GRHL3/GET1 and Trithorax Group Members Collaborate to Activate the Epidermal Progenitor Differentiation Program

1. SchuettengruberBMartinezAMIovinoNCavalliG 2011 Trithorax group proteins: switching genes on and keeping them active. Nat Rev Mol Cell Biol 12 799 814

2. BreilingASessaLOrlandoV 2007 Biology of polycomb and trithorax group proteins. Int Rev Cytol 258 83 136

3. SchuettengruberBChourroutDVervoortMLeblancBCavalliG 2007 Genome regulation by polycomb and trithorax proteins. Cell 128 735 745

4. AkamM 1987 The molecular basis for metameric pattern in the Drosophila embryo. Development 101 1 22

5. BeckSFaradjiFBrockHPeronnetF 2010 Maintenance of Hox gene expression patterns. Adv Exp Med Biol 689 41 62

6. SegreJ 2003 Complex redundancy to build a simple epidermal permeability barrier. Curr Opin Cell Biol 15 776 782

7. DaiXSegreJA 2004 Transcriptional control of epidermal specification and differentiation. Curr Opin Genet Dev 14 485 491

8. SegreJABauerCFuchsE 1999 Klf4 is a transcription factor required for establishing the barrier function of the skin. Nat Genet 22 356 360

9. YuZLinKKBhandariASpencerJAXuX 2006 The Grainyhead-like epithelial transactivator Get-1/Grhl3 regulates epidermal terminal differentiation and interacts functionally with LMO4. Dev Biol 299 122 136

10. TingSBCaddyJHislopNWilanowskiTAudenA 2005 A homolog of Drosophila grainy head is essential for epidermal integrity in mice. Science 308 411 413

11. SenGLReuterJAWebsterDEZhuLKhavariPA 2010 DNMT1 maintains progenitor function in self-renewing somatic tissue. Nature 463 563 567

12. LeBoeufMTerrellATrivediSSinhaSEpsteinJA 2010 Hdac1 and Hdac2 act redundantly to control p63 and p53 functions in epidermal progenitor cells. Dev Cell 19 807 818

13. IndraAKDupéVBornertJMMessaddeqNYanivM 2005 Temporally controlled targeted somatic mutagenesis in embryonic surface ectoderm and fetal epidermal keratinocytes unveils two distinct developmental functions of BRG1 in limb morphogenesis and skin barrier formation. Development 132 4533 4544

14. KashiwagiMMorganBAGeorgopoulosK 2007 The chromatin remodeler Mi-2beta is required for establishment of the basal epidermis and normal differentiation of its progeny. Development 134 1571 1582

15. FessingMYMardaryevANGdulaMRSharovAASharovaTY 2011 p63 regulates Satb1 to control tissue-specific chromatin remodeling during development of the epidermis. J Cell Biol 194 825 839

16. EzhkovaEPasolliHAParkerJSStokesNSuIH 2009 Ezh2 orchestrates gene expression for the stepwise differentiation of tissue-specific stem cells. Cell 136 1122 1135

17. MejettaSMoreyLPascualGKueblerBMysliwiecMR 2011 Jarid2 regulates mouse epidermal stem cell activation and differentiation. EMBO J 30 3635 3646

18. LuisNMMoreyLMejettaSPascualGJanichP 2011 Regulation of human epidermal stem cell proliferation and senescence requires polycomb- dependent and -independent functions of Cbx4. Cell Stem Cell 9 233 246

19. SenGLWebsterDEBarraganDIChangHYKhavariPA 2008 Control of differentiation in a self-renewing mammalian tissue by the histone demethylase JMJD3. Genes Dev 22 1865 1870

20. MaceKAPearsonJCMcGinnisW 2005 An epidermal barrier wound repair pathway in Drosophila is mediated by grainy head. Science 308 381 385

21. BraySJKafatosFC 1991 Developmental function of Elf-1: an essential transcription factor during embryogenesis in Drosophila. Genes Dev 5 1672 1683

22. TingSBCaddyJWilanowskiTAudenACunninghamJM 2005 The epidermis of grhl3-null mice displays altered lipid processing and cellular hyperproliferation. Organogenesis 2 33 35

23. YamadaKMatsukiMMorishimaYUedaETabataK 1997 Activation of the human transglutaminase 1 promoter in transgenic mice: terminal differentiation-specific expression of the TGM1-lacZ transgene in keratinized stratified squamous epithelia. Hum Mol Genet 6 2223 2231

24. ChangWYAndrewsJCarterDEDagninoL 2006 Differentiation and injury-repair signals modulate the interaction of E2F and pRB proteins with novel target genes in keratinocytes. Cell Cycle 5 1872 1879

25. DavisAJYanZMartinezBMumbyMC 2008 Protein phosphatase 2A is targeted to cell division control protein 6 by a calcium-binding regulatory subunit. J Biol Chem 283 16104 16114

26. EckertRLCrishJFBanksEBWelterJF 1997 The epidermis: genes on - genes off. J Invest Dermatol 109 501 509

27. FuchsE 2007 Scratching the surface of skin development. Nature 445 834 842

28. WattFMLo CelsoCSilva-VargasV 2006 Epidermal stem cells: an update. Curr Opin Genet Dev 16 518 524

29. VerdoniAMIkedaSIkedaA 2010 Serum response factor is essential for the proper development of skin epithelium. Mamm Genome 21 64 76

30. Le ProvostFMiyoshiKVilotteJLBierieBRobinsonGW 2005 SOCS3 promotes apoptosis of mammary differentiated cells. Biochem Biophys Res Commun 338 1696 1701

31. LacroixMCaramelJGoguet-RubioPLinaresLKEstrachS 2010 Transcription factor E4F1 is essential for epidermal stem cell maintenance and skin homeostasis. Proc Natl Acad Sci U S A 107 21076 21081

32. XieXRigorPBaldiP 2009 MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinformatics 25 167 174

33. KuMKocheRPRheinbayEMendenhallEMEndohM 2008 Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 4 e1000242 doi:10.1371/journal.pgen.1000242

34. MendenhallEMKocheRPTruongTZhouVWIssacB 2010 GC-rich sequence elements recruit PRC2 in mammalian ES cells. PLoS Genet 6 e1001244 doi:10.1371/journal.pgen.1001244

35. TanayAO'DonnellAHDamelinMBestorTH 2007 Hyperconserved CpG domains underlie Polycomb-binding sites. Proc Natl Acad Sci U S A 104 5521 5526

36. AngYSTsaiSYLeeDFMonkJSuJ 2011 Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell 145 183 197

37. AnsariKIMishraBPMandalSS 2009 MLL histone methylases in gene expression, hormone signaling and cell cycle. Front Biosci 14 3483 3495

38. GlaserSSchaftJLubitzSVinterstenKvan der HoevenF 2006 Multiple epigenetic maintenance factors implicated by the loss of Mll2 in mouse development. Development 133 1423 1432

39. LeeSLeeDKDouYLeeJLeeB 2006 Coactivator as a target gene specificity determinant for histone H3 lysine 4 methyltransferases. Proc Natl Acad Sci U S A 103 15392 15397

40. YuBDHessJLHorningSEBrownGAKorsmeyerSJ 1995 Altered Hox expression and segmental identity in Mll-mutant mice. Nature 378 505 508

41. NgSBBighamAWBuckinghamKJHannibalMCMcMillinMJ 2010 Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 42 790 793

42. HannibalMCBuckinghamKJNgSBMingJEBeckAE 2011 Spectrum of MLL2 (ALR) mutations in 110 cases of Kabuki syndrome. Am J Med Genet A 155A 1511 1516

43. LiYBögershausenNAlanayYSimsek KiperPOPlumeN 2011 A mutation screen in patients with Kabuki syndrome. Hum Genet

44. MicaleLAugelloBFuscoCSelicorniALoviglioMN 2011 Mutation spectrum of MLL2 in a cohort of Kabuki syndrome patients. Orphanet J Rare Dis 6 38

45. PaulussenADStegmannAPBlokMJTserpelisDPosma-VelterC 2011 MLL2 mutation spectrum in 45 patients with Kabuki syndrome. Hum Mutat 32 E2018 2025

46. BankaSVeeramachaneniRReardonWHowardEBunstoneS 2012 How genetically heterogeneous is Kabuki syndrome?: MLL2 testing in 116 patients, review and analyses of mutation and phenotypic spectrum. Eur J Hum Genet 20 381 388

47. BokinniY 2012 Kabuki syndrome revisited. J Hum Genet 57 223 227

48. YuZMannikJSotoALinKKAndersenB 2009 The epidermal differentiation-associated Grainyhead gene Get1/Grhl3 also regulates urothelial differentiation. EMBO J 28 1890 1903

49. KennisonJATamkunJW 1988 Dosage-dependent modifiers of polycomb and antennapedia mutations in Drosophila. Proc Natl Acad Sci U S A 85 8136 8140

50. DouYMilneTATackettAJSmithERFukudaA 2005 Physical association and coordinate function of the H3 K4 methyltransferase MLL1 and the H4 K16 acetyltransferase MOF. Cell 121 873 885

51. SierraJYoshidaTJoazeiroCAJonesKA 2006 The APC tumor suppressor counteracts beta-catenin activation and H3K4 methylation at Wnt target genes. Genes Dev 20 586 600

52. OnoderaAYamashitaMEndoYKuwaharaMTofukujiS 2010 STAT6-mediated displacement of polycomb by trithorax complex establishes long-term maintenance of GATA3 expression in T helper type 2 cells. J Exp Med 207 2493 2506

53. YuZLinKKBhandariASpencerJAXuX 2006 The Grainyhead-like epithelial transactivator Get-1/Grhl3 regulates epidermal terminal differentiation and interacts functionally with LMO4. Dev Biol 299 122 136

54. LinKKChudovaDHatfieldGWSmythPAndersenB 2004 Identification of hair cycle-associated genes from time-course gene expression profile data by using replicate variance. Proc Natl Acad Sci U S A 101 15955 15960

55. SaeedAISharovVWhiteJLiJLiangW 2003 TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34 374 378

56. SaeedAIBhagabatiNKBraistedJCLiangWSharovV 2006 TM4 microarray software suite. Methods Enzymol 411 134 193

57. LongADMangalamHJChanBYTolleriLHatfieldGW 2001 Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276 19937 19944

58. HuangdWShermanBTZhengXYangJImamichiT 2009 Extracting biological meaning from large gene lists with DAVID. Curr Protoc Bioinformatics Chapter 13 Unit 13.11

59. HuangdWShermanBTLempickiRA 2009 Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4 44 57

60. EdgarRDomrachevMLashAE 2002 Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30 207 210

61. SchmidtDWilsonMDSpyrouCBrownGDHadfieldJ 2009 ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48 240 248

62. LangmeadBTrapnellCPopMSalzbergSL 2009 Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10 R25

63. ZhangYLiuTMeyerCAEeckhouteJJohnsonDS 2008 Model-based analysis of ChIP-Seq (MACS). Genome Biol 9 R137

64. BlankenbergDVon KusterGCoraorNAnandaGLazarusR 2010 Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol Chapter 19 Unit 19.10.11 21

65. GiardineBRiemerCHardisonRCBurhansRElnitskiL 2005 Galaxy: a platform for interactive large-scale genome analysis. Genome Res 15 1451 1455

66. GoecksJNekrutenkoATaylorJTeamG 2010 Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11 R86