R6F6R6NG6S

R.efevev\'ce.s

IX. REFERENCES

1. Alberts B, Wilson J, Johnson A, Hunt, Lewis J, Raff M, Roberts K (2008).

Molecular biology o/the cell. Fifth Edn: 549.

20 Albrecht KH, Eicher EM (2001). Evidence that Sry is expressed in pre-Sertoli cells

and Sertoli and granulosa cells have a common precursor. Dev Bioi 240:92-107.

3. AI-Khouri AM, Ma Y, Togo SH, Williams S, Mustelin T (2005). Cooperative

phosphorylation of the tumor suppressor phosphatase and tensin homologue

(PTEN) by casein kinases and glycogen synthase kinase 3beta. J Bioi Chern

280(42):35195-351202.

4. An J, Beauchemin N, Albanese J, Abney TO, Sullivan AK (1997). Use of a rat

cDNA probe specific for the Y chromosome to detect male-derived cells. J Androl

18(3): 289-293.

5. Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N,

Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, Chien M, Russo JJ,

Ju J, Sheridan R, Sander C, Zavolan M, Tuschl T (2006). A novel class of small

RNAs bind to MILl protein in mouse testes. Nature 442: 203-207.

6. Aravin AA, Hannon GJ, Brennecke J (2007).The piwi-piRNA pathway provides

an adaptive defense in the transposon arms race. Science 318: 761-764.

7. Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,

Gaasterland T, Meyer J, Tuschl T (2003). The small RNA profile during

Drosophila melanogaster development. Dev Cell 5:337-350.

8. Aravin AA, Sachidanandam R, Bourc'his D, Schaefer C, Pezic D, Toth KF, Bestor

T, Hannon GJ (2008). A piRNA pathway primed by individual transposons is

linked to de novo DNA methylation in mice. Mol Cell 31:785-799.

9. Aravin AA, Sachidanandam R, Girard A, Fejes-Toth K, Hannon GJ (2007).

Developmentally regulated piRNA clusters implicate MILl in transposon control.

Science, 316: 744 - 747.

10. Arena S, Benvenuti Sand Bardelli A (2005). Genetic analysis of the kinome and

phosphatome in cancer. Cell Mol Lift Sci 62: 2092-2099.

11. Assis R, Kondrashov AS (2009). Rapid repetitive element-mediated expansion of

piRNA clusters in mammalian evolution. Proc Natl Acad Sci USA 106: 7079-

7082.

201

RefeveVl-c,es.

12. Assumpcao JG, Benedetti CE, Maciel-Guerra AT, Guerra Jr G, Baptista MT,

Scolfaro MR., De Mello MP (2002). Novel mutations affecting SRY DNA-binding

activity: the HMG box N65H associated with 46, XY pure gonadal dysgenesis and

the familial non-HMO box R30I associated with variable phenotypes. J Mol Med

80: 782-790.

13. Auffray C, Rougeon F (1980). Purification of mouse immunoglobulin heavy-chain

messenger RNAs from total myeloma tumor RNA. Eur J Biochem 107(2):303-314.

14. Babich V, Aksenov N, Alexeenko V, Oei SL, Buchlow G, Tomilin N (1999).

Association of some potential hormone response elements in human genes with

Alu family repeats. Gene 239: 341-349.

15. Bajaj GD (2002). Molecular cloning and characterization of human cDNAs by a

simple repeat DNA probe: identification of novel candidate genes. Ph.D thesis

School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.

16. Barrionuevo F, Bagheri-Fam S, Klattig J, Kist R, Taketo MM, Englert C, Scherer

G, (2006). Homozygous inactivation of Sox9 causes complete XY sex reversal in

mice. Bioi Reprod74(1): 195-201.

17. Bartel DP (2004). MicroRNAs: genomics, biogenesis, mechanism, and function.

Cell 116: 281-297.

18. Bartel DP (2009). MicroRNAs: target recognition and regulatory functions. Cell

136: 215-233.

19. Bass BL (2002). RNA editing by adenosine deaminases that act on RNA. Annu

Rev Biochem 71: 817-846.

20. Batzer MA, Deininger PL (2002). Alu repeats and human genomic diversity. Nat

Rev Genet 3:370-379.

21. Behlke MA, Bogan JS, Page DC (1993). Evidence that the SRY protein is encoded

by a single exon on the human Y chromosome. Genomics 17:736-739.

22. Belancio VP, Hedges DJ, Deininger P (2008). Mammalian non-LTR

retrotransposons: for better or worse, in sickness and in health. Genome Res 18:

343-358.

23. Belgnaoui SM, Gosden RG, Semmes OJ, Haoudi A (2006). Human LINE-l

retrotransposon induces DNA damage and apoptosis in cancer cells. Cancer Cell

Int 6: 13.

24. Bennett M, Onnebo SM, Azevedo C, Saiardi A (2006). Inositol pyrophosphates:

metabolism and signaling. Cell Mol Life Sci 63(5):552-564.

202

R.efey-eV\,c,es

25. Berta P, Hawkins JR, Sinclair AH, Taylor A, Griffiths BL, Goodfellow PN,

Fellous M (1990). Genetic evidence equating SRY and the testis-determining

factor. Nature 348(6300):448-450.

26. Bessman MJ, Frick DN, and O'Handley SF (1996) The MutT proteins or "Nudix"

hydro lases, a family of versatile, widely distributed, "housecleaning" enzymes. J

Bioi Chern 271(41): 25059-25062.

27. Bianchi ME, Agresti A (2005). HMG proteins: dynamic players in gene regulation

and differentiation. Curr Opin Genet Dev 15(5):496-506.

28. Birney E et al. (2007). Identification and analysis of functional elements in 1 % of

the human genome by the ENCODE pilot project. Nature 447:799-816.

29. Bohnsack MT, Czaplinski K, Gorlich D (2004). Exportin 5 is a RanGTP­

dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs.

RNA 10: 185-191.

30. Borchert GM, Lanier W, Davidson BL (2006). RNA polymerase III transcribes

human microRNAs. Nat Struct Mol Bioi 13:1097-1101.

31. Bowles J, Cooper L, Berkman J, Koopman P (1999). Sry requires a CAG repeat

domain for male sex determination in Mus musculus. Nat Genet 22: 405-408.

32. Bracht J, Hunter S, Eachus R, Weeks P, Pasquinelli AE (2004). Trans-splicing and

polyadenylation of let-7 microRNA primary transcripts. RNA 10: 1586-1594.

33. Bradford ST, Hiramatsu R, Maddugoda MP, Bernard P, Chaboissier MC, Sinclair

A, Schedl A, Harley V, Kanai Y, Koopman P, Wilhelm D (2009). The cerebellin 4

precursor gene is a direct target of SRY and SOX9 in mice. Bioi Reprod 80: 1178-

1188.

34. Brennan J, Tilmann C, Capel B (2003). Pdgfr-alpha mediates testis cord

organization and fetal Leydig cell development in the XV gonad. Genes Dev 17:

800-810.

35. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanadam R, Hannon GJ

(2007). Discrete small RNA-generating loci as master regulators of transposon

activity in Drosophilia. Cell 128: 1089-1103.

36. Brown TA (1999). Genomes. John Wiley & Sons (ASIA) PTE LTD: 1-472.

37. BUhler M, Verde I A, Moazed D (2006). Tethering RITS to a nascent transcript

initiates RNAi- and heterochromatin-dependent gene silencing. Cell 125(5): 873-

886.

203

RefeyeV\,ces.

38. Caffrey n, Safrany ST, Yang XN, Shears SB (2000). Discovery of molecular and

catalytic diversity among human diphosphoinositol-polyphosphate

phosphohydrolases - an expanding NUDT family. J Bioi Chern 275: 12730-12736.

39. Caffrey n, Shears SB (2001). Genetic rationale for microheterogeneity of human

diphosphoinositol polyphosphate phosphohydrolase type 2. Gene 269(1-2):53-60.

40. Carl DN, Phillip AS (2004). The RNAi revolution. Nature 430: 161-164.

41. Carmell MA, Girard A, van de Kant HJG, Bourc'his D, Bestor TH, de Rooij DG,

Hannon GJ (2007). MIWI2 is essential for spermatogenesis and repression of

transposons in the mouse male germline. Dev Cell 12:503-514.

42. Caminci P et al. (2005). The transcriptional landscape of the mammalian genome.

Science 309:1559-1563.

43. Carthew RW, Sontheimer EJ (2009). Origins and Mechanisms of miRNAs and

siRNAs. Cell 136: 642-655.

44. Cartwright JL, Safrany ST, Dixon LK, Darzynkiewicz E, Stepinski J, Burke R,

McLennan AG (2002). The g5R (D250) gene of African swine fever virus encodes

a Nudix hydrolase that preferentially degrades diphosphoinositol polyphosphates. J

Viro/76(3):1415-1412I.

45. Chang CJ, Mulholland DJ, Valamehr B, Mosessian S, Sellers WR, Wu H (2008).

PTEN nuclear localization is regulated by oxidative stress and mediates p53-

dependent tumor suppression. Mol Cell Bioi 28(10):3281-3289.

46. Chappell WH, Green TD, Spengeman JD, McCubrey JA, Akula SM, Bertrand FE

(2005). Increased protein expression ofthe PTEN tumor suppressor in the presence

of constitutively active Notch-I. Cell Cycle 4(10):1389-1395.

47. Chen C, Ara T, Gautheret D (2008). Using Alu elements as polyadenylation sites:

a case ofretroposon exaptation. Mol Bioi Evo/26: 327-334.

48. Chen H, Rossier C, Morris MA, Scott HS, Gos A, Bairoch A, Antonarakis SE

(1999). A testis-specific gene, TPTE, encodes a putative transmembrane tyrosine

phosphatase and maps to the peri centromeric region of human chromosomes 21

and 13, and to chromosomes 15,22, and Y. Hum Genet 105: 399-409.

49. Chen LL, DeCerbo IN, Carmichael GG (2008). Alu element-mediated gene

silencing. EMBOJ27:1694-1705.

50. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stem D,

Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK,

Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR (2005). Transcriptional

204

R.efevelMes.

maps of 10 human chromosomes at 5-nucleotide resolution. Science 308: 1149-

11540

51. Choi K, Mollapour E, Shears SB (2005). Signal transduction during environmental

stress: InsP8 operates within highly restricted contexts. Cell Signal 17(12): 1533-

1541.

520 Chu C, Alapat D, Wen XP, Timo K, Burstein D, Lisanti M, Shears S, Kohtz DS

(2004) Ectopic expression of murine diphosphoinositol polyphosphate

phosphohydrolase 1 attenuates signaling through the ERK1I2 pathway. Cell Signal

16(9): 1045-1059.

53. Chu CY, Rana TM (2007). Small RNAs: Regulators and guardians of the genome.

JCell PhysioI213(2):412-419.

54. Chung JH, Ostrowski MC, Romigh T, Minaguchi T, Waite KA, Eng C (2006). The

ERK1I2 pathway modulates nuclear PTEN-mediated cell cycle arrest by cyclin Dl

transcriptional regulation. Human Mol Genet 15(17): 2553-2559.

55. Church GM, Gilbert W (1984). Genomic sequencing. Proc Natl Acad Sci USA,

81: 1991-1995.

56. Clepet C, Schafer AJ, Sinclair AH, Palmer MS, Lovell-Badge R, Goodfellow PN

(1993). The human SRY transcript. Hum Mol Genet 2: 2007-2012

57. Cohen DR, Sinclair AH, McGovern JD (1994). SRY protein enhances

transcription of Fos-related antigen 1 promoter constructs. Proc Natl Acad Sci

USA 91:4372-4376.

58. Colvin JS, Green RP, Schmahl J, Capel B, Ornitz DM (2001). Male-to-female sex

reversal in mice lacking fibroblast growth factor 9. Cell 104:875-889.

59. Comeaux MS, Roy-Engel AM, Hedges DJ, Deininger PL (2009). Diverse cis

factors controlling Alu retrotransposition: What causes Alu elements to die?

Genome Res 19: 545-555.

60. Costa FF (2008). Non-coding RNAs, epigenetics and complexity. Gene 410: 9-17.

61. Cristofano AD, Pesce B, Cordon-Cardo C, Pandolfi PP (1998). Pten is essential for

embryonic development and tumour suppression. Nat Genet 19(4): 348-355.

62. Cully M, You H, Levine AJ, Mak TW (2006). Beyond PTEN mutations: the PI3K

pathway as an integrator of multiple inputs during tumorigenesis. Nat Rev Cancer

6: 184-192.

63. DeCerbo J, Carmichael GG (2005). SINES point to abundant human editing.

Genome Bioi 6: 216-217.

205

RefereV\,ces

64. Deng Wei, Lin Haifan (2002). miwi, a Murine Homolog of piwi, Encodes a

Cytoplasmic Protein Essential for Spermatogenesis. Dev Cell 2: 819-830.

65. Denli AM, Tops BB, Pia sterk RH, Ketting RF, Hannon GJ (2004). Processing of

primary microRNAs by the Microprocessor complex. Nature 432: 231-235.

66. Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ. (2004). A micrococcal

nuclease homologue in RNAi effector complexes. Nature 432(7014): 231-235.

67. De-Santa Barbara P, Bonneaud N, Boizet B, Desclozeaux M, Moniot B, Sudbeck

P, Scherer G, Poulat F, Berta P (1998). Direct interaction of SRY-related protein

SOX9 and steroidogenic factor 1 regulates transcription of the human anti­

Mullerian hormone gene. Mol Cell Bioi 18: 6653-6665.

68. Desclozeaux M, Poulat F, de Santa Barbara P, Capony JP, Turowski P, Jay P,

Mejean C, Moniot B, Boizet B, Berta P (1998). Phosphorylation of an N-terminal

motif enhances DNA-binding activity of the human SRY protein. J Bioi Chem

273:7988-7995.

69. Dewing P, Chiang CW, Sinchak K, Sim H, Femagut PO, Kelly S, Chesselet MF,

Micevych PE, Albrecht KH, Harley VR, Vilain E (2006). Direct regulation of adult

brain function by the male-specific factor SRY. Curr Bioi 16: 415-420.

70. Dey I (2000). A Study of Chromatin Structure and Transcription using LINE DNA

and Simple Repeat DNA Probes. Ph.D thesis School of Life Sciences, Jawaharlal

Nehru University, New Delhi 110067, India.

71. Dey I, Rath PC (2005). A novel rat genomic simple repeat DNA with RNA­

homology shows triplex (H-DNA)-like structure and tissue-specific RNA

expression. Biochem Biophys Res Commun 327: 276-286.

72. Dey I, Rath PC (2005). Correlation between alterations in nucleosomal

organization of LINEs in the promoter of cytochrome P450 2B1I2 gene and

induction of CYP 2B 1I2B2 mRNA expression by phenobarbitone in rat liver. DNA

Cell Bioi 24(6):359-370.

73. Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A (2007).The

expanding RNA polymerase III transcriptome. Trends Genet 23: 614-622.

74. Doench JG, Sharp PA (2004). Specificity of microRNA target selection in

translational repression. Genes Dev 18: 504-511.

75. Dubin RA, Ostrer H (1994) Sry is a transcriptional activator. Mol EndocrinoI8(9):

1182-1192.

206

RefereV\,ces.

76. Ely D, Milsted A, Bertram J, Ciotti M, Dunphy G, Turner ME (2007). Sry delivery

to the adrenal medulla increases blood pressure and adrenal medullary tyrosine

hydroxylase of normotensive WKY rats. BMC Cardiovasc Disord7: 6.

77. Epplen JT, Kyas A, Maueler W (1996). Genomic simple repetitive DNAs are

targets for differential binding of nuclear proteins. FEBS Letters 389:92-95.

78. Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA (2004). B2 RNA binds

directly to RNA polymerase II to repress transcript synthesis. Nat Struct Mol Bioi

11:822-829.

79. Faehnle CR, Joshua-Tor L (2007). Argonautes confront new small RNAs. Curr

Opin Chern Bioi 11(5):569-577.

80. Ferrari S, Harley VR, Pontiggia A, Goodfellow PN, Lovell-Badge R, Bianchi ME

(1992). SRY, like HMG1, recognizes sharp angles in DNA. EMBO J 11: 4497-

4506.

81. Filipowicz W, Bhattacharyya SN, Sonenberg N (2008). Mechanisms of post­

transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet

9:102-114.

82. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998). Potent

and specific genetic interference by double-strandedRNAin Caenorhabditis

elegans. Nature 391, 806-811.

83. Forwood JK, Harley VR, and Jans DA (2001). The C-terminal nuclear localization

signal of the sex-determining region Y (SRY) high mobility group domain

mediates nuclear import through importin 131. J Bioi Chern 276(49): 46575-46582.

84. Freeman DJ, Li AG, Wei G, Li HR, Kertesz N, Lesche R, Whale AD, Martinez­

Diaz H, Rozengurt N, Cardiff RD, Liu X, Wu H (2003). PTEN tumor suppressor

regulates p53 protein levels and activity through phosphatase-dependent and -

independent mechanisms. Cancer Cell 3: 117-130.

85. Gao F, Maiti S, Alam N, Zhang Z, Deng lM, Behringer RR, Lecureuil C, Guillou

F, Huff V (2006). The Wilms tumor gene, Wtl, is required for Sox9 expression

and maintenance of tubular architecture in the developing testis. Proc Natl Acad

Sci USA 103: 11987-11992.

86. Gasior SL, Wakeman TP, Xu B, Deininger PL (2006). The human LINE-l

retrotransposon creates DNA double-strand breaks. J Mol Bioi 357: 1383-1393.

207

RefeveV\..c,es.

87. Georgescu MM, Kirsch KH, Kaloudis P, Yang H, Pavletich NP, Hanafusa H

(2000). Stabilization and productive positioning roles of the C2 domain of PTEN

tumor suppressor. Cancer Res 60(24):7033-7038.

88. Gibbs RA et aI., (2004). Genome sequence of the brown norway rat yields insights

into mammalian evolution. Nature 428: 493-521.

89. Giese K, Cox J, Grosschedl R (1992). The HMG domain of Lymphoid Enhancer

Factor 1 bends DNA and facilitates assembly of functional nucleoprotein

structures. Cell 69: 185-195.

90. Giese K, Pagel J, Grosschedl R (1994). Distinct DNA-binding properties of the

high mobility group domain of murine and human SRY sex-determining factors.

Proc Natl Acad Sci USA 91:3368-3372.

91. Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, Baskerville S,

Hammond SM, Bartel DP, Schier AF (2005). MicroRNAs regulate brain

morphogenesis in zebrafish. Science 308: 833-838.

92. Girard A, Sachidanandam R, Hannon GJ, Carmell MA (2006). A germ line-specific

class of small RNAs binds mammalian Piwi proteins. Nature 442:199-202.

93. Goodier JL, Kazazian HH, Jr (2008). Retrotransposons revisited: the restraint and

rehabilitation of parasites. Cell 135: 23-35.

94. Goodier JL, Zhang L, Vetter MR. Kazazian HH Jr. (2007). LINE-l ORFI protein

localizes in stress granules with other RNA-binding proteins, including

components of RNA interference RNA-induced silencing complex. Mol Cell BioI

27: 6469-6483.

95. Green K, Lewis A, Dawson C, Dean W, Reinhart B, Chaillet JR, Reik W. 2007. A

developmental window of opportunity for imprinted gene silencing mediated by

DNA methylation and the Kcnqlotl noncoding RNA. Mammalian Genome 18:32-

42.

96. Greenman C, Stephens P, Smith R, et al. (2007). Patterns of somatic mutation in

human cancer genomes. Nature 446(7132): 153-158.

97. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N,

Shiekhattar R (2004). The Microprocessor complex mediates the genesis of

microRNAs. Nature 432: 235-240.

98. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A,

Ruvkun G, Mello CC (2001). Genes and mechanisms related to RNA interference

208

regulate expression of the small temporal RNAs that control C. elegans

developmental timing. Cell 106:23-34.

99. Grivna ST, Beyret E, Wang Z, Lin H (2006). A novel class of small RNAs in

mouse spermatogenic cells. Genes Dev 20: 1709-1714.

100. Grivna ST, Pyhtila B, Lin H (2006). MIWI associates with translational machinery

and PIWI-interacting RNAs (piRNAs) in regulating spermatogenesis. Proc Natl

Acad Sci USA 103:13415-13420.

101. Gu J, Tamura M, Yamada KM. (1998). Tumor suppressor PTEN inhibits integrin­

and growth factor-mediated mitogen-activated protein (MAP) kinase signaling

pathways. J Cell Bioi 143(5): 1375-1383.

102. Guipponi M, Tapparel C, Jousson 0, Scamuffa N, Mas C, Rossier C, Hutter P,

Meda P, Lyle R, Reymond A, Antonarakis SE (2001). The murine orthologue of

the Golgi-Iocalized TPTE protein provides clues to the evolutionary history of the

human TPTE gene provides clues to the evolutionary history of the human TPTE

gene family. Hum Genet 109: 569-575.

103. Gunawardane LS, Saito K, Nishida KM, Miyoshi K, Kawamura Y, Nagami T,

Siomi H, Siomi MC (2007). A slicer-mediated mechanism for repeat-associated

siRNA 5' end formation in Drosophila. Science 315: 1587-1590.

104. Gustafson S, Zbuk KM, Scacheri C, Eng C (2007). Cowden syndrome. Semin

OncoI34(5):428-434.

105. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk 0,

Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen

N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES (2009).Chromatin

signature reveals over a thousand highly conserved large non-coding RNAs in

mammals. Nature 458: 223-227.

106. Ha M, Pang M, Agarwal V, Chen ZJ (2008), Interspecies regulation of microRNAs

and their targets, Biochim Biophys Acta 1779(11):735-742.

107. Hacker A, Capel B, Goodfellow P, Lovell-Badge R (1995). Expression ofSry, the

mouse sex determining gene. Development 121: 1603-1614.

108. Hammes A, Guo JK, Lutsch G, Leheste JR, Landrock D, Ziegler U, Gubler MC,

Schedl A (2001). Two splice variants of the Wilms' tumor 1 gene have distinct

functions during sex determination and nephron formation. Cell 106:319-329.

109. Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN (2004). The Drosha-DGCR8

complex in primary microRNA processing. Genes Dev 18: 3016-3027.

209

Refevelll,ces.

110, Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, Sohn SY, Cho Y, Zhang BT,

Kim VN (2006). Molecular basis for the recognition of primary microRNAs by the

Drosha-DGCR8 complex, Cell 125: 887-901.

111. Hanahan D (1985). DNA cloning volume 1, Glover D, ed., IRL Press Ltd.,

London, UK.

112. Hancock 1M, Simon M (2005). Simple sequence repeats in proteins and their

significance for network evolution. Gene 345(1): 113-118.

113. Hanley NA, Hagan DM, Clement-Jones M, Ball SG, Strachan T, Salas-Cortes L,

McElreavey K, Lindsay S, Robson S, Bullen P, Ostrer H, Wilson DI (2000) SRY,

SOX9, and DAXI expression patterns during human sex determination and

gonadal development. Mech Dev 91:403-407.

114. Hanley NA, Hagan DM, M. Clement-Jones, Ball SG, Strachan T, Salas-Cortes L,

McElreavey K, Lindsay S, Robson S, Bullen P, Ostrer H, Wilson DI (2000). SRY,

SOX9, and DAXI expression patterns during human sex determination and

gonadal development. Mech Dev 91: 403-407.

115. Harley VR, Jackson DI, Hextall PJ, Hawkins JR, Berkovitz GD, Sockanathan S,

Lovell-Badge R, Goodfellow PN (1992). DNA binding activity of recombinant

SRY from normal males and XY females. Science 255(5043):453-456.

116. Harley VR, Layfield S, Mitchell CL, Forwood JK, John AP, Briggs LJ, McDowall

SG and Jans DA (2003). Defective importin f3 recognition and nuclear import of

the sex-determining factor SRY are associated with XY sex reversing mutations.

Proc Natl Acad Sci USA 100(12): 7045-7050.

117. Harley VR, Lovell-Badge R, Goodfellow PN, Hextall PJ (1996). The HMG box of

SRY is a calmodulin binding domain. FEBS Letters 391: 24-28.

118. Harley VR, Mitchell CL and Argentaro A (2003). The molecular action and

regulation of the testis-determining factors, SRY (Sex-Determining Region on the

Y Chromosome) and SOX9 [SRY-Related High-Mobility Group (HMG) Box 9].

Endocr Rev 24(4): 466-487.

119. Hartig N, Tomari Y, Forstemann K (2007). piRNAs-the ancient hunters of

genome invaders. Genes Dev 21: 1707-1713.

120. Hartman RK, Bindereif A, Schon A, Weshof E (2009). Handbook of RNA

Biochemistry, Student Edn. Wiley-VCH Verlag GMBH & Co: 1-931.

210

121. Hawkins JR (1993). Mutational analysis of SRY in XY females. Hum Mutat

2(5):347-350.

122. Hawkins JR, Taylor A, Berta P, Levilliers J, Van der Auwera B, Goodfellow PN

(1992). Mutational analysis of SRY: nonsense and missense mutations in XY sex

reversal. Hum Genet 88 (4):471-474,

123, Hefferon TW, Groman JD, Yurk CE, Cutting GR (2004). A variable dinucleotide

repeat in the CFTR gene contributes to phenotype diversity by forming RNA

secondary structures that alter splicing. Proc Nat! Acad Sci USA 101: 3504-3509.

124. Hess P, Pihan G, Sawyers CL, Flavell RA, and Davis RJ (2002). Survival signaling

mediated by c-Jun NH(2)-terminal kinase in transformed B lymphoblasts. Nat

Genet 32(1): 201-205.

125. Hidaka K, Caffrey n, Hua L, Zhang T, Falck JR, Nickel GC, Carrel L, Barnes LD,

Shears SB (2002). An adjacent pair of human NUDT genes on chromosome X are

preferentially expressed in testis and encode two new isoforms of

diphosphoinositol polyphosphate phosphohydrolase. J Bio! Chern 277(36): 32730-

32738.

126. Hidaka K., Caffrey J. J., Hua L., Zhang T., Falck J. R., Nickel G. C. et al. (2002)

An adjacent pair of human NUDT genes on chromosome X are preferentially

expressed in testis and encode two new isoforms of diphosphoinositol

polyphosphate phosphohydrolase. J Bio! Chern 277: 32730-32738.

127. Hinderliter A, Almeida PFF, Creutz CE, Biltonen RL (2001). Domain formation in

a fluid mixed lipid bilayer modulated through binding of the C2 protein motif.

Biochemistry 40(13):4181-4191.

128. Horwich MD, Li C, Matranga C, Vagin V, Farley G, Wang P, Zamore PD (2007).

The Drosophila RNA methyltransferase, DmHen 1, modifies germ line piRNAs and

single-stranded siRNAs in RISC. Curr Bio!17:1265-1272.

129. Houwing S, Berezikov E, Ketting RF (2008). Zili is required for germ cell

differentiation and meiosis in zebrafish. EMBO J27:2702-2711.

130. Houwing S, Kamminga, LM, Berezikov E, Cronembold D, Girard A, van den Elst

H, Filippov DV, Blaser H, Raz E, Moens CB, Plasterk RH, Hannon GJ, Draper

BW, Ketting RF (2007). A role for Piwi and piRNAs in germ cell maintenance and

transposon silencing in zebrafish. Cell 129: 69-82.

131. Hua LV, Hidaka K, Pesesse X, Barnes LD and Shears SB (2003). Paralogous

murine NudtlO and Nudtll genes have differential expression patterns but encode

211

RefereV\,ces.

identical proteins that are physiologically competent diphosphoinositol

polyphosphate phosphohydrolases. Biochem J373: 81-89.

132. HutvAgner G, McLachlan J, Pasquinelli AE, BAlint E, Tuschl T, Zamore PD

(2001). A cellular function for the RNA-interference enzyme Dicer in the

maturation of the let-7 small temporal RNA. Science 293(5531):834-838.

133. Ishikawa F, Matunis MJ, Dreyfuss G, Cechl TR (1993). Nuclear proteins that bind

the pre-mRNA 3' splice site sequence r(UUAG/G) and the human telomeric DNA

sequence d(TTAGGG)n. Mol Cell Bioi 13(7):4301-4310.

134. Jackson IJ (1991). A reappraisal of non-consensus mRNA splice sites. Nucleic

Acids Res 19: 3795-3798.

135. Jager RJ, Anvret M, Hall K, Scherer G (1990). A human XY female with a frame

shift mutation in the candidate testis-determining gene SRY. Nature

348(6300):452-454.

136. Jeyasuria P Ikeda Y, Jamin SP, Zhao L, De Rooij DG, Themmen AP, Behringer

RR, Parker KL (2004). Cell-specific knockout of steroidogenic factor 1 reveals its

essential roles in gonadal function. Mol EndocrinoI18(7): 1610-1619.

137. Johnson SM, Grosshans H, Shingara J, Byrom M, Jarvis R, Cheng A, Labourier E,

Reinert KL, Brown D, Slack FJ (2005). RAS is regulated by the let-7 microRNA

family. Cell 120: 635- 647.

138. Jovanovic A, Jovanovic S, Mays DC, Lipsky JJ, Terzic A (1998). Diadenosine

5',5"-Pl,P5-pentaphosphate harbors the properties of a signaling molecule in the

heart. FEBS Lett 423(3):314-318.

139. Kang-Park S, Lee YI (2003). PTEN modulates insulin-like growth factor II (IGF­

II)-mediated signaling; the protein phosphatase activity of PTEN downregulates

IGF-II expression in hepatoma cells. FEBS Lett 545(2-3): 203-208.

140. Kapranov P, Cawley E, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP,

Gingeras TR (2002). Large-scale transcriptional activity in chromosomes 21 and

22. Science 296: 916-919.

141. Kessler MA, Yang M, Gollom KL, Jin H, Iacovitti L (2003). The human tyrosine

hydroxylase gene promoter. Mol Brain Res 112: 8-23.

142. Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ, Plasterk RH (2001).

Dicer functions in RNA interference and in synthesis of small RNA involved in

developmental timing in C. elegans. Genes Dev 15:2654-2659.

212

143. Khvorova A, Reynolds A, Jayasena SD (2003). Functional siRNAs and miRNAs

exhibit strand bias. Cell 115:209-216.

144. Kim DD, Kim IT, Walsh T, Kobayashi Y, Matise TC, Buyske S, Gabriel A

(2004). Widespread RNA editing of embedded alu elements in the human

transcriptome. Genome Res 14: 1719-1725.

145. Kim DS, Kim TH, Huh JW, Kim IC, Kim SW, Park HS, Kim HS (2006). LINE

FUSION GENES: a database of LINE expression in human genes. BMC Genomics

7:139.

146. Kim SM, Yang JW, Park MJ, Lee JK, Kim SU, Lee YS, Lee MA (2006).

Regulation of human tyrosine hydroxylase gene by neuron-restrictive silencer

factor. Biochem Biophys Res Commun 346(2):426-35.

147. Kim TE, Park MJ, Choi EJ, Lee HS, Lee SH, Yoon SR, Oh CK, Lee BJ, Kim SU,

Lee YS, Lee MA (2003). Cloning and cell type-specific regulation of the human

tyrosine hydroxylase gene promoter. Biochem Biophys Res Commun 312(4):1123-

1131.

148. Kim VN (2005). microRNA biogenesis: coordinatinated cropping and dicing. Nat.

Rev. Mol. Cell Bioi. 6(5):376-385.

149. Kim VN (2006). Small RNAs just got bigger: Piwi-interacting RNAs (piRNAs) in

mammalian testes. Genes Dev 20(15): 1993-1997.

150. Kim Y, Bingham N, Sekido R, Parker KL, Lovell-Badge R, Capel B (2007).

Fibriblast growth factor receptor 2 regulates proliferation and Sertoli

differentiation during male sex determination. Proc Natl Acad Sci USA 104(42):

16558-16563.

151. Kim Y, Kobayashi A, Sekido R, DiNapoli L, Brennan J, Chaboissier MC, Poulat

F, Behringer RR, Lovell-Badge R, Capel B (2006). Fgf9 and Wnt4 act as

antagonistic signals to regulate mammalian sex determination. PLoS Bioi 4(6):

e187.

152. King CY, Weiss MA (1993). The SRY high-mobilitygroup box recognizes DNA

by partial intercalation in the minor groove: a topological mechanism of sequence

specificity, Proc Nat! Acad Sci USA, 90: 11990-11994.

153. Kissil JL, Deiss LP, Bayewitch M, Raveh T, Khaspekov G, Kimchi A (1995).

Isolation of DAP3, a novel mediator of interferon-gamma-induced cell death. J

Bioi Chem 270: 27932-27936.

213

RefereV\,ces.

154. Klenov MS, Lavrov SA, Stolyarenko AD, Ryazansky SS, Aravin AA, Tuschl T,

Gvozdev V A (2007). Repeat-associated siRNAs cause chromatin silencing of

retrotransposons in the Drosophila melanogaster germline. Nucleic Acids Res

35(6): 5430-5438.

155. Komili S, Silver PA (2008). Coupling and coordination in gene expression

processes: a systems biology view. Nat Rev Genet 9(1): 38-48.

156. Koopman P, Gubbay J, Vivian N, Goodfellow P, and Lovell- Badge R (1991).

Male development of chromosomally female mice transgenic for Sry. Nature 351:

117-121.

157. Koopman P, Munsterberg A, Capel B, Vivian N, Lovell-Badge R (1990).

Expression of a candidate sex-determining gene during mouse testis

differentiation. Nature 348:450-452.

158. Koritschoner NP, Bocco JL, Panzetta-Dutari GM, Dumur CI, Flury A, Patrito

LC (1997). A novel human zinc finger protein that interacts with the core promoter

element of a TAT A box-less gene. J Bioi Chern 272: 9573-9580.

159. Kumari D, Usdin K (2009). Chromatin remodeling in the noncoding repeat

expansion diseases. J Bioi Chern 274: 7413-7417.

160. Kumer SC, Vrana KE (1996). Intricate regulation of tyrosine hydroxylase activity

and gene expression, J Neurochern 67: 443-462.

161. Kunkel LM, Monaco AP, Middlesworth W, Ochs RD, Lart SA (1985). Specific

cloning of DNA fragments absent from the DNA of a male patient with X

chromosome deletion. Proc Natl Acad Sci USA, 82: 4778-4782.

162. Kurihara Y, Watanabe Y. (2004). Arabidopsis micro-RNA biogenesis through

Dicer-like 1 protein functions. Proc Nat! Acad Sci USA 101(34): 12753-12658.

163. Laemmli UK (1970). Cleavage of structural proteins during the assembly of the

head of bacteriophage T4. Nature 227(259): 680-685.

164. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001). Identification of

novel genes coding for small expressed RNAs. Science 294: 853-858.

165. Lahr G, Maxson SC, Mayer A, Just W, Pilgrim C, Reisert I (1995). Transcription

of the Y chromosomal gene, Sry, in adult mouse brain. Brain Res Mol Brain Res

33(1): 179-82.

166. Lander ES et aI., (2001). Initial sequencing and analysis of the human genome.

Nature 409: 860-921.

214

RefereV\,ces.

167. Lau NC, Seto AG, Kim J, Kuramochi-Miyagawa S, Nakano T, Bartel DP,

Kingston RE (2006). Characterization of the piRNA complex from rat testes.

Science 313:363-367.

168. Laudet V, Stehelin D, Clevers H (1993). Ancestry and diversity of the HMG box

superfamily. Nucleic Acids Res 21:2493-2501.

169. Lee JO, Yang H, Georgescu MM, Di Cristofano A, Maehama T, Shi Y, Dixon JE,

Pandolfi P, Pavletich NP (1999). Crystal structure of the PTEN tumor suppressor:

implications for its phosphoinositide phosphatase activity and membrane

association. Cell 99(3):323-334.

170. Lee RC, Feinbaum RL, Ambros V (1993). The C. elegans heterochronic gene lin-4

encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.

171. Lee SR, Collins K (2006). Two classes of endogenous small RNAs in

Tetrahymena thermophila. Genes Dev: 20:28-33.

172. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark 0, Kim S,

Kim VN (2003). The nuclear RNase III Drosha initiates microRNA processing.

Nature 425: 415-419.

173. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN. (2004).MicroRNA

genes are transcribed by RNA polymerase II. EMBO J23: 4051-4060.

174. Lehnert L, Van LP, Thilakarathne PJ, Marynen P, Verbeke G, Schuit FC (2009).

Evidence for co-evolution between human MicroRNAs and Alu-repeats. PLoS

ONE 4: e4456.

175. Leslie NR, Downes CP (2004). PTEN function: how normal cells control it and

tumour cells lose it. Biochem J 382(Pt 1): 1-11.

176. Leslie NR, McLennan AG, Safrany ST (2002). Cloning and characterisation of

hAps 1 and hAps2, human diadenosine polyphosphate-metabolising Nudix

hydrolases. BMC Biochem 3: 20.

177. Leslie NR, Yang X, Downes CP, Weijer CJ (2007). Ptdlns(3,4,5)P3-dependent and

independent roles for PTEN in the control of cell migration. Curr BioI 17: 115-

125.

178. Levanon EY, Eisenberg E, Yelin R, Nemzer S, Hallegger M, Shemesh R,

Fligelman ZY, Shoshan A, Pollock SR, Sztybel D, Olshansky M, Rechavi G,

Jantsch MF (2004). Systematic identification of abundant A-to-I editing sites in the

human transcriptome. Nat Biotechnol22: 1001-1005.

215

Refe ye V\..c,es.

179. Li AG, Piluso LG, Cai X, Wei G, Sellers WR, Liu X (2006). Mechanistic insights

into maintenance of high p53 acetylation by PTEN. Mol Cell 23(4): 575-587.

180. U D, Day KV, Yu S, Shi G, Uu S, Guo M, Xu Y, Sreedharan S, O'Malley BW Jr

(2002). The role of adenovirus-mediated retinoblastoma 94 in the treatment of head

and neck cancer. Cancer res 62(16): 4637-4644.

181. Li DM and Sun H (1997). TEPl, Encoded by a Candidate Tumor Suppressor

Locus, Is a Novel Protein Tyrosine Phosphatase Regulated by Transforming

Growth Factor beta. Cancer Res 57: 2124-2129.

182. Li J, Yen C, Liaw D, Podsypanina K, Bose S, Wang SI et al. (1997). PTEN, a

putative protein tyrosine phosphatase gene mutated in human brain, breast, and

prostate cancer. Science 275: 1943-1947.

183. Li PTX, Vieregg J, Tinoco I, Jr (2008). How RNA Unfolds and Refolds. Annu Rev

Biochem 77:77-100.

184. Li T, Spearow J, Rubin CM, Schmid CW (1999) Physiological stresses increase

mouse short interspersed element (SINE) RNA expression in vivo. Gene 239:367-

372.

185. Li Y, Guessous F, Kwon S, Kumar M, Ibidapo 0, Fuller L, Johnson E, Lal B,

Hussaini I, Bao Y, Laterra J, Schiff D, Abounader R (2008). PTEN has tumor­

promoting properties in the setting of gain-of-function p53 mutations. Cancer Res

68(6): 1723-1731.

186. Li Y, Oh HJ, Lau YC (2006). The poly(ADP-ribose) polymerase 1 interacts with

Sry and modulates its biological functions. Mol Cell EndocrinoI257-258: 35-46.

187. Liaw D, Marsh DJ, Li J, Dahia PL, Wang SI, Zheng Z, Bose S, Call KM, Tsou

HC, Peacocke M, Eng C, Parsons R (1997). Germline mutations of the PTEN gene

in Cowden disease, an inherited breast and thyroid cancer syndrome. Nat Genet

16(1):64-67.

188. Liaw D, Marsh DJ, Li J, Dahia PL, Wang SI, Zheng Z, Bose S, Call KM, Tsou

HC, Peacocke M, Eng C, Parsons R (1997). Germline mutations of the PTEN gene

in Cowden disease, an inherited breast and thyroid cancer syndrome. Nat Genet

16(1):64-67.

189. Lillest01 RK, Redder P, Garrett RA, Brugger K (2006). A putative viral defence

mechanism in archaeal cells. Archaea 2:59-72.

190. Lin H (2007). piRNAs in the Germ Line. Science 316 (5823): 397.

216

19L Linding R, Russell RB, Neduva V, Gibson TJ (2003). GlobPlot: Exploring protein

sequences for gIobularity and disorder. Nucleic Acids Res 31: 3701-3708.

192. Lippman Z, Martienssen R (2004). The role of RNA interference in

heterochromatic silencing. Nature 431: 364-370.

193. Liu X, Fortin K, Mourelatos Z (2008). MicroRNAs: biogenesis and molecular

functions. Brain Pathol18: 13-121.

194. Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL,

Darnell J (2004). Molecular Cell Biology W.H. Freeman & company, Newyork: 1-

973.

195. Love JJ, Li X, Case DA, Giese K, Grosschedl R, and Wright PE (1995). Structural

basis for DNA bending by the architectural transcription factor LEF-l. Nature 376:

791-795.

196. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A,

Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR

(2005). MicroRNA expression profiles classify human cancers. Nature 435: 834-

838.

197. Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U (2004). Nuclear export of

microRNA precursors. Science 303: 95-98.

198. Lunyak VV, Prefontaine GG, Nunez E, Cramer T, Ju BG, Ohgi KA, Hutt K, Roy

R, Garcia-Diaz A, Zhu X, Yung Y, Montoliu L, Glass CK, Rosenfeld MG (2007).

Developmentally regulated activation of a SINE B2 repeat as a domain boundary

in organogenesis. Science 317(5835):248-251.

199. Ma JB, Ye K, Patel DJ (2004). Structural basis for overhang-specific small

interfering RNA recognition by the PAZ domain. Nature 429:318-322.

200. Maccario H, Perera NM, Davidson L, Downs CP, Leslie NR (2007). PTEN is

destabilized by phosphorylation on Th~66. Biochern J 405: 439-444.

201. Maehama T, Dixon JE (1998). The tumor suppressor, PTENIMMAC1,

dephosphorylates the lipid second messenger, phosphatidylinositol 3,4,5-

trisphosphate. J Bioi Chern, 273(22):13375-13378.

202. Maier D, Jones G, Li X, SchOnthal AH, Gratzl 0, Van Meir EG, Merlo A (1999).

The PTEN lipid phosphatase domain is not required to inhibit invasion of glioma

cells. Cancer Res 59(21): 5479-5482.

203. Maiti R, Domselaar GHV, Zhang H, Wishart DS (2004). SuperPose: a simple

server for sophisticated structural superposition. Nucleic Acids Res 32: W590-594.

217

RefeY"eJll,c,es

204. Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF,

Goodrich JA (2008) Human Alu RNA is a modular transacting repressor of mRNA

transcription during heat shock. Mol Cell 29:499-509.

205. Matsuzawa-Watanabe Y, Inoue J and Semba K (2003). Transcriptional activity of

testis-determining factor SRY is modulated by the Wilms' Tumor 1 gene product,

WTl.0ncogene 22(39): 7900-7904.

206. Mattick JS (2009). The Genetic Signatures of Non coding RNAs. PLoS Genet 5(4):

el000459.

207. Mattick JS, Makunin IV (2005). Small regulatory RNAs in mammals. Hum Mol

Genet 14: RI21-R132.

208. Matzke MA, Birchler JA (2005). RNAi-mediated pathways in the nucleus. Nat Rev

Genet 6:24-35.

209. Mayer A, Lahr G, Swaab DF, Pilgrim C, Reisert I (1998). The Y-chromosomal

genes SRY and ZFY are transcribed in adult human brain. Neurogenetics 1: 281-

288.

210. McCorda RA, Broccoli D (2008). Telomeric chromatin: Roles in aging, cancer and

hereditary disease. Mut Res 647:86-93.

211. McLaren A (2003). Primordial germ cells in the mouse. Dev Bioi 262: 1-15.

212. McLennan AG (1999) The MutT motif family of nucleotide phosphohydrolases in

man and human pathogens. Int J Mol Med 4(1): 79-89.

213. McLennan AG (2006). The Nudix hydrolase superfamily. Cell Mol Life Sci 63(2):

123-143.

214. Megosh HB, Cox DN, Campbell C, Lin H (2006). The role of PIWI and the

miRNA machinery in Drosophila germline determination. Curr Bioi 16: 1884-

1894.

215. Mehenni H, Lin-Marq N, Buchet-Poyau K, Reymond A, Collart MA, Picard D,

Antonarakis SE (2005). LKBI interacts with and phosphorylates PTEN: a

functional link between two proteins involved in cancer predisposing syndromes.

Hum Mol Genet 14(15):2209-2219.

216. Mello CC (2007). Return to the RNAi world: rethinking gene expression and

evolution. Cell Death Differ 14(12): 2013-2020.

217. Mello CC and Conte D Jr (2004). Revealing the world of RNA interference.

Nature 431(7006): 338-342.

218

RefeveVl-ces

218. Mendes Soares LM, Valcarcel J. (2006). The expanding transcriptome: the genome

as the 'Book of Sand'. EMBO J25(5): 923-931.

219. Menniti FS, Miller RN, Putney JW Jr, Shears SB (1993). Turnover of inositol

polyphosphate pyrophosphates in pancreatoma cells. J Bioi Chern 268(6):3850-

3856.

220. Meuillet EJ, Mahadevan D, Berggren M, Coon A and Garth Powis (2004).

Thioredoxin-l binds to the C2 domain of PTEN inhibiting PTENOs lipid

phosphatase activity and membrane binding: a mechanism for the functional loss

ofPTEN's tumor suppressor activity. Arch Biochern Biophys 429(2):123-133.

221. Miller SJ, Lou DY, Seldin DC, Lane WS and Neel BG (2002). Direct

identification ofPTEN phosphorylation sites. FEBS Lett 528: 145-153.

222. Milsted A, Serova L, Sabban EL, Dunphy G, Turner ME, Ely DL (2004).

Regulation of tyrosine hydroxylase gene transcription by Sry. Neurosci Lett

369(3):203-207.

223. Miyamoto Y, Taniguchi H, Hamel F, Silversides DW, Viger RS (2008). A

GATA4/WTl cooperation regulates transcription of genes required for mammalian

sex determination and differentiation. BMC Molecular Biology 9:44.

224. Modi D, Shah C, Sachdeva G, Gadkar S, Bhartiya D and Puri C (2005). Ontogeny

and cellular localization of SRY transcripts in the human testes and its detection in

spermatozoa. Reproduction 130: 603-613.

225. Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC (2007).

miRNAs control gene expression in the single-cell alga Chlamydomonas

reinhardtii. Nature 447: 1126-1129.

226. Morlando M, Ballarino M, Gromak N, Pagano F, Bozzoni I, Proudfoot NJ (2008).

Primary microRNA transcripts are processed co-transcriptionally. Nat Struct Mol

Bioi 15: 902-909.

227. Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J,

Mann M, Dreyfuss G (2002). miRNPs: a novel class of ribonucleoproteins

containing numerous microRNAs. Genes Dev 16:720-728.

228. Munshi N, Agalioti T, Lomvardas S, Merika M, Chen G, Thanos D (2001)

Coordination of a transcriptional switch by HMGI(Y) acetylation. Science 293:

1133-1136.

219

Refevev\'ces

229. Myers MP, Stolarov JP, Eng C, Li J, Wang SI, Wigler MH, Parsons R, and Tonks

NK (1997). P-TEN, the tumor suppressor from human chromosome 10q23, is a

dual-specificity phosphatase. Proc Natl Acad Sci USA, 94(17): 9052-9057.

230. Nakaya HI, Amaral PP, Louro R, Lopes A, Fachel AA, Moreira VB, El-Jundi TA,

da Silva AM, Reis EM, Verjovski-Almeida S. (2007). Genome mapping and

expression analyses of human intronic noncoding RNAs reveal tissue-specific

patterns and enrichment in genes related to regulation of transcription. Genome

Biology 8:R43.

231. Napoli C, Lemieux C, Jorgensen R (1990). Introduction of a Chimeric Chalcone

Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous

Genes in trans. Plant Cell 2(4):279-289.

232. Nef S, Parada LF, (2000). Hormones in male sexual development. Genes & Dev

14: 3075-3086.

233. Neidle S, Parkinson GN (2003). The structure of telomeric DNA. Curr Opin Stru

Bio 13:275-283.

234. Ng KW, Ridgway P, Cohen DR, Tremethick DJ (1997). The binding of a Fos/Jun

heterodimer can completely disrupt the structure of a nucleosome. EMBO J

16:2072-2085.

235. Nigumann P, Redik K, Matlik K, Speek M (2002). Many human genes are

transcribed from the antisense promoter of Ll retrotransposon. Genomics 79:628-

634.

236. Norris J, Fan D, Aleman C, Marks JR, Futreal PA, Wiseman RW, Iglehart JD,

Deininger PL, McDonnell DP (1995). Identification ofa new subclass of Alu DNA

repeats which can function as estrogen receptordependent transcriptional

enhancers. J BioI Chem 270: 22777-22782.

237. O'Rourke JR, Swanson MS (2009). Mechanisms of RNA-mediated Disease. J BioI

Chem 284: 7419-7423.

238. O'Donnell KA, Boeke JD (2007). Mighty Piwis defend the germline against

genome intruders Cell. 129:37-44.

239. Odriozola L, Singh G, Hoang T, Chan AM (2007). Regulation ofPTEN activity by

its carboxyl-terminal autoinhibitory domain. J BioI Chem 282(32):23306-23315.

240. Oh HJ, Lau YF (2006). KRAB: A partner for SRY action on chromatin. Mol Cell

EndocrinoI247(1-2):47-52.

220

RefereV\,ces

241. Oh HJ, Li Y and Lau Yun-Fai C (2005). SRY associates with the heterochromatin

protein 1 complex by interacting with a KRAB domain protein. Bioi Reprod 72(2):

407-415.

242. Ohara T, Sakaguchi Y, Suzuki T, Veda H, Miyauchi K, Suzuki T (2007). The 3'

termini of mouse Piwi-interacting RNAs are 2' -O-methylated. Nat Struct Mol Bioi

14: 349-350 ..

243. Okahara F, Ikawa H, Kanaho Y, Maehama T (2004). Regulation of PTEN

phosphorylation and stability by a tumor suppressor candidate protein. J Bioi Chern

279(44):45300-45303.

244. Orr HT, Zoghbi HY (2007). Trinucleotide Repeat Disorders. Annu Rev Neurosci

30:575-621.

245. Ota T et al. (2004). Complete sequencing and characterization of 21,243 full­

length human cDNAs. Nat Genet 36: 40-45.

246. Palomero T, Dominguez M, Ferrando AA (2008).The role of the PTEN/AKT

Pathway in NOTCHI-induced leukemia. Cell Cycle 7(8):965-970.

247. Palomero T, Sulis ML, Cortina M, Real PJ, Barnes K, Ciofani M, Caparros E,

Buteau J, Brown K, Perkins SL, Bhagat G, Agarwal AM, Basso G, Castillo M,

Nagase S, Cordon-Cardo C, Parsons R, Zuniga-PflUcker JC, Dominguez M,

Ferrando AA (2007). Mutational loss of PTEN induces resistance to NOTCHI

inhibition in T-cell leukemia. Nat Med 13(10):1203-1210.

248. Pang K, Stephen S, Dinger EM, Engstro MG (2007) RNAdb 2.0 an expanded

database of mammalian non-coding RNAs. Nucleic Acids Res 35: D 178-D 182.

249. Park MJ, Kim MS, Park IC, Kang HS, Yoo H, Park SH Rhee CH, Hong SI, Lee

SH (2002). PTEN suppresses hyaluronic acid-induced matrix metalloproteinase- 9

expression in V87MG glioblastoma cells through focal adhesion kinase

dephosphorylation. Cancer Res 62(21): 6318-6322.

250. Payer B, Lee JT (2008). X chromosome Dosage Compensation: How Mammals

Keep the Balance. Annu Rev Genet 42: 733-772.

251. Phillips NB, Nikolskaya, T, Jancso-Radek A, Ittah V, Jiang F, Singh R, Haas E

and Weiss MA (2004). Sry-directed sex reversal in transgenic mice is robust with

respect to enhanced DNA bending: comparison of human and murine HMG boxes.

Biochemistry 43: 7066-7081.

252. Podsypanina K, Ellenson LH,Nemes A, Gu J, TamuraM, Yamada KM, Cordon­

Cardo C, Catoretti G, Fisher PE, Parsons R (1999). Mutation of PtenlMmac 1 in

221

Refevev\'ces

mice causes neoplasia in multiple organ systems. Proc Natl Acad Sci USA 96(4):

1563-1568.

253. Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS,

Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr,

Vanderhaeghen P, Haussler D (2006). An RNA gene expressed during cortical

development evolved rapidly in humans. Nature 443: 167-172.

254. Poulat F, Barbara Pascal de Santa, Desclozeaux M, Soullier S, Moniot B,

Bonneaud N, Boizet B, and Berta P (1997). The human testis determining factor

SRY binds a nuclear factor containing PDZ protein interaction domains. J BioI

Chern 272(11): 7167-7172.

255. Poulat F, Girard F, Chevron MP, Goze C, Rebillard X, Calas B, Lamb N, Berta P

(1995). Nuclear localization of the testis determining gene product SRY. J BioI

Chern 128(5):737-748.

256. Prasanth KV, Prasanth SG, Xuan Z, Hearn S, Freier SM, Bennett CF, Zhang MQ,

Spector DL (2005). Regulating gene expression through RNA nuclear retention.

Cell 123:249-263.

257. Qin Y, Bishop CE (2005). Sox9 is sufficient for functional testis development

producing fertile male mice in the absence of Sry. Hum Mol Genet 14(9):1221-

1229.

258. Radomska HS, Gonzalez DA, Okuno Y, Iwasaki H, Nagy A, Akashi K, Tenen DG,

Huettner CS (2002). Transgenic targeting with regulatory elements of the human

CD34 gene. Blood 100:4410-4419.

259. Raftopoulou M, Etienne-Manneville S, Self A, Nicholls S, Hall A (2004).

Regulation of cell migration by the C2 domain of the tumor suppressor PTEN.

Science 303: 1179-1181.

260. Ravasi T, Suzuki H, Pang KC, Katayama S, Furuno M,Okunishi R, Fukuda S,

Ru K, Frith MC, Gongora MM, Grimmond SM, Hume DA, Hayashizaki Y,

Mattick JS (2006). Experimental validation of the regulated expression of large

numbers of non-coding RNAs from the mouse genome. Genome Res 16: 11-19.

261. Reddien PW, Oviedo NJ, Jennings JR, Jenkin JC, Sanchez Alvarado A (2005).

SMEDWI-2 is a PIWI-like protein that regulates planarian stem cells. Science

310(5752): 1327-1330.

262. Rizo J, SUdhof TC (1998). C2 domain, structure and function of a universal Ca2+-

binding domain. J BioI Chern 273(26): 15879-15882.

222

RefereV\,ces

263. Ro S, Park C, Song R, Nguyen D, Jin J, Sanders KM, McCarrey JR, Van W

(2007). Cloning and expression profiling of testis-expressed piRNA-like RNAs.

RNA 13:1693-1702.

264. Ro S, Song R, Park C, Zheng H, Sanders KM, Van W (2007). Cloning and

expression profiling of small RNAs expressed in the mouse ovary. RNA 13:2366-

2380.

265. Ross AJ and Capel B (2005). Signaling at the crossroads off gonad development.

TRENDS in Endocrinology and Metabolism 16(1): 19-25.

266. Ross J (1996). Control of messenger RNA stability in higher Eukaryotes. Trends

Genet 12(5): 171-175.

267. Ryazansky SS, Gvozdev VA (2008). Small RNAs and Cancerogenesis.

Biochemistry 73: 514-527.

268. Safrany ST, Caffrey JJ, Yang XN, Bembenek ME, Moyer MB, Burkhart WA,

Shears SB (1998). A novel context for the 'MutT' module, a guardian of cell

integrity, in a diphosphoinositol polyphosphate phosphohydrolase. EMBO J

17(22):6599-6607.

269. Safrany ST, Ingram SW, Cartwright JL, Falck JR, McLennan AG, Barnes LD,

Shears SB (1999). The diadenosine hexaphosphate hydro lases from

Schizosaccharomyces pombe and Saccharomyces cerevisiae are homologues of the

human diphosphoinositol polyphosphate phosphohydrolase - overlapping substrate

specificities in a MutT-type protein. J BioI Chern 274(31): 21735-21740.

270. Saito K, Nishida KM, Mori T, Kawamura Y, Miyoshi K, Nagami T, Siomi H,

Siomi MC (2006). Specific association of Piwi with rasiRNAs derived from

retrotransposon and heterochromatic regions in the Drosophila genome. Genes

Dev. 15,20(16),2214-2222.

271. Saito K, Sakaguchi Y, Suzuki T, Suzuki T, Siomi H, Siomi MC (2007). Pi met, the

Drosophila homolog of HENl, mediates 2'-O-methylation of Piwi- interacting

RNAs at their 3' ends. Genes Dev 21:1603-1608.

272. Saito Y, Suzuki H, Tsugawa H, Nakagawa I, Matsuzaki J, Kanai Y, Hibi T (2009).

Chromatin remodeling at Alu repeats by epigenetic treatment activates silenced

microRNA-512-5p with downregulation of Mc1-1 in human gastric cancer cells.

Oncogene [Epub ahead of print].

223

Refey-eVl.-ces

273. Salas-Cortes L, Jaubert F, Barbaux S, Nessmann C, Bono MR, Fellous M,

McElreavey K, and Rosemblatt M (1999). The human SRY protein is present in

fetal and adult Sertoli cells and germ cells. Int J Dev BioI 43 (2): 135-140.

274. Sambrook J, Russell DW (2001). Molecular Cloning, A laboratory manual, Cold

Spring Harbor Press. New York.

275. Sanchez-Moreno I, Canto P, Munguia P, de Le6n MB, Cisneros B, Vilchis F,

Reyes E, Mendez JP (2009). DNA binding activity studies and computational

approach of mutant SRY in patients with 46, XY complete pure gonadal

dysgenesis. Mol Cell EndocrinoI299(2):212-218.

276. Sansal I, Sellers WR (2004). The biology and clinical relevance of the PTEN

tumor suppressor pathway. J Clin OncoI22(14):2954-2963.

277. Scherer SW et al. (2003). Human chromosome 7: DNA sequence and biology.

Science 300: 767-772.

278. Schmahl J, Eicher EM, Washburn LL and Capel Blanche (2000). Sry induces cell

proliferation in the mouse gonad. Development 127: 65-73.

279. Schmahl J, Kim Y, Colvin JS, Ornitz DM, Capel B (2004). Fgf9 induces

proliferation and nuclear localization of FGFR2 in Sertoli precursors during male

sex determination. Development 131(15): 3627-3636.

280. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N (2003). Asymmetry in the

assembly ofthe RNAi enzyme complex. Cell 115(2):199-208.

281. Sekido R, Bar I, Narva'ez V, Penny V, Lovell-Badge Robin (2004). SOX9 is up

regulated by the transient expression of SRY specifically in Sertoli cell precursors.

Dev BioI 274: 271-279.

282. Sekido R, Bar I, Narvaez V, Penny G, Lovell-Badge R (2004). SOX9 is

upregulated by the transient expression of SRY specifically in Sertoli cell

precursors. Dev BioI 274: 271-279.

283. Sekido R, Lovell-Badge R (2008). Sex determination involves synergistic action of

SRY and SFI on a specific Sox9 enhancer. Nature 453(7197):930-934.

284. Sekido R, Lovell-Badge R (2009). Sex determination and SRY: down to a wink

and a nudge? Trends Genet 25(1): 19-29.

285. Shao C, Novakovic VA, Head JF, Seaton BA, Gilbert GE (2008). Crystal structure

of lactadherin C2 domain at 1.7Ao resolution with mutational and computational

analyses of its membrane-binding motif. J BioI Chem 283: 7230-7241.

224

R.efer-ev\'ces

286. Shapiro JA, Sternberg RV (2005). Why repetitive DNA is essential to genome

function. Bioi Rev 80: 1-24.

287. Shen WH, Balajee AS, Wang J, Wu H, Eng C, Pandolfi PP, Yin Y (2007).

Essential role for nuclear PTEN in maintaining chromosomal integrity. Cell

128(1):157-170.

288. Sinclair AH, Berta P, Palmer MS, Hawkins JR, Griffiths BL, Smith MJ, Foster JW,

Frischauf AM, Lovell-Badge R, Goodfellow PN (1990). A gene from the human

sex-determining region encodes a protein with homology to a conserved DNA­

binding motif. Nature 346(6281):216-217.

289. Smalheiser NR, Torvik VI (2005). Mammalian microRNAs derived from genomic

repeats. Trends Genet 21: 322-326.

290. Smalheiser NR, Torvik VI (2006). Alu elements within human mRNAs are

probable microRNA targets. Trends Genet 22: 532-536.

291. Soullier S, Poulat F, Boizet-Bonhoure B, Cal as, B, Bennes R, Heitz F, Berta P

(1994). The human testis determining factor SRY: A new member of the HMG

box protein family. Biochirnie 76: 1075-1081.

292. Spiegelman BM, Heinrich R (2004). Biological control through regulated

transcriptional coactivators. Cell 119: 157-167.

293. Standart N, Jackson RJ (2007). MicroRNAs repress translation ofm7Gppp-capped

target mRNAs in vitro by inhibiting initiation and promoting deadenylation. Genes

Dev 21: 1975-1982.

294. Steck PA, Pershouse MA, Jasser SA, Yung WK., Lin H, Ligon AH et al. (1997).

Identification of a candidate tumour suppressor gene, MMACl, at chromosome

lOq23.3 that is mutated in multiple advanced cancers. Nat Genet 15: 356-362.

295. Stefani G, Slack FJ (2008). Small non-coding RNAs in animal development. Nat

Rev Mol Cell Bioi 9(3): 219-230.

296. Steinemann M, Steinemann S (2000). Common mechanisms of Y chromosome

evolution. Genetica 109: 1 05-111.

297. Stephens L, Radenberg T, Thiel U, Vogel G, Khoo KH, Dell A, Jackson TR,

Hawkins PT, Mayr GW (1993). The detection, purification, structural

characterization, and metabolism of diphosphoinositol pentakisphosphate(s) and

bisdiphosphoinositol tetrakisphosphate(s). J Bioi Chern 268(6):4009-4015.

225

Refe ve lAces

298. Stewart SA, Weinberg RA. 2006. Telomeres: Cancer to Human Aging. Annu Rev

Cell Dev BioI 22:531-557.

299. Strausberg RL et aI., Mammalian Gene Collection (MGC) Program Team (2002).

Generation and initial analysis of more than 15,000 full-length human and mouse

cDNA sequences. Proc Natl Acad Sci USA 99: 16899-16903.

300. Strobel SA, Cochrane JC (2007). RNA catalysis: ribozymes, ribosomes, and

riboswitches. Current Opinion in Chemical Biology 11(6):636-643.

301. Subauste MC, Nalbant P, Adamson ED, Hahn KM (2005). Vinculin controls

PTEN protein level by maintaining the interaction of the adherens junction protein

beta-catenin with the scaffolding protein MAGI-2. J BioI Chem 280(7):5676-5681.

302. Sucheck SJ, Wong CH (2000). RNA as a target for small molecules. Curr Opin

Chem Bio 4:678-686.

303. Sudbeck P, Scherer G (1997). Two independent nuclear localization signals are

present in the DNA-binding high-mobility group domain ofSRY and SOX9. J BioI

Chem 272:27848-27852.

304. Sweitzer TD, Hanover JA (1996). Calmodulin activates nuclear protein import: a

link between signal transduction and nuclear transport. Proc Natl Acad Sci USA

93:14574-14579.

305. Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E,

Anger M, Sachidanandam R, Schultz RM, Hannon GJ (2008). Pseudogene-derived

small interfering RNAs regulate gene expression in mouse oocytes. Nature

453(7194): 534-538.

306. Tamguney T, Stokoe D (2007). New insights into PTEN. J Cell Sci 120(pt

23):4071-4079.

307. Tamura M, Gu J, Matsumoto K, Aota S, Parsons R, Yamada KN (1998). Inhibition

of cell migration, spreading, and focal adhesions by tumor suppressor PTEN.

Science 280(5369): 1614-1617.

308. Tamura M, Gu J, Takino T, and Yamada KM (l999).Tumor suppressor PTEN

inhibition of cell invasion, migration, and growth: differential involvement of focal

adhesion hinase and p130Cas. Cancer Res, 59: 442-449.

309. Tang G (2005). siRNA and miRNA: an insight into RISCs. TRENDS in Biochem

Sci 30(2): 106-114.

310. Tang Y, Eng C (2006). PTEN autoregulates its expression by stabilization of p53

in a phosphatase-independent manner, Cancer Res 66: 736-742.

226

Refevev.-ces

311. Tapparel C, Reymond A, Girardet C, Guillou L, Lyle R, Lamon C, Hutter P,

Antonarakis SE (2003). The TPTE gene family: cellular expression, subcellular

localization and alternative splicing. Gene 323: 189-199.

312. Thevenet L, Albrecht KH, Malki S, Berta P, Boizet-Bonhoure B (2005).

NHERF2/SIP-l interacts with mouse SRY via a different mechanism than human

SRY. J Bioi Chern 280(46): 38625-38630.

313. Thevenet L, Mejean C, Moniot B, Bonneaud N, Galeotti N, Aldrian-Herrada G,

Poulat F, Berta P, Benkirane M, Boizet-Bonhoure B (2004). Regulation of human

SRY subcellular distribution by its acetylationldeacetylation. EMBO J 23(16):

3336-3345.

314. Tolkachev T, Boddapati M, Sanfiz A, Tsuchida K, Kimmelman AC, Chan AM

(2001). Regulation ofPTEN binding to MAGI-2 by two putative phosphorylation

sites at threonine 382 and 383. Cancer Res 61: 4985-4989.

315. Tomari Y, Zamore PD (2005). Perspective: machines for RNAi. Genes Dev 19(5):

517-529.

316. Torres J, Pulido R (2001). The tumor suppressor pten is phosphorylated by the

protein kinase CK2 at Its C terminus. Implications for PTEN stability to

proteasome mediated degradation. J BioI Chern 276: 993-998.

317. Trotman LC, Wang X, Alimonti A, Alimonti A, Chen Z, Teruya-Feldstein J,

Yang H, Pavletich NP, Carver BS, Cordon-Cardo C, Erdjument-Bromage H,

Tempst P, Chi S, Misteli T, Jiang X, Pandolfi PP (2007). Ubiquitination

regulates PTEN nuclear import and tumor suppression. Cell 128:141-156.

318. Vagin VV, Sigova A, Li C, Seitz H, Gvozdev V, Zamore PD (2006). A distinct

small RNA pathway silences selfish genetic elements in the germ line. Science 313:

320-324.

319. Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R (2006). Control of translation

and mRNA degradation by miRNAs and siRNAs. Genes Dev 20: 515-524.

320. Valiente M, Andres-Pons A, Gomar B, Torres J, Gil A, Tapparel C, Antonarakis

SE, Pulido R (2005). Binding of PTEN to Specific PDZ Domains Contributes to

PTEN Protein Stability and Phosphorylation by Microtubule-associated

Serine/Threonine Kinases. J BioI Chern 280(32):28936-28943.

321. Vazquez F, Grossman SR, Takahashi Y, Rokas MY, Nakamura N, Sellers WR

(2001). Phosphorylation of the PTEN tail acts as an inhibitory switch by

preventing its recruitment into a protein complex. J BioI Chern 276: 48627-48630.

227

Refevelll,ces

322. Vazquez F, Ramaswamy S, Nakamura N, Sellers W R (2000). Phosphorylation of

the PTEN tail regulates protein stability and function. Mol Cell Bioi 20: 5010-

5018.

323. Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC,

Hilbert JL, Bartel DP, Crete P (2004). Endogenous trans-acting siRNAs regulate

the accumulation of Arabidopsis mRNAs. Mol Cell 16: 69-79.

324. Venter CJ et aI., (2001), The sequence of the human genome. Science 291: 1304-

1351.

325. Ventura A, Jacks T (2009). MicroRNAs and cancer: short RNAs go a long way.

Cell 136: 586-591.

326. Versteeg R, van Schaik BD, van Batenburg MF, Roos M, Monajemi R, Caron H,

Bussemaker HJ, van Kampen AH (2003). The human transcriptome map reveals

extremes in gene density, intron length, GC content, and repeat pattern for domains

of highly and weakly expressed genes. Genome Res 13: 1998-2004.

327. Vivanco I, Palaskas N, Tran C, Finn SP, Getz G, Kennedy NJ, Jiao J, Rose J, Xie

W, Loda M, Golub T, Mellinghoff IK, Davis RJ, Wu H, Sawyers CL (2007).

Identification of the JNK signaling pathway as a functional target of the tumor

suppressor PTEN. Cancer Cell 11(6):555-569.

328. Wahl MC, Will CL, Luhrmann R (2009). The Spliceosome: Design Principles of a

Dynamic RNP Machine. Cell 136:701-718.

329. Walker SM, Downes CP, Leslie NR (2001). TPIP: a novel phosphoinositide 3-

phosphatase. Biochem J360: 277-283.

330. Wallace N, Wagstaff BJ, Deininger PL, Roy-Engel AM (2008). LINE-l ORFI

protein enhances Alu SINE retrotransposition. Gene 419: 1-6.

331. Wang X, Jiang X (2008). PTEN: a default gate-keeping tumor suppressor with a

versatile tail. Cell Res 18(8):807-816.

332. Wang X, Shi Y, Wang J, Huang G, Jiang X (2008). Crucial role of the C-terminus

of PTEN in antagonizing NEDD4-1-mediated PTEN ubiquitination and

degradation. Biochem J 414(2): 221-229.

333. Wang X, Trotman LC, Koppie T, Alimonti A, Chen Z, Gao Z, Wang J, Erdjument­

Bromage H, Tempst P, Cordon-Cardo C, Pandolfi P, Jiang X. NEDD4-1 is a

protooncogenic ubiquitin ligase for PTEN. Cell 128:129-139.

334. Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N,

Imai H (2006). Identification and characterization of two novel classes of small

228

R.efereV\,c,es,

RNAs in the mouse gennline: retrotransposon-derived siRNAs in oocytes and

gennline small RNAs in testes. Genes Dev 20:1732-1743.

335, Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y,

Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y, Sasaki H (2008).

Endogenous siRNAs from naturally fonned dsRNAs regulate transcripts in mouse

oocytes. Nature 453(7194): 539-543.

336. Waterston RH et aI., (2002). Initial sequencing and comparative analysis of the

mouse genome. Nature 420: 520-562.

337. Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R (2008). Molecular

Biology of the Gene. 6th Edn. Pearson Int. Edn : 1-841.

338. Wechsler-Reya R, Scott MP (2001). The developmental biology of brain tumors.

Annu Rev Neurosci 24: 385-428.

339. Weng LP, Brown JL, Baker KM, Ostrowski MC, Eng C (2002). PTEN blocks

insulin-mediated ETS-2 phosphorylation through MAP kinase, independently of

the phosphoinositide 3-kinase pathway. Hum Mol Genet 11(15): 1687-1696.

340. Werner MR, Bianchi ME, Gronenborn AM, Clore GM (1995). NMR spectroscopic

analysis of the DNA confonnation induced by the human testis detennining factor

SRY. Biochemistry 34(37):11998-12004.

341. Wetering MV and Clevers H (1992). Sequence-specific interaction of the HMG

box proteins TCF-l and SRY occurs within the minor groove of a Watson-Crick

double helix. EMBO J 11(8): pp.3039-3044.

342. Whitfield LS, Lovell-Badge R, Goodfellow PN (1993). Rapid sequence evolution

ofthe mammalian sex-detennining gene SRY. Nature 364:713-715.

343. Wightman B, Ha I, Ruvkun G (1993). Posttranscriptional regulation of the

heterochronic gene lin-14 by lin-4 mediates temporal pattern fonnation in C.

elegans. Cell 75: 855-862.

344. Wilhelm D and Englert C (2002). The Wilms tumor suppressor WTl regulates

early gonad development by activation ofSfl. Genes Dev 16: 1839-1851.

345. Wilhelm D and Koopman P, (2006). The makings of maleness: towards an

integrated view of male sexual development. Nat Rev Genet 7(8): 620-631.

346. Wilhelm D, Martinson F, Bradford S, Wilson MJ, Combes AN, Beverdam A,

Bowles J, Mizusaki H, Koopman P (2005). Sertoli cell differentiation is induced

both cell-autonomously and through prostaglandin signaling during mammalian

sex detennination. Dev BioI 287: 111-124.

229

347. Wilhelm D, Palmer P and Koopman P (2007). Sex determination and gonadal

development in mammals. Physiol Rev 87: 1-28.

348. Williams RW, Rubin GM (2002). ARGONAUTEI is required for efficient RNA

interference in Drosophila embryos. Proc Natl Acad Sci USA 99: 6889-6894.

349. Willingham AT and Gingeras TR (2006). TUF Love for "Junk" DNA. Cell 125:

1215-1220.

350. Woiwode A, Johnson SA, Zhong S, Zhang C, Roeder RG, Teichmann M, Johnson

DL. (2008). PTEN represses RNA polymerase III-dependent transcription by

targeting the TFIIIB complex. Mol Cell Bio!28(12):4204-4214.

351. Wu H, Goel V, Haluska FG (2003). PTEN signaling pathways in melanoma.

Oncogene 22(20):3113-22.

352. Wu L, Fan J, Belasco JG (2006). MicroRNAs direct rapid deadenylation of

mRNA. Proc Natl A cad Sci USA 103: 4034-4039.

353. Wu X, Senechal K, Neshat MS, Whang YE, Sawyers CL (1998). The

PTENIMMAC 1 tumor suppressor phosphatase functions as a negative regulator of

the phosphoinositide 3-kinase/Akt pathway. Proc Nat! Acad Sci USA

95(26): 15587-15591.

354. Wu Y, Dowbenko D, Pisabarro M, Dillard-Telm L, Koeppen H, Lasky LA (2001).

PTEN 2, a Golgi-associated testis-specific homologue of the PTEN tumor

suppressor lipid phosphatase. J Bio! Chern 276(24): 21745-21753.

355. Yakovchuk P, Goodrich YA, Kugel JF (2009). B2 RNA and Alu RNA repress

transcription by disrupting contacts between RNA polymerase II and promoter

DNA within assembled complexes. Proc Nat! Acad Sci USA 106: 5695-5574.

356. Yamada KM, Araki M (2001). Tumor suppressor PTEN: modulator of cell

signaling, growth, migration and apoptosis. J Cell Sci 114(Pt 13): 2375-2382.

357. Yang XN, Safrany ST, Shears SB (1999). Site-directed mutagenesis of

diphosphoinositol polyphosphate phosphohydrolase, a dual specificity NUDT

enzyme that attacks diadenosine polyphosphates and diphosphoinositol

polyphosphates. J Bio! Chern 274(50): 35434-35440.

358. Yang Z, Boffelli D, Boonmark N, Schwartz K, Lawn R (1998). Apolipoprotein(a)

Gene Enhancer Resides within a LINE Element, J Bio! Chern 273: 891-897.

359. Yang Z, Ebright YW, Yu B, Chen X (2006). HENI recognizes 21-24 nt small

RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal

nucleotide. Nucleic Acids Res 34: 667-675.

230

Refevelll.us.

360. Yekta S, Shih IH, Bartel DP (2004). MicroRNA-directed cleavage of HOXB8

mRNA. Science 304:594-596.

361. Yigit E, Batista PJ, Bei Y, Pang KM, Chen CC, Tolia NH, Joshua-Tor L, Mitani S,

Simard MJ, Mello CC (2006). Analysis of the C. elegans Argonaute family reveals

that distinct Argonautes act sequentially during RNAi. Cell 127: 747-757.

362. Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, Chen X

(2005). Methylation as a crucial step in plant microRNA biogenesis. Science 307:

932-935.

363. Yuan X, Lu ML, Li T and Balk SP (2001). SRY interacts with and negatively

regulates androgen receptor transcriptional activity. J BioI Chern 276(49): 46647-

46654.

364. Zamore PD, Haley B. (2005). Ribo-gnome: the big world of small RNAs. Science

309: 1519-1524.

365. Zbuk KM, Eng C (2007). Cancer phenomics: RET and PTEN as illustrative

models. Nat Rev Cancer 7: 35-45.

366. Zeng Y, Yi R, Cullen BR (2005). Recognition and cleavage of primary microRNA

precursors by the nuclear processing enzyme Drosha. EMBO J 24: 138148.

367. Zhang B, Wang Q, Pan X (2007). MicroRNAs and their regulatory roles in animals

and plants. J cell Physiol210: 279-289.

368. Zhang C, Comai L, Johnson DL (2005). PTEN represses RNA polymerase I

transcription by disrupting the SLI complex. Mol Cell BioI 25(16):6899-6911.

369. Zhou M, Gu L, Findley HW, Jiang R, Woods WG (2003). PTEN reverses MDM2-

mediated chemotherapy resistance by interacting with p53 in acute lymphoblastic

leukemia cells. Cancer Res 63(19):6357-6362.

370. Zhou X, Liao Z, Jia Q, Cheng L, Li F (2007). Identification and characterization of

piwi subfamily in insects. Biochern Biophys Res Cornrnun 362: 126-131.

371. Zwingman T, Erickson RP, Boyer T, Ao A (1993). Transcription of the sex­

determining region genes Sry and Zfy in the mouse preimplantation embryo. Proc

Natl Acad Sci USA 90:814-817.

231