review article lncrnas in stem cells -...

Review ArticleLncRNAs in Stem Cells

Shanshan Hu and Ge Shan

School of Life Sciences and CAS Key Laboratory of Brain Function and Disease University of Science and Technology of ChinaHefei Anhui 230027 China

Correspondence should be addressed to Ge Shan shangeustceducn

Received 5 September 2015 Accepted 3 December 2015

Academic Editor Yujing Li

Copyright copy 2016 S Hu and G Shan 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

Noncoding RNAs are critical regulatory factors in essentially all forms of life Stem cells occupy a special position in cell biologyand Biomedicine and emerging results show that multiple ncRNAs play essential roles in stem cells We discuss some of the knownncRNAs in stem cells such as embryonic stem cells induced pluripotent stem cells mesenchymal stem cells adult stem cells andcancer stem cells with a focus on long ncRNAs Roles and functional mechanisms of these lncRNAs are summarized and insightsinto current and future studies are presented

1 Introduction

Less than 2 of human genome is composed of protein-coding genes but transcription is widespread and corre-sponding to more than sim80 of the genome [1 2] Withthe development of deep sequencing and bioinformatics alarge number of noncoding RNAs (ncRNAs) are identified ineukaryotic cells [3 4] NcRNAs greater than 200 nucleotidesare grouped as long noncoding RNAs Majority of lncRNAsare intergenic transcripts and sense or antisense to othertranscripts Similar to mRNAs most lncRNAs are Pol IItranscripts which have a poly-A tail and 51015840 cap But comparedto protein-coding genes lncRNAs show lower evolutionaryconservation and lower expression level LncRNAs are pre-dominantly localized in nucleus [5ndash7] LncRNAs have beenassociated with significant roles in diverse biological eventssuch as chromatin modifications transcriptional regulationand posttranscriptional regulation [8ndash10]

Stem cells are undifferentiated cells that can either self-renew or differentiate into specialized cells Stem cells are ofgreat interest to both basic and biomedical research due totheir unique properties in cell biology [11ndash13] In recent yearsresearchers are paying more and more attention to roles ofncRNAs in stem cells

In this review we will discuss some of the known roles ofncRNAs in stem cells including embryonic stem cells (ESCs)induced pluripotent stem cells (iPSCs) mesenchymal stem

cells (MSCs) adult stem cells and cancer stem cells Table 1gives a brief summary to key properties of each stem cell typeThe focus is on lncRNAs and for roles of small ncRNAs suchas microRNAs and piRNAs in stem cells readers are referredto other articles [14ndash17]

2 LncRNAs in ESCs

Mohamed et al performed a genome-wide screen to identifylncRNAs transcriptionally regulated by Oct4 and Nanog inmouse ESCs (mESCs) by combining themESC transcriptomewith the chromatin immunoprecipitation genomic locationmaps of Oct4 and Nanog [18] Two conserved lncRNAsAK028326 and AK141205 were further confirmed to bedirectly activated by Oct4 or suppressed by Nanog respec-tively In fact AK028326 might be a coactivator of Oct4Later a systematic survey for lincRNAs which are a subclassof lncRNAs transcribed from intergenic regions of codinggenes was conducted with several murine cell lines includingESCs [19] More than a thousand lincRNAs were identifiedand many of them might possess putative functions in thepluripotency or proliferation of ESCs Transcription of somelincRNAswas also regulated by key transcription factors suchas Sox2 Oct4 and Nanog in ESCs

In human ESCs (hESCs) multiple ESC specific lncRNAswere identified with microarray assays [20] Some of these

Hindawi Publishing CorporationStem Cells InternationalVolume 2016 Article ID 2681925 8 pageshttpdxdoiorg10115520162681925

2 Stem Cells International

Table 1 Key properties of each stem cell type

Stem cell Key properties

Embryonic stem cell Derived from the blastocyst stage early mammalian embryos and has the ability to differentiate into anycell type and propagate

Induced pluripotent stem cellA type of pluripotent stem cell that can be generated directly from adult cells classic four specific genesencoding transcription factors (Oct4 Sox2 cMyc and Klf) could convert adult cells into iPSCs holdinggreat promise in the field of regenerative medicine because of indefinite propagation

Mesenchymal stem cell Multipotent stromal cells that can differentiate into a variety of cell types including osteoblastschondrocytes myocytes and adipocytes

Adult stem cell Undifferentiated cells which are found throughout the body after development can divide or self-renewindefinitely and generate all the cell types of the organ from which they originate

Cancer stem cell Cancer cells that possess the ability to give rise to all cell types found in particular cancer samples and cangenerate tumors through the stem cell processes of self-renewal and differentiation into multiple cell types

lncRNAs were involved in pluripotency maintenance andinteracted with SOX2 and SUZ12 (a subunit of PRC2 com-plex) A subset of the identified lncRNAs was involved inneurogenesis of ESCs and these lncRNAs potentially playedneurogenic roles via physical interaction with importantepigenetic factors such as REST and SUZ12 One of thelncRNAs identified in this study rhabdomyosarcoma 2-associated transcript (RMST) was further investigated ina later study [21 22] RMST interacted directly with andserved as a transcriptional coregulator of SOX2 to modulatethe transcription of a number of SOX2 downstream genesRecently the long terminal repeats of human specific endoge-nous retrovirus subfamilyH (HERVH) which is transposableelements expressed preferentially in hESCs was found tofunction as nuclear lncRNAs with associations with OCT4coactivators such as p300 and Mediator subunits [23]

A recent report showed that pluripotency-associatedtranscription factor SOX2 has an overlapping long non-coding transcript SOX2OT which was highly expressed inembryonic stem cells and downregulated upon the inductionof differentiation [24] SOX2OT had a potential role inmodulating pluripotency through the regulation of SOX2expression

Another lincRNA linc-RoR might function as micro-RNA sponge to prevent mRNA of some key transcriptionfactors in hESCs from microRNA mediated regulation [25]Thus this lncRNA played a role in ESC maintenance anddifferentiation in the cytoplasm

These results implicated that lncRNAs could modulatethe pluripotency and differentiation of ESCs via interveningthe transcriptional and epigenetic regulatory networks in thenucleus or tuning the microRNA functions in the cytoplasmOther cytoplasmic and nuclear roles of lncRNAs in ESCs arewaiting for further investigations

3 LncRNAs in iPSCs

The conversion of lineage-committed cells to iPSCs is aprocess called reprogramming In a 2010 paper Rinn Labcharacterized the transcriptional reorganization of lincR-NAs and identified a vast number of lincRNAs associating

with reprogramming of human iPSCs (hiPSCs) [26] TheselincRNAs were overexpressed in both hESCs and hiPSCsbut showed an elevated level in iPSCs compared to ESCssuggesting that their activation might promote the iPSCsOne of the lincRNAs named lincRNA-RoR for ldquoregulator ofreprogrammingrdquo was regulated by pluripotency transcriptionfactors such as OCT4 SOX2 and NANOG Knockdownof lincRNA-RoR resulted in an inhibition in reprogram-ming Interestingly linc-RoR was later found to functionas a competing endogenous RNA in hESCs as alreadydiscussed

By analyzing single-cell transcriptomes during somaticcell reprogramming more than 400 hundred lncRNAs werecharacterized that were dynamically expressed at definedstages of reprogramming [27] During reprogramming setsof relevant lncRNAs were activated to modulate signal-ing pathways repress lineage-specific genes and regulatemetabolic gene expression

The reprogramming process is accompanied by globalepigenetic remodeling [28] The lncRNA Xist responsible forX chromosome inactivation (XCI) has been investigated as aclassic epigenetic regulator in the context of reprogramming[29 30] Female mESCs have low Xist expression and twoactive X chromosomes Successfully reprogrammed femalemurine iPSCs (miPSCs) have undergone X chromosomereactivation and have the same feature in Xist expressionas mESCs Upon differentiation female mESCs and miPSCsinitiate Xist expression and XCI Surprisingly hESCs andhiPSCs can be divided into three classes based on theirdifferent states of Xist expression Class I hESCs and hiPSCsbehave just like mESCs andmiPSCs Class II human pluripo-tent stem cells express Xist and exhibit random XCI evenbefore differentiation Class III cells have lost XIST expres-sion but have already initiated XCI regardless of whetherthey are in the undifferentiated or differentiating conditions[31]

It seems that lncRNAs play essential roles in the repro-gramming process A better understanding in lncRNAs andmore broadly ncRNAs in the context of iPSCswould certainlybenefit future biomedical research aiming to utilize iPSCs inthe clinic

Stem Cells International 3

4 LncRNAs in MSCs andthe Mesodermal Lineage

Mesenchyme is connective tissue derived from the meso-derm during animal development MSCs are first identi-fied in the bone marrow (BM) stroma BM MSCs providemicroenvironment for hematopoietic stem cells and can alsodifferentiate into various mesodermal lineages Later MSCsare found in many tissues such as placenta umbilical cordblood adipose tissue muscle corneal stroma and the dentalpulp of deciduous baby teeth These MSCs with differentorigins all possess property to differentiate into mesodermallineages Thus MSCs are an important source of multipotentcells with great potential of clinic applications LncRNAs inMSCs have significant regulatory roles and potentially can beused as biomarkers for disease or therapeutic targets Wanget al performed differential expression profiles of lncRNAsandmRNAs of undifferentiated versus chondrodifferentiatedhuman BM MSCs using microarray in 2015 [32] Someof the identified lncRNAs could be important regulatorsin chondrogenic differentiation The same group identifiedlncRNAs with differential expression and putative functionsduring the osteogenic differentiation of human BM MSCs[33] A total of 1206 differentially expressed lncRNAs wereidentified and among them 687 were upregulated and 519downregulated more than twofold

Some lncRNAs are functionally required during adipo-genesis [34] Brown adipose tissue (BAT) and white adiposetissue (WAT) are differentiated fromMSCs in adipose tissuesSun et al performed RNA sequencing and identified 175lncRNAs in total from in vitro cultured brown and whitepreadipocytes in vitro differentiated mature brown andwhite adipocytes and primary brown and white matureadipocytes directly isolated from mice [34] These lncRNAswere up- or downregulated during differentiation of bothbrown and white adipocytes Activation of some transcrip-tional factors and cofactors such as peroxisome proliferator-activated receptor 120574 (PPAR120574) and CCAATenhancer-bindingprotein 120572 (CEBP120572) is the hallmark of brown adipocytedifferentiation These lncRNAs have promoters with bindingof PPAR120574 andor CEBP120572 key transcription factors RNAi-mediated loss-of-function identified the top 20 lncRNAs thatmay be involved in the proper differentiation of adipocyteprecursors Later in 2014 substantially more lncRNAs wereidentified and may be functionally required during properadipogenesis [35] Zhao and colleagues identified induciblelncRNAs involved in brown fat development and thermogen-esis using transcriptional profiling in adipose tissues and cellsduring brown adipocyte differentiation [36] Twenty-onelncRNAs were found to be enriched in BAT and among themAK038898 significantly impaired brown adipogenesis uponRNAi knocking downThis lncRNAwas then renamedbrownfat lncRNA 1 (Blnc1) The expression of Blnc1 was highlyinduced during brown and beige adipogenesisThe inductionwas correlated with the stimulation of the thermogenic geneprogram and in consistency with the expression of keythermogenicmarkers such as Ucp1 in adipose tissues Blnc1 is

primarily localized in the nucleus and forms a ribonucleopro-tein complexwith EBF2 which is amember of the EBF familyof transcription factors that has been implicated in the controlof adipogenesis [37] Blnc1 itself is also a target of EBF2thereby forming a feed-forward regulatory loop to regulateadipocyte gene expression Knowing the distinct roles andfunctional mechanisms of lncRNAs in adipogenesis havegreat values in developing new approaches to fight obesityand other related pathological consequences

LncRNAs also regulate cardiomyocyte differentiationZhu et al identified multiple lncRNAs involved in thedevelopment of the lateral mesoderm and in the differenti-ation of cardiomyocytes with P19 cells which were isolatedfrom embryo-derived mouse teratocarcinoma and coulddifferentiate into cardiacmyocytes [38] Forty differentiallyexpressed lncRNAs 28 upregulated and 12 downregulatedwere identified using microarrays In another researchMatkovich and colleagues used genome-wide sequencingand improved bioinformatics to measure dynamic lncRNAregulation during the transition between embryo and adultmouse hearts and identified numerous cardiac-specific lncR-NAs [39] Analyses indicated a broad role of regulatedcardiac lncRNAs asmodulators of key cardiac transcriptionalpathways Two lncRNAs Fendrr and Braveheart were laterfound to be involved in the development of the lateralmesoderm in the heart and the differentiation of cardiacmyocytes respectively [40 41] Fendrr was discovered in asurvey of differentially expressed lncRNAs in six differenttissues dissected from early somite-stage of mouse embryosby using RNA-seq and ChIP-seq [40] Knocking out Fendrrby homologous recombination was embryonic lethal TheChIP data showed that Fendrr interacts directly with thePRC2 andor TrxGMLL complexes in mouse embryosindicating that it acts as a modulator of chromatin signaturesdefining gene activity in embryonic development Braveheartalso plays roles as an epigenetic factor [41] This lncRNA isrequired for the progression of nascent mesoderm towards acardiac fate by interacting with SUZ12 a component of PRC2to alter cardiomyocyte differentiation and retain the cardiacphenotype in neonatal cardiomyocyte [41] Cardiovasculardiseases are currently themain cause ofmorbidityworldwideand researches on these lncRNAs are critical to achievinga better understanding of heart development and designingnew ways for the diagnosis and treatment of cardiac relateddiseases

Several important lncRNAs play critical roles in myo-genesis [42] Linc-MD1 is a muscle-specific long noncodingRNA expressed during early phases of muscle differentiationIt promotes the switch of muscle differentiation from earlyto later stages by acting as a miR-133 and miR-135 sponge[43] What is more interesting is that linc-MD1 is also theprimary transcript of miR-133b [44] The process of linc-MD1 as a pri-microRNA by Drosha is controlled by HuRThe binding of HuR to linc-MD1 suppresses Drosha cleavageof linc-MD1 and leads to accumulation of linc-MD1 whichfurther inhibits the functions of miR-133 as a sponge sothat this microRNA could not target the HuR mRNA ThusHuR and linc-MD1 form an elegant feed-forward positive


loop [45] Another lncRNA YAM-1 affects myogenesis viaepigenetic transcriptional activation [42] The transcriptionfactor Yin Yang 1 (YY1) regulates expression multiple genesin myoblasts and YAM-1 is positively regulated by YY1YAM-1 expression is downregulated during myogenesis andits expression inhibits myoblast differentiation YAM-1 reg-ulates the transcription of miR-715 in cis and miR-715 isa microRNA that targets Wnt7b an important signalingmodulator of myogenesis [42]

5 LncRNAs in Adult Stem Cells

A series of studies focused on lncRNAs in adult stem cellssuch as hematopoietic stem cells and adult neural stem cellsThe milestone discovery of lincRNA HOTAIR in 2007 wascarried out with primary human fibroblasts which are a kindof somatic stem cell [45] In this and following researchesHOTAIR was found to bind both the polycomb repressivecomplex 2 (PRC2) and the LSD1CoRESTREST complexand thus to modulate histone modifications on target genes[45 46] The lncRNA ANCR (antidifferentiation noncodingRNA)was also characterized by epidermal progenitors versusdifferentiating cells [47] Knocking down ANCR alone ledto rapid expression of differentiation genes ANCR wasthought to be essential for the undifferentiated state althoughthe exact molecular mechanism requires further investiga-tion [47] On the other hand an lncRNA called terminaldifferentiation-induced noncoding RNA (TINCR) promotedepidermal differentiation [48] TINCR had a very low levelin epidermal stem cells but it was dramatically inducedupon differentiation As a cytoplasmic ncRNA TINCR couldinteract with mRNAs of many differentiation genes such asKRT80 and RNA-binding protein STAU1 to mediate mRNAstabilization through binding TINCR box

In a systematic analysis of adult neural stem cell lineagein the mouse subventricular zone for lncRNA with potentialroles in adult neurogenesis Ramos et al identified twolncRNAs Six3os andDlx1as playing crucial roles in the lineagespecification of adult stem cells [49] The same lab latercharacterized a neural-specific lncRNA named Pnky whichlocalized in the nucleus of human and mouse neural stemcells [50] With knockdown of Pnky neuronal differentiationincreased both in vitro and in vivo Pnky interacted with thesplicing regulator PTBP1 and thus regulated the expressionand alternative splicing

Recently Luo et al identified 159 unannotated lncRNAsenriched in hematopoietic stem cells with RNA sequencingKnocking down two of these lncRNAs showed effects onself-renewal and lineage commitment of hematopoietic stemcells [51] Interestingly the genomic binding sites of onelncRNA overlapped significantly with binding sites of akey hematopoietic transcription factor E2A indicating thislncRNA might be a cofactor of the transcription factor

It is obvious that lncRNAs possess vital roles in a varietyof somatic stem cells with diverse mechanisms Consideringthe large number of lncRNAs identified we still have a long

way to understand the full range of roles of these regulatorsin adult stem cells as well as in the other eukaryotic cells

6 LncRNAs in Cancer Stem Cells

Cancer stem cells (CSCs) play critical roles in tumor initi-ation progression metastasis chemoresistance and recur-rence [52 53] Some studies showed that lncRNAs might beinvolved in regulating stem cell signaling in CSCs

A novel lncRNA HIF2PUT (hypoxia-inducible factor-2120572promoter upstream transcript) was identified in a kind ofCSCs the osteosarcoma stem cells [54] HIF2PUT expressionlevels were positively correlated with its parent gene HIF-2120572 in osteosarcoma tissues indicating a regulatory roleof HIF2PUT through HIF-2120572 Knocking down HIF2PUTenhanced the proliferation migration and self-renewal ofosteosarcoma stem cells while overexpression of HIF2PUTdecreased the proliferation migration and self-renewal [54]In liver CSCs lncTCF7 was identified and it recruited theSWISNF complex and further activated the Wnt signalingto promote self-renewal of liver CSCs and tumor propagation[55]

The lncRNA MALAT-1 (metastasis-associated lung ade-nocarcinoma transcript 1) was found to be upregulated inCSCs and high expression levels of this lncRNA positivelycorrelated with the proportion of CSCs in pancreatic can-cer cells [10 56 57] MALAT-1 might serve as an onco-genic lncRNA in pancreatic cancer by promoting epithelial-mesenchymal transition and stimulating the expression ofself-renewal factors such as Sox2

An lncRNA H19 known for more than two decades alsofunctions in cancer and cancer stem cells [58 59] H19 isan imprinting gene in both mice and human [60 61] H19RNA was identified as a tumor suppressor and was involvedin Wilmsrsquo tumor long time ago in early 1990s [62 63]Despite the fact that H19 is one of the first identified mostabundant and conserved ncRNAs in mammals its actuallyphysiological functions and functionalmechanism have beenelusive for a long time In 2007 and then in 2012 compellinglines of evidence showed that H19 is the primary transcriptof a microRNA miR-675 [64 65] Overexpression of miR-675 in embryonic and extraembryonic cell lines reducedproliferation Just like the linc-MD1 (the primary transcriptof miR-133b) the processing of H19 into miR-675 is alsoregulated by HuR What makes H19 more intriguing is thefinding that H19 could be sponge of let-7 and miR-106a(a miR-17-5p family member) [66 67] HOTAIR with highexpression level was always involved in various cancers aswellas CSCs via promoting tumorigenesis cell proliferation ortumor metastasis and could be a novel epigenetic moleculartarget for therapeutics [68 69] Linc00617 may be anotherpotential therapeutic target for breast cancer because offunctioning as a key regulator of EMT and promotes cancerprogression and metastasis via activating the transcription ofSox2 [70]

Knowing the roles of lncRNAs in tumor cells andespecially in CSCs would help the development of tumor


Table 2 Regulatory roles of lncRNAs in different stem cells

LncRNA Stem cell types Regulations and functionsAK028326 ESCs Transcriptionally regulated by Oct4 and NanogAK141205 ESCs A coactivator of Oct4RMST ESCs Involved in pluripotency maintenance and interacting with SOX2 and SUZ12

HERVH ESCs Function as nuclear lncRNAs with associations with OCT4 coactivators such as p300 andMediator subunits

SOX2OT ESCs Modulate pluripotency through the regulation of SOX2 expressionLinc-RoR ESCs iPSCs Function as microRNA sponge to prevent mRNA of some key transcription factorsXist ESCs iPSCs An epigenetic regulator of X chromosome inactivation

Blnc1 MSCs Highly induced during brown and beige adipogenesis and form a feed-forward regulatory loopwith EBF2 to regulate adipocyte gene expression

Fendrr MSCs Interact directly with the PRC2 andor TrxGMLL complexes and act as a modulator ofchromatin signatures defining gene activity in embryonic development

Braveheart MSCs An epigenetic factor required for the progression of nascent mesoderm towards a cardiac fate byinteracting with SUZ12

Linc-MD1 MSCs Promote the switch of muscle differentiation from early to later stages by acting as miR-133 andmiR-135 sponge

YAM-1 MSCs Affect myogenesis via epigenetic transcriptional activation

HOTAIR ASCs CSCs Bind both the polycomb repressive complex 2 (PRC2) and the LSD1CoRESTREST complex andthus modulate histone modifications on target genes

ANCR ASCs Essential for the undifferentiated state

TINCR ASCs Interact with mRNAs of many differentiation genes such as KRT80 and RNA-binding proteinSTAU1 to mediate mRNA stabilization through binding TINCR box

Six3os ASCs Play crucial roles in the lineage specification of adult stem cellsDlx1as ASCs Play crucial roles in the lineage specification of adult stem cellsPnky ASCs Interact with the splicing regulator PTBP1 and regulate the expression and alternative splicingHIF2PUT CSCs A regulatory role through HIF-2120572

lncTCF7 CSCs Recruit the SWISNF complex and further activated the Wnt signaling to promote self-renewal ofliver CSCs and tumor propagation

MALAT-1 CSCs Serve as an oncogenic lncRNA in pancreatic cancer by promoting epithelial-mesenchymaltransition and stimulating the expression of self-renewal factors such as Sox2

H19 CSCs Primary transcript of a microRNA miR-675 processing of H19 into miR-675 is also regulated byHuR

Linc00617 CSCs Function as a key regulator of EMT and promote cancer progression and metastasis via activatingthe transcription of Sox2

diagnosis and therapeutics [71] So far lncRNA researchin cancer and CSCs is just emerging and more efforts arerequired to push the field forward Table 2 lists lncRNAs theirregulatory roles and stem cells where they exert functions

7 Conclusions and Perspectives

LncRNAs and other ncRNAs play substantial roles in diversestem cell types Here we have summarized some of thelncRNAs in five classes of stem cells although we are nottrying to summarize all the known lncRNAs in all kindsof stem cells and have to miss a lot of researches aboutlncRNAs in multiple other somatic and germline stem cellsLncRNAs could participate in the biology of stem cells withdiverse mechanisms by serving as transcriptional coactivator

or corepressor modular scaffold for chromatin modifiersfactors of tuning splicing primary transcripts of microRNAscompeting endogenous RNAs of microRNAs and so on(Figure 1) We need to keep in mind that the functions andmechanisms of a vast majority of lncRNAs in stem cellsremain unknownThe pervasive transcription of the genomeand the growing inventory of ncRNAs with newly identifiedncRNAs such as circRNAs and EIciRNAs also make a call forenormous future efforts to investigate ncRNAs in stem cells[72ndash77] Nevertheless the field of ncRNA research in stemcells has emerged and has been making progress towards asystematic understanding of stem cell biology Researches inthis area would eventually bring benefit to the understandingof lncRNAs and Biomedicine


PTBP1

Pnky

Xist

Nucleus

Cytoplasm

mir-145

linc-ROR

TF mRNA

RISC

Ribosome

(a)(b)

(c)

(g)

Oct4

cMycNanog

Sox2

(d)

AAA

TINCR box

TINCRSTAU1

(f) mRNA

EBF2

EBF2

Blnc1

Blnc1

DroshaHuR

Drosha

HuR

(e) Linc-MD1H19

Figure 1 Some known functional mechanisms of lncRNAs in stem cells (a) Pnky localizes to the nucleus and interacts with the mRNAsplicing regulator PTBP1 to regulate splicing of key transcripts (b) some lncRNAs serve as cofactors of key transcription factors (TF) toregulate gene transcription (c) Xist as an epigenetic regulator of X chromosome inactivation plays roles in female ESCs and iPSCs (d) Blnc1is activated by EBF2 and functions as a coactivator of EBF2 (e) linc-MD1 is the primary transcript of miR-133b and H19 is the primarytranscript of miR-675 and the Drosha processing of both is regulated by HuR (f) TINCR interacts with STAU1 and multiple mRNAs via anRNA motif called TINCR box (g) linc-ROR functions as a mir-145 sponge

Conflict of Interests

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

References

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[43] M Cesana D Cacchiarelli I Legnini et al ldquoA long noncodingRNA controls muscle differentiation by functioning as a com-peting endogenous RNArdquo Cell vol 147 no 2 pp 358ndash369 2011

[44] I Legnini M Morlando A Mangiavacchi A Fatica and IBozzoni ldquoA feedforward regulatory loop between HuR andthe long noncoding RNA linc-MD1 controls early phases ofmyogenesisrdquoMolecular Cell vol 53 no 3 pp 506ndash514 2014


[45] J L RinnM Kertesz J KWang et al ldquoFunctional demarcationof active and silent chromatin domains in human HOX loci bynoncoding RNAsrdquo Cell vol 129 no 7 pp 1311ndash1323 2007

[46] M-C Tsai O Manor Y Wan et al ldquoLong noncoding RNA asmodular scaffold of histone modification complexesrdquo Sciencevol 329 no 5992 pp 689ndash693 2010

[47] M Kretz D E Webster R J Flockhart et al ldquoSuppressionof progenitor differentiation requires the long noncoding RNAANCRrdquo Genes and Development vol 26 no 4 pp 338ndash3432012

[48] M Kretz Z Siprashvili C Chu et al ldquoControl of somatic tissuedifferentiation by the long non-coding RNA TINCRrdquo Naturevol 493 no 7431 pp 231ndash235 2013

[49] A D Ramos A Diaz A Nellore et al ldquoIntegration of genome-wide approaches identifies lncRNAs of adult neural stem cellsand their progeny in vivordquo Cell Stem Cell vol 12 no 5 pp 616ndash628 2013

[50] A D Ramos R E Andersen S J Liu et al ldquoThe longnoncoding RNA Pnky regulates neuronal differentiation ofembryonic and postnatal neural stem cellsrdquo Cell Stem Cell vol16 no 4 pp 439ndash447 2015

[51] M LuoM JeongD Sun et al ldquoLong non-coding RNAs controlhematopoietic stem cell functionrdquo Cell Stem Cell vol 16 no 4pp 426ndash438 2015

[52] F Islam V Gopalan R A Smith and A K-Y Lam ldquoTransla-tional potential of cancer stem cells a review of the detection ofcancer stem cells and their roles in cancer recurrence and cancertreatmentrdquo Experimental Cell Research vol 335 no 1 pp 135ndash147 2015

[53] G A Dashyan V F Semiglazov R V Donskikh T Y Semi-glazova V V Vorotnikov and V S Apollonova ldquoThe role ofbreast cancer stem cells in metastasisrdquo Voprosy Onkologii vol61 no 2 pp 169ndash173 2015

[54] Y Wang J Yao H Meng et al ldquoA novel long non-codingRNA hypoxia-inducible factor-2120572 promoter upstream tran-script functions as an inhibitor of osteosarcoma stem cells invitrordquoMolecular Medicine Reports vol 11 no 4 pp 2534ndash25402015

[55] YWang L He Y Du et al ldquoThe long noncoding RNA lncTCF7promotes self-renewal of human liver cancer stem cells throughactivation of Wnt signalingrdquo Cell Stem Cell vol 16 no 4 pp413ndash425 2015

[56] F Jiao H Hu C Yuan et al ldquoElevated expression level of longnoncoding RNA MALAT-1 facilitates cell growth migrationand invasion in pancreatic cancerrdquo Oncology Reports vol 32no 6 pp 2485ndash2492 2014

[57] F Jiao H Hu T Han et al ldquoLong noncoding RNA MALAT-1enhances stem cell-like phenotypes in pancreatic cancer cellsrdquoInternational Journal of Molecular Sciences vol 16 no 4 pp6677ndash6693 2015

[58] V Pachnis A Belayew and SM Tilghman ldquoLocus unlinked to120572-fetoprotein under the control of themurine raf andRif genesrdquoProceedings of the National Academy of Sciences of the UnitedStates of America vol 81 no 17 pp 5523ndash5527 1984

[59] C I Brannan E C Dees R S Ingram and S M TilghmanldquoThe product of the H19 gene may function as an RNArdquoMolecular and Cellular Biology vol 10 no 1 pp 28ndash36 1990

[60] M S Bartolomei S Zemel and S M Tilghman ldquoParentalimprinting of the mouse H19 generdquo Nature vol 351 no 6322pp 153ndash155 1991

[61] Y Zhang and B Tycko ldquoMonoallelic expression of the humanH19 generdquo Nature Genetics vol 1 no 1 pp 40ndash44 1992

[62] Y Hao T Crenshaw T Moulton E Newcomb and B TyckoldquoTumour-suppressor activity of H19 RNArdquoNature vol 365 no6448 pp 764ndash767 1993

[63] M J C Steenman S Rainier C J Dobry P Grundy I L Horonand A P Feinberg ldquoLoss of imprinting of IGF2 is linked toreduced expression and abnormalmethylation ofH19 inWilmsrsquotumourrdquo Nature Genetics vol 7 no 3 pp 433ndash439 1994

[64] X Cai and B R Cullen ldquoThe imprinted H19 noncoding RNA isa primarymicroRNAprecursorrdquoRNA vol 13 no 3 pp 313ndash3162007

[65] A Keniry D Oxley P Monnier et al ldquoThe H19 lincRNA is adevelopmental reservoir ofmiR-675 that suppresses growth andIgf1rrdquo Nature Cell Biology vol 14 no 7 pp 659ndash665 2012

[66] A N Kallen X-B Zhou J Xu et al ldquoThe imprinted H19lncRNA antagonizes let-7 microRNAsrdquo Molecular Cell vol 52no 1 pp 101ndash112 2013

[67] J Imig A Brunschweiger A Brummer et al ldquomiR-CLIPcapture of a miRNA targetome uncovers a lincRNA H19-miR-106a interactionrdquoNature Chemical Biology vol 11 no 2 pp 107ndash114 2015

[68] Z Yang L Zhou L-MWu et al ldquoOverexpression of long non-coding RNA HOTAIR predicts tumor recurrence in hepatocel-lular carcinomapatients following liver transplantationrdquoAnnalsof Surgical Oncology vol 18 no 5 pp 1243ndash1250 2011

[69] X Li Z Wu Q Mei et al ldquoLong non-coding RNA HOTAIR adriver of malignancy predicts negative prognosis and exhibitsoncogenic activity in oesophageal squamous cell carcinomardquoBritish Journal of Cancer vol 109 no 8 pp 2266ndash2278 2013

[70] H Li L Zhu L Xu et al ldquoLong noncoding RNA linc00617exhibits oncogenic activity in breast cancerrdquoMolecular Carcino-genesis 2015

[71] L Chen F Rashid A Shah et al ldquoThe isolation of anRNA aptamer targeting to p53 protein with single amino acidmutationrdquo Proceedings of the National Academy of Sciences vol112 no 32 pp 10002ndash10007 2015

[72] J Salzman C Gawad P L Wang N Lacayo and P O BrownldquoCircular RNAs are the predominant transcript isoform fromhundreds of human genes in diverse cell typesrdquo PLoS ONE vol7 no 2 Article ID e30733 2012

[73] S Memczak M Jens A Elefsinioti et al ldquoCircular RNAs area large class of animal RNAs with regulatory potencyrdquo Naturevol 495 no 7441 pp 333ndash338 2013

[74] T B Hansen T I Jensen B H Clausen et al ldquoNatural RNAcircles function as efficient microRNA spongesrdquo Nature vol495 no 7441 pp 384ndash388 2013

[75] Z Li C Huang C Bao et al ldquoExon-intron circular RNAsregulate transcription in the nucleusrdquo Nature Structural andMolecular Biology vol 22 no 3 pp 256ndash264 2015

[76] H Liu X Wang H-DWang et al ldquoEscherichia coli noncodingRNAs can affect gene expression and physiology of Caenorhab-ditis elegansrdquo Nature Communications vol 3 article 1073 2012

[77] S Hu J Wu L Chen and G Shan ldquoSignals from noncodingRNAs unconventional roles for conventional pol III tran-scriptsrdquo International Journal of Biochemistry and Cell Biologyvol 44 no 11 pp 1847ndash1851 2012

Submit your manuscripts athttpwwwhindawicom

Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014

Anatomy Research International

PeptidesInternational Journal of


Hindawi Publishing Corporation httpwwwhindawicom

International Journal of

Volume 2014

Zoology


Molecular Biology International

GenomicsInternational Journal of


The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014


BioinformaticsAdvances in

Marine BiologyJournal of



Signal TransductionJournal of


BioMed Research International

Evolutionary BiologyInternational Journal of



Biochemistry Research International

ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014


Genetics Research International


Advances in

Virolog y

Hindawi Publishing Corporationhttpwwwhindawicom

Nucleic AcidsJournal of

Volume 2014

Stem CellsInternational



Enzyme Research



Microbiology


Table 1 Key properties of each stem cell type

Stem cell Key properties

Embryonic stem cell Derived from the blastocyst stage early mammalian embryos and has the ability to differentiate into anycell type and propagate

Induced pluripotent stem cellA type of pluripotent stem cell that can be generated directly from adult cells classic four specific genesencoding transcription factors (Oct4 Sox2 cMyc and Klf) could convert adult cells into iPSCs holdinggreat promise in the field of regenerative medicine because of indefinite propagation

Mesenchymal stem cell Multipotent stromal cells that can differentiate into a variety of cell types including osteoblastschondrocytes myocytes and adipocytes

Adult stem cell Undifferentiated cells which are found throughout the body after development can divide or self-renewindefinitely and generate all the cell types of the organ from which they originate

Cancer stem cell Cancer cells that possess the ability to give rise to all cell types found in particular cancer samples and cangenerate tumors through the stem cell processes of self-renewal and differentiation into multiple cell types

lncRNAs were involved in pluripotency maintenance andinteracted with SOX2 and SUZ12 (a subunit of PRC2 com-plex) A subset of the identified lncRNAs was involved inneurogenesis of ESCs and these lncRNAs potentially playedneurogenic roles via physical interaction with importantepigenetic factors such as REST and SUZ12 One of thelncRNAs identified in this study rhabdomyosarcoma 2-associated transcript (RMST) was further investigated ina later study [21 22] RMST interacted directly with andserved as a transcriptional coregulator of SOX2 to modulatethe transcription of a number of SOX2 downstream genesRecently the long terminal repeats of human specific endoge-nous retrovirus subfamilyH (HERVH) which is transposableelements expressed preferentially in hESCs was found tofunction as nuclear lncRNAs with associations with OCT4coactivators such as p300 and Mediator subunits [23]

A recent report showed that pluripotency-associatedtranscription factor SOX2 has an overlapping long non-coding transcript SOX2OT which was highly expressed inembryonic stem cells and downregulated upon the inductionof differentiation [24] SOX2OT had a potential role inmodulating pluripotency through the regulation of SOX2expression

Another lincRNA linc-RoR might function as micro-RNA sponge to prevent mRNA of some key transcriptionfactors in hESCs from microRNA mediated regulation [25]Thus this lncRNA played a role in ESC maintenance anddifferentiation in the cytoplasm

These results implicated that lncRNAs could modulatethe pluripotency and differentiation of ESCs via interveningthe transcriptional and epigenetic regulatory networks in thenucleus or tuning the microRNA functions in the cytoplasmOther cytoplasmic and nuclear roles of lncRNAs in ESCs arewaiting for further investigations

3 LncRNAs in iPSCs

The conversion of lineage-committed cells to iPSCs is aprocess called reprogramming In a 2010 paper Rinn Labcharacterized the transcriptional reorganization of lincR-NAs and identified a vast number of lincRNAs associating

with reprogramming of human iPSCs (hiPSCs) [26] TheselincRNAs were overexpressed in both hESCs and hiPSCsbut showed an elevated level in iPSCs compared to ESCssuggesting that their activation might promote the iPSCsOne of the lincRNAs named lincRNA-RoR for ldquoregulator ofreprogrammingrdquo was regulated by pluripotency transcriptionfactors such as OCT4 SOX2 and NANOG Knockdownof lincRNA-RoR resulted in an inhibition in reprogram-ming Interestingly linc-RoR was later found to functionas a competing endogenous RNA in hESCs as alreadydiscussed

By analyzing single-cell transcriptomes during somaticcell reprogramming more than 400 hundred lncRNAs werecharacterized that were dynamically expressed at definedstages of reprogramming [27] During reprogramming setsof relevant lncRNAs were activated to modulate signal-ing pathways repress lineage-specific genes and regulatemetabolic gene expression

The reprogramming process is accompanied by globalepigenetic remodeling [28] The lncRNA Xist responsible forX chromosome inactivation (XCI) has been investigated as aclassic epigenetic regulator in the context of reprogramming[29 30] Female mESCs have low Xist expression and twoactive X chromosomes Successfully reprogrammed femalemurine iPSCs (miPSCs) have undergone X chromosomereactivation and have the same feature in Xist expressionas mESCs Upon differentiation female mESCs and miPSCsinitiate Xist expression and XCI Surprisingly hESCs andhiPSCs can be divided into three classes based on theirdifferent states of Xist expression Class I hESCs and hiPSCsbehave just like mESCs andmiPSCs Class II human pluripo-tent stem cells express Xist and exhibit random XCI evenbefore differentiation Class III cells have lost XIST expres-sion but have already initiated XCI regardless of whetherthey are in the undifferentiated or differentiating conditions[31]

It seems that lncRNAs play essential roles in the repro-gramming process A better understanding in lncRNAs andmore broadly ncRNAs in the context of iPSCswould certainlybenefit future biomedical research aiming to utilize iPSCs inthe clinic













































PTBP1

Pnky

Xist

Nucleus

Cytoplasm

mir-145

linc-ROR

TF mRNA

RISC

Ribosome

(a)(b)

(c)

(g)

Oct4

cMycNanog

Sox2

(d)

AAA

TINCR box

TINCRSTAU1

(f) mRNA

EBF2

EBF2

Blnc1

Blnc1

DroshaHuR

Drosha

HuR

(e) Linc-MD1H19




References























































































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology













































PTBP1

Pnky

Xist

Nucleus

Cytoplasm

mir-145

linc-ROR

TF mRNA

RISC

Ribosome

(a)(b)

(c)

(g)

Oct4

cMycNanog

Sox2

(d)

AAA

TINCR box

TINCRSTAU1

(f) mRNA

EBF2

EBF2

Blnc1

Blnc1

DroshaHuR

Drosha

HuR

(e) Linc-MD1H19




References























































































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology











































































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology

review article lncrnas in stem cells -...

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