distinct Snf2 subfamilies with con-served structural motifsrdquoNucleic Acids Research vol 34 no 10pp 2887ndash2905 2006

[6] P B Becker and J L Workman ldquoNucleosome remodeling andepigeneticsrdquo Cold Spring Harbor Perspectives in Biology vol 5no 9 2013

[7] C R Clapier and B R Cairns ldquoThe biology of chromatinremodeling complexesrdquo Annual Review of Biochemistry vol 78pp 273ndash304 2009

[8] S H Orkin and L I Zon ldquoHematopoiesis an evolvingparadigm for stem cell biologyrdquoCell vol 132 no 4 pp 631ndash6442008

[9] J I Sive and B Gottgens ldquoTranscriptional network controlof normal and leukaemic haematopoiesisrdquo Experimental CellResearch vol 329 no 2 pp 255ndash264 2014

[10] D Lara-Astiaso A Weiner E Lorenzo-Vivas et al ldquoImmuno-genetics Chromatin state dynamics during blood formationrdquoScience vol 345 no 6199 pp 943ndash949 2014

[11] A Valouev S M Johnson S D Boyd C L Smith A Z Fireand A Sidow ldquoDeterminants of nucleosome organization inprimary human cellsrdquo Nature vol 474 no 7352 pp 516ndash5202011

[12] A Luyten C Zang X S Liu and R A Shivdasani ldquoActiveenhancers are delineated de novo during hematopoiesis withlimited lineage fidelity among specified primary blood cellsrdquoGenes amp Development vol 28 no 16 pp 1827ndash1839 2014

[13] H T Huang K L Kathrein A Barton et al ldquoA network ofepigenetic regulators guides developmental haematopoiesis invivordquo Nature Cell Biology vol 15 no 12 pp 1516ndash1525 2013

[14] J A Martens and F Winston ldquoRecent advances in under-standing chromatin remodeling by SwiSnf complexesrdquoCurrentOpinion in Genetics and Development vol 13 no 2 pp 136ndash1422003


[15] W Wang J Cote Y Xue et al ldquoPurification and biochemicalheterogeneity of the mammalian SWI-SNF complexrdquo TheEMBO Journal vol 15 no 19 pp 5370ndash5382 1996

[16] Y Xue J C Canman C S Lee et al ldquoThe human SWISNF-Bchromatin-remodeling complex is related to yeast Rsc andlocalizes at kinetochores of mitotic chromosomesrdquo Proceedingsof the National Academy of Sciences of the United States ofAmerica vol 97 no 24 pp 13015ndash13020 2000

[17] J C Reyes J Barra C Muchardt A Camus C Babinet andMYaniv ldquoAltered control of cellular proliferation in the absence ofmammalian brahma (SNF2alpha)rdquo The EMBO Journal vol 17no 23 pp 6979ndash6991 1998

[18] L Ho and G R Crabtree ldquoChromatin remodelling duringdevelopmentrdquo Nature vol 463 no 7280 pp 474ndash484 2010

[19] M Ko D H Sohn H Chung and R H Seong ldquoChromatinremodeling development and diseaserdquoMutation Research vol647 no 1-2 pp 59ndash67 2008

[20] V Krasteva M Buscarlet A Diaz-Tellez M-A Bernard G RCrabtree and J A Lessard ldquoThe BAF53a subunit of SWISNF-like BAF complexes is essential for hemopoietic stem cellfunctionrdquo Blood vol 120 no 24 pp 4720ndash4732 2012

[21] J A Armstrong J J Bieker and B M Emerson ldquoA SWISNF-related chromatin remodeling complex E-RC1 is required fortissue-specific transcriptional regulation by EKLF in vitrordquoCellvol 95 no 1 pp 93ndash104 1998

[22] T C Gebuhr G I Kovalev S Bultman V Godfrey L Su and TMagnuson ldquoThe role of Brg1 a catalytic subunit of mammalianchromatin-remodeling complexes in T cell developmentrdquo Jour-nal of Experimental Medicine vol 198 no 12 pp 1937ndash19492003

[23] D Vradii S Wagner D N Doan et al ldquoBrg1 the ATPasesubunit of the SWISNF chromatin remodeling complex isrequired for myeloid differentiation to granulocytesrdquo Journal ofCellular Physiology vol 206 no 1 pp 112ndash118 2006

[24] D H Sohn K Y Lee C Lee et al ldquoSRG3 interacts directly withthe major components of the SWISNF chromatin remodelingcomplex and protects them from proteasomal degradationrdquoJournal of Biological Chemistry vol 282 no 14 pp 10614ndash106242007

[25] J K Kim S-O Huh H Choi et al ldquoSrg3 a mouse homolog ofyeast SWI3 is essential for early embryogenesis and involved inbrain developmentrdquoMolecular and Cellular Biology vol 21 no22 pp 7787ndash7795 2001

[26] D Han S Jeon D H Sohn et al ldquoSRG3 a core componentof mouse SWISNF complex is essential for extra-embryonicvascular developmentrdquo Developmental Biology vol 315 no 1pp 136ndash146 2008

[27] C W M Roberts M M Leroux M D Fleming and S HOrkin ldquoHighly penetrant rapid tumorigenesis through condi-tional inversion of the tumor suppressor gene Snf5rdquoCancer Cellvol 2 no 5 pp 415ndash425 2002

[28] P Prasad M Ronnerblad E Arner et al ldquoHigh-throughputtranscription profiling identifies putative epigenetic regulatorsof hematopoiesisrdquo Blood vol 123 no 17 pp e46ndashe57 2014

[29] S J Bultman T C Gebuhr and T Magnuson ldquoA Brg1 mutationthat uncouples ATPase activity from chromatin remodelingreveals an essential role for SWISNF-related complexes in120573-globin expression and erythroid developmentrdquo Genes ampDevelopment vol 19 no 23 pp 2849ndash2861 2005

[30] C T Griffin J Brennan and T Magnuson ldquoThe chromatin-remodeling enzyme BRG1 plays an essential role in primitive

erythropoiesis and vascular developmentrdquo Development vol135 no 3 pp 493ndash500 2008

[31] T H Chi M Wan P P Lee et al ldquoSequential roles of Brg theATPase subunit of BAF chromatin remodeling complexes inthymocyte developmentrdquo Immunity vol 19 no 2 pp 169ndash1822003

[32] T Chi ldquoA BAF-centred view of the immune systemrdquo NatureReviews Immunology vol 4 no 12 pp 965ndash977 2004

[33] K Zhao W Wang O J Rando et al ldquoRapid and phos-phoinositol-dependent binding of the SWISNF-like BAF com-plex to chromatin after T lymphocyte receptor signalingrdquo Cellvol 95 no 5 pp 625ndash636 1998

[34] I Taniuchi W Ellmeier and D R Littman ldquoThe CD4CD8lineage choice new insights into epigenetic regulation during Tcell developmentrdquo Advances in Immunology vol 83 pp 55ndash892004

[35] T H Chi M Wan K Zhao et al ldquoReciprocal regulation ofCD4CD8 expression by SWISNF-like BAF complexesrdquoNature vol 418 no 6894 pp 195ndash199 2002

[36] M Wan J Zhang D Lai et al ldquoMolecular basis of CD4repression by the SwiSnf-like BAF chromatin remodeling com-plexrdquo European Journal of Immunology vol 39 no 2 pp 580ndash588 2009

[37] A F Holloway S Rao X Chen and M F Shannon ldquoChangesin chromatin accessibility across the GM-CSF promoter upon Tcell activation are dependent on nuclear factor 120581B proteinsrdquoJournal of Experimental Medicine vol 197 no 4 pp 413ndash4232003

[38] J ChoiM Ko S Jeon et al ldquoThe SWISNF-like BAF complex isessential for early B cell developmentrdquo Journal of Immunologyvol 188 no 8 pp 3791ndash3803 2012

[39] J Tsukada Y Yoshida Y Kominato and P E Auron ldquoTheCCAATenhancer (CEBP) family of basic-leucine zipper(bZIP) transcription factors is a multifaceted highly-regulatedsystem for gene regulationrdquo Cytokine vol 54 no 1 pp 6ndash192011

[40] L M Scott C I Civin P Rorth and A D Friedman ldquoA noveltemporal expression pattern of three CEBP family members indifferentiating myelomonocytic cellsrdquo Blood vol 80 no 7 pp1725ndash1735 1992

[41] E Kowenz-Leutz and A Leutz ldquoA CEBP120573 isoform recruits theSWISNF complex to activate myeloid genesrdquo Molecular Cellvol 4 no 5 pp 735ndash743 1999

[42] F Erdel and K Rippe ldquoChromatin remodelling in mammaliancells by ISWI-type complexesmdashwhere when and whyrdquo TheFEBS Journal vol 278 no 19 pp 3608ndash3618 2011

[43] B Bartholomew ldquoISWI chromatin remodeling one primaryactor or a coordinated effortrdquo Current Opinion in StructuralBiology vol 24 no 1 pp 150ndash155 2014

[44] B Bartholomew ldquoRegulating the chromatin landscape struc-tural andmechanistic perspectivesrdquoAnnual Review of Biochem-istry vol 83 no 1 pp 671ndash696 2014

[45] T Stopka and A I Skoultchi ldquoThe ISWI ATPase Snf2h isrequired for early mouse developmentrdquo Proceedings of theNational Academy of Sciences of the United States of Americavol 100 no 2 pp 14097ndash14102 2003

[46] J W Landry S Banerjee B Taylor P D Aplan A Singer andC Wu ldquoChromatin remodeling complex NURF regulates thy-mocyte maturationrdquo Genes amp Development vol 25 no 3 pp275ndash286 2011


[47] J K Sims and P A Wade ldquoSnapShot chromatin remodelingCHDrdquo Cell vol 144 no 4 p 626 2011

[48] S Qin Y Liu W Tempel et al ldquoStructural basis for histonemimicry and hijacking of host proteins by influenza virusprotein NS1rdquo Nature Communications vol 5 article 3952 2014

[49] J C Eissenberg ldquoStructural biology of the chromodomainform and functionrdquo Gene vol 496 no 2 pp 69ndash78 2012

[50] J Ramırez and J Hagman ldquoTheMi-2NuRD complex a criticalepigenetic regulator of hematopoietic development differenti-ation and cancerrdquo Epigenetics vol 4 no 8 pp 532ndash536 2009

[51] R Bajpai D A Chen A Rada-Iglesias et al ldquoCHD7 cooperateswith PBAF to control multipotent neural crest formationrdquoNature vol 463 no 7283 pp 958ndash962 2010

[52] M Radman-Livaja T K Quan L Valenzuela et al ldquoA key rolefor Chd1 in histone H3 dynamics at the 31015840 ends of long genes inyeastrdquo PLoS Genetics vol 8 no 7 Article ID e1002811 2012

[53] M Lange S Demajo P Jain and L di Croce ldquoCombinatorialassembly and function of chromatin regulatory complexesrdquoEpigenomics vol 3 no 5 pp 567ndash580 2011

[54] A Gaspar-Maia A Alajem F Polesso et al ldquoChd1 regulatesopen chromatin and pluripotency of embryonic stem cellsrdquoNature vol 460 no 7257 pp 863ndash868 2009

[55] J Pointner J Persson P Prasad et al ldquoCHD1 remodelers regu-late nucleosome spacing in vitro and align nucleosomal arraysover gene coding regions in S pomberdquoThe EMBO Journal vol31 no 23 pp 4388ndash4403 2012

[56] T Gkikopoulos P Schofield V Singh et al ldquoA role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleo-some organizationrdquo Science vol 333 no 6050 pp 1758ndash17602011

[57] Y-X Chen J Yan K Keeshan et al ldquoThe tumor suppressormenin regulates hematopoiesis and myeloid transformation byinfluencing Hox gene expressionrdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 103 no4 pp 1018ndash1023 2006

[58] P Nagarajan TMOnami S Rajagopalan S Kania R Donnelland S Venkatachalam ldquoRole of chromodomain helicase DNA-binding protein 2 in DNA damage response signaling andtumorigenesisrdquo Oncogene vol 28 no 8 pp 1053ndash1062 2009

[59] N J Bowen N Fujita M Kajita and P A Wade ldquoMi-2NuRD multiple complexes for many purposesrdquo Biochimica etBiophysica ActamdashGene Structure and Expression vol 1677 no1ndash3 pp 52ndash57 2004

[60] C Dege and J Hagman ldquoMi-2NuRD chromatin remodelingcomplexes regulate B and T-lymphocyte development andfunctionrdquo Immunological Reviews vol 261 no 1 pp 126ndash1402014

[61] T Yoshida I Hazan J Zhang et al ldquoThe role of the chromatinremodeler Mi-2120573 in hematopoietic stem cell self-renewal andmultilineage differentiationrdquo Genes amp Development vol 22 no9 pp 1174ndash1189 2008

[62] R Sridharan and S T Smale ldquoPredominant interaction ofboth Ikaros and Helios with the NuRD complex in immaturethymocytesrdquo The Journal of Biological Chemistry vol 282 no41 pp 30227ndash30238 2007

[63] J Zhang A F Jackson T Naito et al ldquoHarnessing of thenucleosome-remodeling-deacetylase complex controls lym-phocyte development and prevents leukemogenesisrdquo NatureImmunology vol 13 no 1 pp 86ndash94 2012

[64] HMaier ROstraatHGao et al ldquoEarly B cell factor cooperateswith Runx1 and mediates epigenetic changes associated with

mb-1 transcriptionrdquoNature Immunology vol 5 no 10 pp 1069ndash1077 2004

[65] HGao K Lukin J Ramırez S Fields D Lopez and J HagmanldquoOpposing effects of SWISNF and Mi-2NuRD chromatinremodeling complexes on epigenetic reprogramming by EBFand Pax5rdquo Proceedings of the National Academy of Sciences ofthe United States of America vol 106 no 27 pp 11258ndash112632009

[66] V R Ramirez-Carrozzi A A Nazarian C C Li et al ldquoSelectiveand antagonistic functions of SWISNF and Mi-2beta nucleo-some remodeling complexes during an inflammatory responserdquoGenes amp Development vol 20 no 3 pp 282ndash296 2006

[67] C J Williams T Naito P Gomez-Del Arco et al ldquoThechromatin remodelerMi-2120573 is required for CD4 expression andT cell developmentrdquo Immunity vol 20 no 6 pp 719ndash733 2004

[68] V B Cismasiu K Adamo J Gecewicz J Duque Q Lin and DAvram ldquoBCL11B functionally associates with the NuRD com-plex in T lymphocytes to repress targeted promoterrdquo Oncogenevol 24 no 45 pp 6753ndash6764 2005

[69] T M Geiman and K Muegge ldquoLsh an SNF2helicase familymember is required for proliferation ofmature T lymphocytesrdquoProceedings of the National Academy of Sciences of the UnitedStates of America vol 97 no 9 pp 4772ndash4777 2000

[70] T Ueda R Watanabe-fukunaga H Ogawa et al ldquoCriticalrole of the p400mDomino chromatin-remodeling ATPase inembryonic hematopoiesisrdquoGenes to Cells vol 12 no 5 pp 581ndash592 2007

[71] T Fujii T Ueda S Nagata and R Fukunaga ldquoEssential roleof p400mDomino chromatin-remodeling ATPase in bonemarrow hematopoiesis and cell-cycle progressionrdquo Journal ofBiological Chemistry vol 285 no 39 pp 30214ndash30223 2010

[72] O Barak M A Lazzaro N S Cooch D J Picketts and RShiekhattar ldquoA tissue-specific naturally occurring humanSNF2L variant inactivates chromatin remodelingrdquo The Journalof Biological Chemistry vol 279 no 43 pp 45130ndash45138 2004

[73] P M Thompson T Gotoh M Kok P S White and G MBrodeur ldquoCHD5 a new member of the chromodomain genefamily is preferentially expressed in the nervous systemrdquoOncogene vol 22 no 7 pp 1002ndash1011 2003

[74] J I Wu J Lessard I A Olave et al ldquoRegulation of dendriticdevelopment by neuron-specific chromatin remodeling com-plexesrdquo Neuron vol 56 no 1 pp 94ndash108 2007

[75] M Lange B Kaynak U B Forster et al ldquoRegulation ofmuscle development by DPF3 a novel histone acetylation andmethylation reader of the BAF chromatin remodeling complexrdquoGenes and Development vol 22 no 17 pp 2370ndash2384 2008

[76] H Lickert J K Takeuchi I von Both et al ldquoBaf60c is essentialfor function of BAF chromatin remodelling complexes in heartdevelopmentrdquo Nature vol 432 no 7013 pp 107ndash112 2004

[77] S Kadam and B M Emerson ldquoTranscriptional specificityof human SWISNF BRG1 and BRM chromatin remodelingcomplexesrdquoMolecular Cell vol 11 no 2 pp 377ndash389 2003

[78] M L Phelan S Sif G J Narlikar andR E Kingston ldquoReconsti-tution of a core chromatin remodeling complex from SWISNFsubunitsrdquoMolecular Cell vol 3 no 2 pp 247ndash253 1999

[79] I J Miller and J J Bieker ldquoA novel erythroid cell-specificmurine transcription factor that binds to the CACCC elementand is related to the Kruppel family of nuclear proteinsrdquoMolecular and Cellular Biology vol 13 no 5 pp 2776ndash27861993


[80] C-H Lee M R Murphy J-S Lee and J H Chung ldquoTargetinga SWISNF-related chromatin remodeling complex to the 120573-globin promoter in erythroid cellsrdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 96 no22 pp 12311ndash12315 1999

[81] PMcDonel I Costello and BHendrich ldquoKeeping things quietroles of NuRD and Sin3 co-repressor complexes during mam-malian developmentrdquo International Journal of Biochemistry andCell Biology vol 41 no 1 pp 108ndash116 2009

[82] X Li S Jia S Wang Y Wang and A Meng ldquoMta3-NuRDcomplex is a master regulator for initiation of primitivehematopoiesis in vertebrate embryosrdquo Blood vol 114 no 27 pp5464ndash5472 2009

[83] N Fujita D L Jaye C Geigerman et al ldquoMTA3 and the Mi-2NuRD complex regulate cell fate during B lymphocyte differen-tiationrdquo Cell vol 119 no 1 pp 75ndash86 2004

[84] X LeGuezennecMVermeulen A B Brinkman et al ldquoMBD2NuRD andMBD3NuRD two distinct complexes with differentbiochemical and functional propertiesrdquoMolecular and CellularBiology vol 26 no 3 pp 843ndash851 2006

[85] B Hendrich J Guy B Ramsahoye V A Wilson and A BirdldquoClosely related proteins MBD2 and MBD3 play distinctive butinteracting roles in mouse developmentrdquo Genes and Develop-ment vol 15 no 6 pp 710ndash723 2001

[86] K Kaji I M Caballero R MacLeod J Nichols V A Wilsonand B Hendrich ldquoThe NuRD component Mbd3 is required forpluripotency of embryonic stem cellsrdquo Nature Cell Biology vol8 no 3 pp 285ndash292 2006

[87] Y Shi F Lan CMatson et al ldquoHistone demethylationmediatedby the nuclear amine oxidase homolog LSD1rdquo Cell vol 119 no7 pp 941ndash953 2004

[88] S Y R Dent and J Chandra ldquoThe lasting influence of LSD1 inthe bloodrdquo eLife vol 2013 no 2 Article ID e00963 2013

[89] N Pottier W Yang M Assem et al ldquoThe SWISNF chromatin-remodeling complex and glucocorticoid resistance in acutelymphoblastic leukemiardquo Journal of the National Cancer Insti-tute vol 100 no 24 pp 1792ndash1803 2008

[90] C Plass S M Pfister A M Lindroth O Bogatyrova R Clausand P Lichter ldquoMutations in regulators of the epigenome andtheir connections to global chromatin patterns in cancerrdquoNature Reviews Genetics vol 14 no 11 pp 765ndash780 2013

[91] Y Qu A Lennartsson V I Gaidzik et al ldquoDifferential methy-lation in CN-AML preferentially targets non-CGI regions andis dictated by DNMT3A mutational status and associated withpredominant hypomethylation of HOX genesrdquo Epigenetics vol9 no 8 pp 1108ndash1119 2014

[92] The Cancer Genome Atlas Research Network ldquoGenomic andepigenomic landscapes of adult de novo acute myeloidleukemiardquo The New England Journal of Medicine vol 368 no22 pp 2059ndash2074 2013

[93] V I Kashuba R Z Gizatullin A I Protopopov et al ldquoNotIlinkingjumping clones of human chromosome 3 mapping ofthe TFRC RAB7 and HAUSP genes to regions rearranged inleukemia and deleted in solid tumorsrdquo FEBS Letters vol 419no 2-3 pp 181ndash185 1997

[94] A Rynditch Y Pekarsky S Schnittger and K GardinerldquoLeukemia breakpoint region in 3q21 is gene richrdquo Gene vol193 no 1 pp 49ndash57 1997

[95] T Stopka D Zakova O Fuchs et al ldquoChromatin remodelinggene SMARCA5 is dysregulated in primitive hematopoieticcells of acute leukemiardquo Leukemia vol 14 no 7 pp 1247ndash12522000

[96] V Torrano I Chernukhin F Docquier et al ldquoCTCF regu-lates growth and erythroid differentiation of human myeloidleukemia cellsrdquoThe Journal of Biological Chemistry vol 280 no30 pp 28152ndash28161 2005

[97] F Rosenbauer S Koschmieder U Steidl and D G TenenldquoEffect of transcription-factor concentrations on leukemic stemcellsrdquo Blood vol 106 no 5 pp 1519ndash1524 2005

[98] M Dluhosova N Curik J Vargova A Jonasova T Zikmundand T Stopka ldquoEpigenetic control of SPI1 gene by CTCF andISWI ATPase SMARCA5rdquo PLoS ONE vol 9 no 2 Article IDe87448 2014

[99] I V Tereshchenko H Zhong M A Chekmareva et al ldquoERGand CHD1 heterogeneity in prostate cancer use of confocalmicroscopy in assessment ofmicroscopic focirdquoTheProstate vol74 no 15 pp 1551ndash1559 2014

[100] S C Baca D Prandi M S Lawrence et al ldquoPunctuated evolu-tion of prostate cancer genomesrdquo Cell vol 153 no 3 pp 666ndash677 2013

[101] J Burrage A Termanis A Geissner K Myant K Gordonand I Stancheva ldquoThe SNF2 family ATPase LSH promotesphosphorylation of H2AX and efficient repair of DNA double-strand breaks in mammalian cellsrdquo Journal of Cell Science vol125 no 22 pp 5524ndash5534 2012

[102] K Myant and I Stancheva ldquoLSH cooperates with DNAmethyl-transferases to repress transcriptionrdquo Molecular and CellularBiology vol 28 no 1 pp 215ndash226 2008

[103] K Myant A Termanis A Y M Sundaram et al ldquoLSH andG9aGLP complex are required for developmentally pro-grammed DNA methylationrdquo Genome Research vol 21 no 1pp 83ndash94 2011

[104] S Xi H Zhu H Xu A Schmidtmann T M Geiman and KMuegge ldquoLsh controlsHox gene silencing during developmentrdquoProceedings of the National Academy of Sciences of the UnitedStates of America vol 104 no 36 pp 14366ndash14371 2007

[105] R A Alharbi R Pettengell H S Pandha and R Morgan ldquoTherole of HOX genes in normal hematopoiesis and acuteleukemiardquo Leukemia vol 27 no 5 pp 1000ndash1008 2013

[106] J Krosl A Mamo J Chagraoui et al ldquoAmutant allele of theSwiSnfmember BAF250a determines the pool size of fetal liverhemopoietic stem cell populationsrdquo Blood vol 116 no 10 pp1678ndash1684 2010

[107] H Huang S-M Chen L-B Pan J Yao and H-T Ma ldquoLossof function of SWISNF chromatin remodeling genes leads togenome instability of human lung cancerrdquoOncology Reports pp283ndash291 2014

[108] M Khursheed J N Kolla V Kotapalli et al ldquoARID1B a mem-ber of the human SWISNF chromatin remodeling complexexhibits tumour-suppressor activities in pancreatic cancer celllinesrdquo British Journal of Cancer vol 108 no 10 pp 2056ndash20622013

[109] M Buscarlet V Krasteva L Ho et al ldquoEssential role of BRGthe ATPase subunit of BAF chromatin remodeling complexesin leukemia maintenancerdquo Blood vol 123 no 11 pp 1720ndash17282014

[110] J Shi W A Whyte C J Zepeda-Mendoza et al ldquoRole ofSWISNF in acute leukemia maintenance and enhancer-mediatedMyc regulationrdquoGenes ampDevelopment vol 27 no 24pp 2648ndash2662 2013

[111] DW Lee K Zhang Z-Q Ning et al ldquoProliferation-associatedSNF2-like gene (PASG) a SNF2 family member altered inleukemiardquoCancer Research vol 60 no 13 pp 3612ndash3622 2000


[112] F Grand S Kulkarni A Chase JM GoldmanMGordon andN C P Cross ldquoFrequent deletion of hSNF5INI1 a componentof the SWISNF complex in chronic myeloid leukemiardquoCancerResearch vol 59 no 16 pp 3870ndash3874 1999

[113] B G Wilson and C W M Roberts ldquoSWISNF nucleosomeremodellers and cancerrdquo Nature Reviews Cancer vol 11 no 7pp 481ndash492 2011

[114] A H Shain and J R Pollack ldquoThe spectrum of SWISNFmuta-tions ubiquitous in human cancersrdquo PLoS ONE vol 8 no 1Article ID e55119 2013

[115] F O Bagger N Rapin K Theilgaard-Monch et al ldquoHemaEx-plorer a database of mRNA expression profiles in normal andmalignant haematopoiesisrdquo Nucleic Acids Research vol 41 ppD1034ndashD1039 2013

Submit your manuscripts athttpwwwhindawicom

Stem CellsInternational

Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014


MEDIATORSINFLAMMATION

of


Behavioural Neurology

EndocrinologyInternational Journal of



Disease Markers


BioMed Research International

OncologyJournal of



Oxidative Medicine and Cellular Longevity


PPAR Research

The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014

Immunology ResearchHindawi Publishing Corporationhttpwwwhindawicom Volume 2014

Journal of

ObesityJournal of



Computational and Mathematical Methods in Medicine

OphthalmologyJournal of


Diabetes ResearchJournal of



Research and TreatmentAIDS


Gastroenterology Research and Practice


Parkinsonrsquos Disease

Evidence-Based Complementary and Alternative Medicine

Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom


Helicase-like superfamily 2 (SF2)

ATP

Nucleosome sliding

Nuclesome spacing Nucleosome assembly

Histone dimer exchange

DNA accessibility

ncRNA expression

Transcription regulation

Histone eviction

Histone turnover

Outcome of chromatin remodeling

DEAD boxhelicases

RecGhelicases

Snf2 Type IIIIrestrictionenzymes

DEAHDExHhelicases

Snf2-like Swr1-like SSO1653-like Rad54-like Rad516-like SMARCAL1ALC1IswiCHD7Chd1Mi-2LshSnf2

EP400Swr1Ino80Etl1

ERCC6SSO1653Mot1

ATRXArip4JBP2DRD1Rad54

LodestarRad516Ris1SHPRH

ADP + Pi

(a)

B-cell

Monocytemacrophage

Neutrophil

Eosinophil

NK cell

Basophil

Mast cells

RBC

Megakaryocytes

HSC

CLP

CMP

GMP

MEP

CD4+ T-cell

CD8+ T-cell

(b)Figure 1 Classification of SNF2 enzymes and schema of mammalian hematopoiesis SNF2-like chromatin remodelers belong to SF2superfamily and are classified based on conserved structure of the ATPase domain as discussed in Flaus et al [5] (a) Overview of mammalianhematopoietic cell development and differentiation Dashed arrows show intermediate stages of hematopoietic development which is notshown in the figure for simplicity purpose (b)

chromatin For example the SNF2 enzyme SMARCA4Brg1is targeted via a Bromodomain [6 7]

Numerous in vivo and biochemical studies have beenemployed using different model organisms to address thedetailed effects of SNF2 enzymes on chromatin The chro-matin remodeling reaction can lead to nucleosome slidinghistone exchange histone eviction (disassembly) and nucle-osome spacing to form regular arrays or nucleosome assem-bly depending on both which SNF2 enzyme is used andwhether other cofactors such as histone chaperones areadded to the experiments (recently reviewed in [6]) Thedisassembly function is particularly important in gene regu-lation to ensure that promoter and enhancer DNA sequencesare accessible for transcription factors epigenetic modifiersand RNA polymerase II SNF2 enzymes are often part ofmultisubunit chromatin remodeling complexes (CRC) con-taining several auxiliary subunits

2 Chromatin Reorganizationduring Hematopoiesis

The hematopoietic system consists of two main cell lineagesthe myeloid and the lymphoid which both originate from

hematopoietic stem cells (HSCs) (Figure 1(b)) BrieflymultipotentHSCs differentiate to give rise to commonmyeloidprogenitors (CMPs) and common lymphoid progenitors(CLPs) Further differentiation ofCMPs yieldsmegakaryocyteerythroid progenitor (MEP) and granulocyte-monocyteprogenitor (GMP) The MEP differentiates and matures intoerythrocytes and megakaryocytes whereas the GMP dif-ferentiates into monocytes and granulocytes (neutrophilseosinophils and basophils) which are the first line of defenseagainst infections [8] CLPs give rise to T-cells B-cells andNatural Killer (NK) cells The lymphoid subtypes ofhematopoietic cells are crucial for adaptive immunity FinalB- T- and NK-cell maturation occur in the peripherallymphoid tissue where antigen selection takes place

Lineage choice and blood cell differentiation are tightlyregulated at several levels Different transcription factors (TFs)have been identified that together form a regulatory networkfor hematopoiesis (reviewed in [9]) Several TFs have beenshown to interact with epigenetic regulators including CRCssuch as theNucleosomeRemodeling anddeacetylase (NuRD)complex (reviewed in [8]) The importance of chromatinremodelers in hematopoiesis was recently suggested by two












RAD54L

EP400

CHD8

SRCAP

INO80

ERCC6

CHD9

CHD6

ATRX

SMARCA4

SHPRH

CHD3

CHD7

SMARCA5

BTAF1

CHD1

SMARCA2

CHD4

CHD2

TTF2

HELLS

ZRANB3

RAD54B

SMARCAD1

CHD1L

SMARCAL1

HLTF

SMARCA1

CHD5

Prog

enito

rs

Mac

roph

ages

Neu

troph

ils

Eosin

ophi

ls

Baso

phils

Mon

ocyt

es

B-ce

lls

CD4

T-ce

lls

CD8

T-ce

lls

NK

cells

000

0

070

0

098

7

127

2

144

3

158

9

181

0

210

1

345

9

(a)

Prog

enito

rs

Mac

roph

ages

Neu

troph

ilsEo

sinop

hils

Baso

phils

Mon

ocyt

es

B-ce

lls

CD4

T-ce

llsCD

8 T-

cells

NK

cells

DPF3


000

0

093

8

113

2

133

3

149

4

163

2

170

8

193

8

281

4

(b)




































SNF2 enzymes

CHD1FC 19CHD2FC 49

HELLSFC 069



ARID1ABAF250aFC 21

SMARCD1BAF60AFC 17

SMARCC2BAF170FC 25

ARID1BBAF250bFC 06

ACTL6ABAF53AFC 04

SMARCE1BAF57FC 07





ACTL

6BM

TA2

CHD

5SM

ARC

A1

DPF

3D

PF1

ACTB

MO

RF4L

2M

ORF

4L1

CHD

2BP

TFEP

C1BA

Z1A

RBBP

4SM

ARC

E1RU

VBL

2A

RID

1ARB

BP7

CHD

1LCH

D9

CHD

1SM

ARC

A2

SMA

RCC1

SMA

RCA

5BR

D8

PHF1

0SM

ARC

A4

POLE

3H

LTF

MTA

1A

RID

2IN

G3

INO

80D

ACTL

6ABR

D7

MEA

F6BT

AF1

ATRX

PBRM

1A

RID

1B

GAT

AD

2AIN

O80

CHD

4

CHD

8SM

ARC

B1M

BD3

GAT

AD

2BSM

ARC

D2

EP40

0RU

VBL

1D

PF2

KAT5

CHD

3TT

F2BR

D9

HEL

LSAT

AD

2IN

O80

CU

CHL5

VPS

72TR

RAP

ACTR

6SH

RPH

CHRA

C1AC

TR8

SMA

RCD

1M

CRS1

INO

80E

NFR

KBCH

D6

YEAT

S4D

AM

P1AC

TR5

TFPT

ZRA

NB3

SMA

RCD

3RA

D54

L2M

TA3

ERCC

6IN

O80

BRA

D54

LRA

D54

B


100 293 325 344 360 374 390 408 555


















Table 3 Continued




8 Conclusions









Acknowledgments



References































































































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of



























RAD54L

EP400

CHD8

SRCAP

INO80

ERCC6

CHD9

CHD6

ATRX

SMARCA4

SHPRH

CHD3

CHD7

SMARCA5

BTAF1

CHD1

SMARCA2

CHD4

CHD2

TTF2

HELLS

ZRANB3

RAD54B

SMARCAD1

CHD1L

SMARCAL1

HLTF

SMARCA1

CHD5

Prog

enito

rs

Mac

roph

ages

Neu

troph

ils

Eosin

ophi

ls

Baso

phils

Mon

ocyt

es

B-ce

lls

CD4

T-ce

lls

CD8

T-ce

lls

NK

cells

000

0

070

0

098

7

127

2

144

3

158

9

181

0

210

1

345

9

(a)

Prog

enito

rs

Mac

roph

ages

Neu

troph

ilsEo

sinop

hils

Baso

phils

Mon

ocyt

es

B-ce

lls

CD4

T-ce

llsCD

8 T-

cells

NK

cells

DPF3


000

0

093

8

113

2

133

3

149

4

163

2

170

8

193

8

281

4

(b)




































SNF2 enzymes

CHD1FC 19CHD2FC 49

HELLSFC 069



ARID1ABAF250aFC 21

SMARCD1BAF60AFC 17

SMARCC2BAF170FC 25

ARID1BBAF250bFC 06

ACTL6ABAF53AFC 04

SMARCE1BAF57FC 07





ACTL

6BM

TA2

CHD

5SM

ARC

A1

DPF

3D

PF1

ACTB

MO

RF4L

2M

ORF

4L1

CHD

2BP

TFEP

C1BA

Z1A

RBBP

4SM

ARC

E1RU

VBL

2A

RID

1ARB

BP7

CHD

1LCH

D9

CHD

1SM

ARC

A2

SMA

RCC1

SMA

RCA

5BR

D8

PHF1

0SM

ARC

A4

POLE

3H

LTF

MTA

1A

RID

2IN

G3

INO

80D

ACTL

6ABR

D7

MEA

F6BT

AF1

ATRX

PBRM

1A

RID

1B

GAT

AD

2AIN

O80

CHD

4

CHD

8SM

ARC

B1M

BD3

GAT

AD

2BSM

ARC

D2

EP40

0RU

VBL

1D

PF2

KAT5

CHD

3TT

F2BR

D9

HEL

LSAT

AD

2IN

O80

CU

CHL5

VPS

72TR

RAP

ACTR

6SH

RPH

CHRA

C1AC

TR8

SMA

RCD

1M

CRS1

INO

80E

NFR

KBCH

D6

YEAT

S4D

AM

P1AC

TR5

TFPT

ZRA

NB3

SMA

RCD

3RA

D54

L2M

TA3

ERCC

6IN

O80

BRA

D54

LRA

D54

B


100 293 325 344 360 374 390 408 555


















Table 3 Continued




8 Conclusions









Acknowledgments



References































































































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of


















































SNF2 enzymes

CHD1FC 19CHD2FC 49

HELLSFC 069



ARID1ABAF250aFC 21

SMARCD1BAF60AFC 17

SMARCC2BAF170FC 25

ARID1BBAF250bFC 06

ACTL6ABAF53AFC 04

SMARCE1BAF57FC 07





ACTL

6BM

TA2

CHD

5SM

ARC

A1

DPF

3D

PF1

ACTB

MO

RF4L

2M

ORF

4L1

CHD

2BP

TFEP

C1BA

Z1A

RBBP

4SM

ARC

E1RU

VBL

2A

RID

1ARB

BP7

CHD

1LCH

D9

CHD

1SM

ARC

A2

SMA

RCC1

SMA

RCA

5BR

D8

PHF1

0SM

ARC

A4

POLE

3H

LTF

MTA

1A

RID

2IN

G3

INO

80D

ACTL

6ABR

D7

MEA

F6BT

AF1

ATRX

PBRM

1A

RID

1B

GAT

AD

2AIN

O80

CHD

4

CHD

8SM

ARC

B1M

BD3

GAT

AD

2BSM

ARC

D2

EP40

0RU

VBL

1D

PF2

KAT5

CHD

3TT

F2BR

D9

HEL

LSAT

AD

2IN

O80

CU

CHL5

VPS

72TR

RAP

ACTR

6SH

RPH

CHRA

C1AC

TR8

SMA

RCD

1M

CRS1

INO

80E

NFR

KBCH

D6

YEAT

S4D

AM

P1AC

TR5

TFPT

ZRA

NB3

SMA

RCD

3RA

D54

L2M

TA3

ERCC

6IN

O80

BRA

D54

LRA

D54

B


100 293 325 344 360 374 390 408 555


















Table 3 Continued




8 Conclusions









Acknowledgments



References































































































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















ACTL

6BM

TA2

CHD

5SM

ARC

A1

DPF

3D

PF1

ACTB

MO

RF4L

2M

ORF

4L1

CHD

2BP

TFEP

C1BA

Z1A

RBBP

4SM

ARC

E1RU

VBL

2A

RID

1ARB

BP7

CHD

1LCH

D9

CHD

1SM

ARC

A2

SMA

RCC1

SMA

RCA

5BR

D8

PHF1

0SM

ARC

A4

POLE

3H

LTF

MTA

1A

RID

2IN

G3

INO

80D

ACTL

6ABR

D7

MEA

F6BT

AF1

ATRX

PBRM

1A

RID

1B

GAT

AD

2AIN

O80

CHD

4

CHD

8SM

ARC

B1M

BD3

GAT

AD

2BSM

ARC

D2

EP40

0RU

VBL

1D

PF2

KAT5

CHD

3TT

F2BR

D9

HEL

LSAT

AD

2IN

O80

CU

CHL5

VPS

72TR

RAP

ACTR

6SH

RPH

CHRA

C1AC

TR8

SMA

RCD

1M

CRS1

INO

80E

NFR

KBCH

D6

YEAT

S4D

AM

P1AC

TR5

TFPT

ZRA

NB3

SMA

RCD

3RA

D54

L2M

TA3

ERCC

6IN

O80

BRA

D54

LRA

D54

B


100 293 325 344 360 374 390 408 555


















Table 3 Continued




8 Conclusions









Acknowledgments



References































































































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of



























Table 3 Continued




8 Conclusions









Acknowledgments



References































































































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of






















Acknowledgments



References































































































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of
































































































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of
















review article the roles of snf2/swi2 nucleosome ...jbp2 drd1 rad54 lodestar rad5/16 ris1 shprh adp...

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