#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

Female Bias in and Regulation by the Histone Demethylase KDM6A


The Rhox cluster on the mouse X chromosome contains reproduction-related homeobox genes expressed in a sexually dimorphic manner. We report that two members of the Rhox cluster, Rhox6 and 9, are regulated by de-methylation of histone H3 at lysine 27 by KDM6A, a histone demethylase with female-biased expression. Consistent with other homeobox genes, Rhox6 and 9 are in bivalent domains prior to embryonic stem cell differentiation and thus poised for activation. In female mouse ES cells, KDM6A is specifically recruited to Rhox6 and 9 for gene activation, a process inhibited by Kdm6a knockdown in a dose-dependent manner. In contrast, KDM6A occupancy at Rhox6 and 9 is low in male ES cells and knockdown has no effect on expression. In mouse ovary where Rhox6 and 9 remain highly expressed, KDM6A occupancy strongly correlates with expression. Our study implicates Kdm6a, a gene that escapes X inactivation, in the regulation of genes important in reproduction, suggesting that KDM6A may play a role in the etiology of developmental and reproduction-related effects of X chromosome anomalies.


Vyšlo v časopise: Female Bias in and Regulation by the Histone Demethylase KDM6A. PLoS Genet 9(5): e32767. doi:10.1371/journal.pgen.1003489
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003489

Souhrn

The Rhox cluster on the mouse X chromosome contains reproduction-related homeobox genes expressed in a sexually dimorphic manner. We report that two members of the Rhox cluster, Rhox6 and 9, are regulated by de-methylation of histone H3 at lysine 27 by KDM6A, a histone demethylase with female-biased expression. Consistent with other homeobox genes, Rhox6 and 9 are in bivalent domains prior to embryonic stem cell differentiation and thus poised for activation. In female mouse ES cells, KDM6A is specifically recruited to Rhox6 and 9 for gene activation, a process inhibited by Kdm6a knockdown in a dose-dependent manner. In contrast, KDM6A occupancy at Rhox6 and 9 is low in male ES cells and knockdown has no effect on expression. In mouse ovary where Rhox6 and 9 remain highly expressed, KDM6A occupancy strongly correlates with expression. Our study implicates Kdm6a, a gene that escapes X inactivation, in the regulation of genes important in reproduction, suggesting that KDM6A may play a role in the etiology of developmental and reproduction-related effects of X chromosome anomalies.


Zdroje

1. WeatherbeeSD, HalderG, KimJ, HudsonA, CarrollS (1998) Ultrabithorax regulates genes at several levels of the wing-patterning hierarchy to shape the development of the Drosophila haltere. Genes Dev 12: 1474–1482.

2. WangJ, MagerJ, SchnedierE, MagnusonT (2002) The mouse PcG gene eed is required for Hox gene repression and extraembryonic development. Mamm Genome 13: 493–503.

3. LanF, BaylissPE, RinnJL, WhetstineJR, WangJK, et al. (2007) A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 449: 689–694.

4. SwigutT, WysockaJ (2007) H3K27 demethylases, at long last. Cell 131: 29–32.

5. ChoYW, HongT, HongS, GuoH, YuH, et al. (2007) PTIP associates with MLL3- and MLL4-containing histone H3 lysine 4 methyltransferase complex. J Biol Chem 282: 20395–20406.

6. IssaevaI, ZonisY, RozovskaiaT, OrlovskyK, CroceCM, et al. (2007) Knockdown of ALR (MLL2) reveals ALR target genes and leads to alterations in cell adhesion and growth. Mol Cell Biol 27: 1889–1903.

7. HongS, ChoYW, YuLR, YuH, VeenstraTD, et al. (2007) Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases. Proc Natl Acad Sci U S A 104: 18439–18444.

8. AggerK, CloosPA, ChristensenJ, PasiniD, RoseS, et al. (2007) UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449: 731–734.

9. WelsteadGG, CreyghtonMP, BilodeauS, ChengAW, MarkoulakiS, et al. (2012) X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner. Proc Natl Acad Sci U S A 109: 13004–13009.

10. SeenundunS, RampalliS, LiuQC, AzizA, PaliiC, et al. (2010) UTX mediates demethylation of H3K27me3 at muscle-specific genes during myogenesis. EMBO J 29: 1401–1411.

11. LeeS, LeeJW, LeeSK (2011) UTX, a Histone H3-Lysine 27 Demethylase, Acts as a Critical Switch to Activate the Cardiac Developmental Program. Dev Cell 22 ((1)): 25–37.

12. MiyakeN, MizunoS, OkamotoN, OhashiH, ShiinaM, et al. (2013) KDM6A Point Mutations Cause Kabuki Syndrome. Hum Mutat 34: 108–110.

13. LedererD, GrisartB, DigilioMC, BenoitV, CrespinM, et al. (2012) Deletion of KDM6A, a histone demethylase interacting with MLL2, in three patients with Kabuki syndrome. Am J Hum Genet 90: 119–124.

14. TerashimaM, IshimuraA, YoshidaM, SuzukiY, SuganoS, et al. (2010) The tumor suppressor Rb and its related Rbl2 genes are regulated by Utx histone demethylase. Biochem Biophys Res Commun 399: 238–244.

15. van HaaftenG, DalglieshGL, DaviesH, ChenL, BignellG, et al. (2009) Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer. Nat Genet 41: 521–523.

16. WartmanLD, LarsonDE, XiangZ, DingL, ChenK, et al. (2011) Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression. J Clin Invest 121: 1445–1455.

17. MarBG, BullingerL, BasuE, SchlisK, SilvermanLB, et al. (2012) Sequencing histone-modifying enzymes identifies UTX mutations in acute lymphoblastic leukemia. Leukemia 26 ((8)): 1881–3.

18. MacLeanJA2nd, WilkinsonMF (2010) The Rhox genes. Reproduction 140: 195–213.

19. MacleanJA2nd, ChenMA, WayneCM, BruceSR, RaoM, et al. (2005) Rhox: a new homeobox gene cluster. Cell 120: 369–382.

20. DaggagH, SvingenT, WesternPS, van den BergenJA, McClivePJ, et al. (2008) The rhox homeobox gene family shows sexually dimorphic and dynamic expression during mouse embryonic gonad development. Biol Reprod 79: 468–474.

21. HogeveenKN, Sassone-CorsiP (2005) Homeobox galore: when reproduction goes RHOX and roll. Cell 120: 287–288.

22. SpitzF, HerkenneC, MorrisMA, DubouleD (2005) Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes. Nat Genet 37: 889–893.

23. ZhanM, MiuraT, XuX, RaoMS (2005) Conservation and variation of gene regulation in embryonic stem cells assessed by comparative genomics. Cell Biochem Biophys 43: 379–405.

24. OdaM, YamagiwaA, YamamotoS, NakayamaT, TsumuraA, et al. (2006) DNA methylation regulates long-range gene silencing of an X-linked homeobox gene cluster in a lineage-specific manner. Genes Dev 20: 3382–3394.

25. MacleanJ, BettegowdaA, KimBJ, LouCH, YangSM, et al. (2011) The Rhox Homeobox Gene Cluster is Imprinted and Selectively Targeted for Regulation by Histone H1 and DNA Methylation. Mol Cell Biol 31 ((6)): 1275–87.

26. GreenfieldA, CarrelL, PennisiD, PhilippeC, QuaderiN, et al. (1998) The UTX gene escapes X inactivation in mice and humans. Hum Mol Genet 7: 737–742.

27. XuJ, BurgoynePS, ArnoldAP (2002) Sex differences in sex chromosome gene expression in mouse brain. Hum Mol Genet 11: 1409–1419.

28. JohnstonCM, LovellFL, LeongamornlertDA, StrangerBE, DermitzakisET, et al. (2008) Large-scale population study of human cell lines indicates that dosage compensation is virtually complete. PLoS Genet 4: e9 doi:10.1371/journal.pgen.0040009.

29. HeardE, DistecheCM (2006) Dosage compensation in mammals: fine-tuning the expression of the X chromosome. Genes Dev 20: 1848–1867.

30. DistecheCM (1995) Escape from X inactivation in human and mouse. Trends Genet 11: 17–22.

31. BerletchJB, YangF, XuJ, CarrelL, DistecheCM (2011) Genes that escape from X inactivation. Hum Genet 130: 237–245.

32. JamesonSA, NatarajanA, CoolJ, DeFalcoT, MaatoukDM, et al. (2012) Temporal transcriptional profiling of somatic and germ cells reveals biased lineage priming of sexual fate in the fetal mouse gonad. PLoS Genet 8: e1002575 doi:10.1371/journal.pgen.1002575.

33. LinH, GuptaV, VermilyeaMD, FalcianiF, LeeJT, et al. (2007) Dosage compensation in the mouse balances up-regulation and silencing of X-linked genes. PLoS Biol 5: e326 doi:10.1371/journal.pbio.0050326.

34. LinH, HalsallJA, AntczakP, O'NeillLP, FalcianiF, et al. (2011) Relative overexpression of X-linked genes in mouse embryonic stem cells is consistent with Ohno's hypothesis. Nat Genet 43: 1169–1170; author reply 1171–1162.

35. XuN, TsaiCL, LeeJT (2006) Transient homologous chromosome pairing marks the onset of X inactivation. Science 311: 1149–1152.

36. AzuaraV, PerryP, SauerS, SpivakovM, JorgensenHF, et al. (2006) Chromatin signatures of pluripotent cell lines. Nat Cell Biol 8: 532–538.

37. BernsteinBE, MikkelsenTS, XieX, KamalM, HuebertDJ, et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315–326.

38. GallardoTD, JohnGB, ShirleyL, ContrerasCM, AkbayEA, et al. (2007) Genomewide discovery and classification of candidate ovarian fertility genes in the mouse. Genetics 177: 179–194.

39. RottscheidtR, HarrB (2007) Extensive additivity of gene expression differentiates subspecies of the house mouse. Genetics 177: 1553–1567.

40. MacleanJA2nd, HayashiK, TurnerTT, WilkinsonMF (2012) The Rhox5 Homeobox Gene Regulates the Region-Specific Expression of Its Paralogs in the Rodent Epididymis. Biol Reprod 86 ((6)): 189.

41. SongHW, DannCT, McCarreyJ, MeistrichM, CornwallG, et al. (2012) Dynamic expression pattern and subcellular localization of the RHOX10 homeobox transcription factor during early germ cell development. Reproduction 143 ((5)) 611–24.

42. Hailesellasse SeneK, PorterCJ, PalidworG, Perez-IratxetaC, MuroEM, et al. (2007) Gene function in early mouse embryonic stem cell differentiation. BMC Genomics 8: 85.

43. ChenS, MaJ, WuF, XiongLJ, MaH, et al. (2012) The histone H3 Lys 27 demethylase JMJD3 regulates gene expression by impacting transcriptional elongation. Genes Dev 26: 1364–1375.

44. LiQ, BartlettDL, GorryMC, O'MalleyME, GuoZS (2009) Three epigenetic drugs up-regulate homeobox gene Rhox5 in cancer cells through overlapping and distinct molecular mechanisms. Mol Pharmacol 76: 1072–1081.

45. SasakiH, HamadaT, UedaT, SekiR, HigashinakagawaT, et al. (1991) Inherited type of allelic methylation variations in a mouse chromosome region where an integrated transgene shows methylation imprinting. Development 111: 573–581.

46. MiquelajaureguiA, Varela-EchavarriaA, CeciML, Garcia-MorenoF, RicanoI, et al. (2010) LIM-homeobox gene Lhx5 is required for normal development of Cajal-Retzius cells. J Neurosci 30: 10551–10562.

47. YangJM, SimSM, KimHY, ParkGT (2010) Expression of the homeobox gene, HOPX, is modulated by cell differentiation in human keratinocytes and is involved in the expression of differentiation markers. Eur J Cell Biol 89: 537–546.

48. LiuC, TsaiP, GarciaAM, LogemanB, TanakaTS (2011) A possible role of Reproductive homeobox 6 in primordial germ cell differentiation. Int J Dev Biol 55: 909–916.

49. TakasakiN, RankinT, DeanJ (2001) Normal gonadal development in mice lacking GPBOX, a homeobox protein expressed in germ cells at the onset of sexual dimorphism. Mol Cell Biol 21: 8197–8202.

50. ChunJY, HanYJ, AhnKY (1999) Psx homeobox gene is X-linked and specifically expressed in trophoblast cells of mouse placenta. Dev Dyn 216: 257–266.

51. MacleanJA2nd, HayashiK, TurnerTT, WilkinsonMF (2012) The rhox5 homeobox gene regulates the region-specific expression of its paralogs in the rodent epididymis. Biol Reprod 86: 189.

52. ThorrezL, Van DeunK, TrancheventLC, Van LommelL, EngelenK, et al. (2008) Using ribosomal protein genes as reference: a tale of caution. PLoS ONE 3: e1854 doi:10.1371/journal.pone.0001854.

53. SuYQ, SugiuraK, WigglesworthK, O'BrienMJ, AffourtitJP, et al. (2008) Oocyte regulation of metabolic cooperativity between mouse cumulus cells and oocytes: BMP15 and GDF9 control cholesterol biosynthesis in cumulus cells. Development 135: 111–121.

54. SugiuraK, SuYQ, LiQ, WigglesworthK, MatzukMM, et al. (2010) Estrogen promotes the development of mouse cumulus cells in coordination with oocyte-derived GDF9 and BMP15. Mol Endocrinol 24: 2303–2314.

55. RaefskiAS, O'NeillMJ (2005) Identification of a cluster of X-linked imprinted genes in mice. Nat Genet 37: 620–624.

56. ShpargelKB, SengokuT, YokoyamaS, MagnusonT (2012) UTX and UTY Demonstrate Histone Demethylase-Independent Function in Mouse Embryonic Development. PLoS Genet 8: e1002964 doi:10.1371/journal.pgen.1002964.

57. WangC, LeeJE, ChoYW, XiaoY, JinQ, et al. (2012) UTX regulates mesoderm differentiation of embryonic stem cells independent of H3K27 demethylase activity. Proc Natl Acad Sci U S A 109: 15324–15329.

58. MillerSA, MohnSE, WeinmannAS (2010) Jmjd3 and UTX play a demethylase-independent role in chromatin remodeling to regulate T-box family member-dependent gene expression. Mol Cell 40: 594–605.

59. WangC, LeeJE, ChoYW, XiaoY, JinQ, et al. (2012) UTX regulates mesoderm differentiation of embryonic stem cells independent of H3K27 demethylase activity. Proc Natl Acad Sci U S A 109 ((38)): 15324–9.

60. MansourAA, GafniO, WeinbergerL, ZviranA, AyyashM, et al. (2012) The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature 488: 409–413.

61. BurgoynePS, BakerTG (1985) Perinatal oocyte loss in XO mice and its implications for the aetiology of gonadal dysgenesis in XO women. J Reprod Fertil 75: 633–645.

62. BondyCA (2009) Turner syndrome 2008. Horm Res 71 Suppl 1: 52–56.

63. IshikawaH, BanzaiM, YamauchiT (1999) Developmental retardation of XO mouse embryos at mid-gestation. J Reprod Fertil 115: 263–267.

64. PennyGD, KayGF, SheardownSA, RastanS, BrockdorffN (1996) Requirement for Xist in X chromosome inactivation. Nature 379: 131–137.

65. HokiY, KimuraN, KanbayashiM, AmakawaY, OhhataT, et al. (2009) A proximal conserved repeat in the Xist gene is essential as a genomic element for X-inactivation in mouse. Development 136: 139–146.

66. NelsonJD, DenisenkoO, SovaP, BomsztykK (2006) Fast chromatin immunoprecipitation assay. Nucleic Acids Res 34: e2.

67. NguyenDK, DistecheCM (2006) Dosage compensation of the active X chromosome in mammals. Nat Genet 38: 47–53.

68. EdgarR, DomrachevM, LashAE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207–210.

69. O'GeenH, NicoletCM, BlahnikK, GreenR, FarnhamPJ (2006) Comparison of sample preparation methods for ChIP-chip assays. Biotechniques 41: 577–580.

Štítky
Genetika Reprodukčná medicína

Článok vyšiel v časopise

PLOS Genetics


2013 Číslo 5
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Aktuální možnosti diagnostiky a léčby litiáz
nový kurz
Autori: MUDr. Tomáš Ürge, PhD.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#