Sex-biased genetic programs in liver metabolism and liver fibrosis are controlled by EZH1 and EZH2
Autoři:
Dana Lau-Corona aff001; Woo Kyun Bae aff002; Lothar Hennighausen aff002; David J. Waxman aff001
Působiště autorů:
Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
aff001; Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
aff002; Department of Internal Medicine, Chonnam National University Medical School, Gwangju, Korea
aff003
Vyšlo v časopise:
Sex-biased genetic programs in liver metabolism and liver fibrosis are controlled by EZH1 and EZH2. PLoS Genet 16(5): e32767. doi:10.1371/journal.pgen.1008796
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1008796
Souhrn
Sex differences in the incidence and progression of many liver diseases, including liver fibrosis and hepatocellular carcinoma, are associated with sex-biased hepatic expression of hundreds of genes. This sexual dimorphism is largely determined by the sex-specific pattern of pituitary growth hormone secretion, which controls a transcriptional regulatory network operative in the context of sex-biased and growth hormone-regulated chromatin states. Histone H3K27-trimethylation yields a major sex-biased repressive chromatin mark deposited at many strongly female-biased genes in male mouse liver, but not at male-biased genes in female liver, and is catalyzed by polycomb repressive complex-2 through its homologous catalytic subunits, Ezh1 and Ezh2. Here, we used Ezh1-knockout mice with a hepatocyte-specific knockout of Ezh2 to investigate the sex bias of liver H3K27-trimethylation and its functional role in regulating sex-differences in the liver. Combined hepatic Ezh1/Ezh2 deficiency led to a significant loss of sex-biased gene expression, particularly in male liver, where many female-biased genes were increased in expression while male-biased genes showed decreased expression. The associated loss of H3K27me3 marks, and increases in the active enhancer marks H3K27ac and H3K4me1, were also more pronounced in male liver. Further, Ezh1/Ezh2 deficiency in male liver, and to a lesser extent in female liver, led to up regulation of many genes linked to liver fibrosis and liver cancer, which may contribute to the observed liver pathologies and the increased sensitivity of these mice to hepatotoxin exposure. Thus, Ezh1/Ezh2-catalyzed H3K27-trimethyation regulates sex-dependent genetic programs in liver metabolism and liver fibrosis through its sex-dependent effects on the epigenome, and may thereby determine the sex-bias in liver disease susceptibility.
Klíčová slova:
Fatty liver – Gene expression – Gene regulation – Histones – Chromatin – Liver diseases – Liver fibrosis – Mouse models
Zdroje
1. Clocchiatti A, Cora E, Zhang Y, Dotto GP. Sexual dimorphism in cancer. Nat Rev Cancer. 2016;16(5):330–9. doi: 10.1038/nrc.2016.30 27079803.
2. El-Serag HB. Epidemiology of viral hepatitis and hepatocellular carcinoma. Gastroenterology. 2012;142(6):1264–73 e1. Epub 2012/04/28. doi: 10.1053/j.gastro.2011.12.061 22537432; PubMed Central PMCID: PMC3338949.
3. Hanna D, Riedmaier AE, Sugamori KS, Grant DM. Influence of sex and developmental stage on acute hepatotoxic and inflammatory responses to liver procarcinogens in the mouse. Toxicology. 2016;373:30–40. doi: 10.1016/j.tox.2016.10.006 27746196.
4. Pramfalk C, Pavlides M, Banerjee R, McNeil CA, Neubauer S, Karpe F, et al. Sex-Specific Differences in Hepatic Fat Oxidation and Synthesis May Explain the Higher Propensity for NAFLD in Men. J Clin Endocrinol Metab. 2015;100(12):4425–33. doi: 10.1210/jc.2015-2649 26414963; PubMed Central PMCID: PMC4667166.
5. Ballestri S, Nascimbeni F, Baldelli E, Marrazzo A, Romagnoli D, Lonardo A. NAFLD as a Sexual Dimorphic Disease: Role of Gender and Reproductive Status in the Development and Progression of Nonalcoholic Fatty Liver Disease and Inherent Cardiovascular Risk. Adv Ther. 2017;34(6):1291–326. doi: 10.1007/s12325-017-0556-1 28526997; PubMed Central PMCID: PMC5487879.
6. Marin V, Rosso N, Dal Ben M, Raseni A, Boschelle M, Degrassi C, et al. An Animal Model for the Juvenile Non-Alcoholic Fatty Liver Disease and Non-Alcoholic Steatohepatitis. PLoS One. 2016;11(7):e0158817. doi: 10.1371/journal.pone.0158817 27391242; PubMed Central PMCID: PMC4938400.
7. Marcos R, Correia-Gomes C, Miranda H, Carneiro F. Liver gender dimorphism—insights from quantitative morphology. Histol Histopathol. 2015;30(12):1431–7. doi: 10.14670/HH-11-648 26196413.
8. Buzzetti E, Parikh PM, Gerussi A, Tsochatzis E. Gender differences in liver disease and the drug-dose gender gap. Pharmacol Res. 2017;120:97–108. doi: 10.1016/j.phrs.2017.03.014 28336373.
9. Waxman DJ, Holloway MG. Sex differences in the expression of hepatic drug metabolizing enzymes. Mol Pharmacol. 2009;76(2):215–28. Epub 2009/06/02. doi: 10.1124/mol.109.056705 19483103; PubMed Central PMCID: PMC2713118.
10. Shapiro BH, Agrawal AK, Pampori NA. Gender differences in drug metabolism regulated by growth hormone. Int J Biochem Cell Biol. 1995;27(1):9–20. doi: 10.1016/1357-2725(94)00056-5 7757886.
11. Clodfelter KH, Holloway MG, Hodor P, Park SH, Ray WJ, Waxman DJ. Sex-dependent liver gene expression is extensive and largely dependent upon signal transducer and activator of transcription 5b (STAT5b): STAT5b-dependent activation of male genes and repression of female genes revealed by microarray analysis. Mol Endocrinol. 2006;20(6):1333–51. Epub 2006/02/14. doi: 10.1210/me.2005-0489 16469768.
12. Holloway MG, Cui Y, Laz EV, Hosui A, Hennighausen L, Waxman DJ. Loss of sexually dimorphic liver gene expression upon hepatocyte-specific deletion of Stat5a-Stat5b locus. Endocrinology. 2007;148(5):1977–86. doi: 10.1210/en.2006-1419 17317776; PubMed Central PMCID: PMC3282149.
13. Conforto TL, Zhang Y, Sherman J, Waxman DJ. Impact of CUX2 on the female mouse liver transcriptome: activation of female-biased genes and repression of male-biased genes. Mol Cell Biol. 2012;32(22):4611–27. Epub 2012/09/12. doi: 10.1128/MCB.00886-12 22966202; PubMed Central PMCID: PMC3486175.
14. Conforto TL, Steinhardt GFt, DJ. Cross Talk Between GH-Regulated Transcription Factors HNF6 and CUX2 in Adult Mouse Liver. Mol Endocrinol. 2015;29(9):1286–302. doi: 10.1210/me.2015-1028 26218442; PubMed Central PMCID: PMC4552435.
15. Melia T, Hao P, Yilmaz F, Waxman DJ. Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone. Mol Cell Biol. 2016;36(1):50–69. doi: 10.1128/MCB.00861-15 26459762; PubMed Central PMCID: PMC4702595.
16. Hao P, Waxman DJ. Functional Roles of Sex-Biased, Growth Hormone-Regulated MicroRNAs miR-1948 and miR-802 in Young Adult Mouse Liver. Endocrinology. 2018;159(3):1377–92. doi: 10.1210/en.2017-03109 29346554; PubMed Central PMCID: PMC5839735.
17. Sugathan A, Waxman DJ. Genome-wide analysis of chromatin states reveals distinct mechanisms of sex-dependent gene regulation in male and female mouse liver. Mol Cell Biol. 2013;33(18):3594–610. Epub 2013/07/10. doi: 10.1128/MCB.00280-13 23836885; PubMed Central PMCID: PMC3753870.
18. Zhang Y, Laz EV, Waxman DJ. Dynamic, sex-differential STAT5 and BCL6 binding to sex-biased, growth hormone-regulated genes in adult mouse liver. Mol Cell Biol. 2012;32(4):880–96. Epub 2011/12/14. doi: 10.1128/MCB.06312-11 22158971; PubMed Central PMCID: PMC3272977.
19. Lau-Corona D, Suvorov A, Waxman DJ. Feminization of Male Mouse Liver by Persistent Growth Hormone Stimulation: Activation of Sex-Biased Transcriptional Networks and Dynamic Changes in Chromatin States. Mol Cell Biol. 2017;37(19). doi: 10.1128/MCB.00301-17 28694329; PubMed Central PMCID: PMC5599723.
20. Holoch D, Margueron R. Mechanisms Regulating PRC2 Recruitment and Enzymatic Activity. Trends in biochemical sciences. 2017;42(7):531–42. Epub 2017/05/10. doi: 10.1016/j.tibs.2017.04.003 28483375.
21. Comet I, Riising EM, Leblanc B, Helin K. Maintaining cell identity: PRC2-mediated regulation of transcription and cancer. Nat Rev Cancer. 2016;16(12):803–10. Epub 2016/11/04. doi: 10.1038/nrc.2016.83 27658528.
22. Reddington JP, Perricone SM, Nestor CE, Reichmann J, Youngson NA, Suzuki M, et al. Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes. Genome Biol. 2013;14(3):R25. doi: 10.1186/gb-2013-14-3-r25 23531360; PubMed Central PMCID: PMC4053768.
23. Margueron R, Li G, Sarma K, Blais A, Zavadil J, Woodcock CL, et al. Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. Molecular cell. 2008;32(4):503–18. doi: 10.1016/j.molcel.2008.11.004 19026781; PubMed Central PMCID: PMC3641558.
24. Aranda S, Mas G, Di Croce L. Regulation of gene transcription by Polycomb proteins. Sci Adv. 2015;1(11):e1500737. doi: 10.1126/sciadv.1500737 26665172; PubMed Central PMCID: PMC4672759.
25. Koike H, Ouchi R, Ueno Y, Nakata S, Obana Y, Sekine K, et al. Polycomb group protein Ezh2 regulates hepatic progenitor cell proliferation and differentiation in murine embryonic liver. PLoS One. 2014;9(8):e104776. doi: 10.1371/journal.pone.0104776 25153170; PubMed Central PMCID: PMC4143191.
26. Lee YY, Mok MT, Kang W, Yang W, Tang W, Wu F, et al. Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis. Nucleic Acids Res. 2018;46(17):8832–47. doi: 10.1093/nar/gky589 29992318; PubMed Central PMCID: PMC6158508.
27. Gao SB, Zheng QF, Xu B, Pan CB, Li KL, Zhao Y, et al. EZH2 represses target genes through H3K27-dependent and H3K27-independent mechanisms in hepatocellular carcinoma. Mol Cancer Res. 2014;12(10):1388–97. doi: 10.1158/1541-7786.MCR-14-0034 24916103.
28. Au SL, Ng IO, Wong CM. Epigenetic dysregulation in hepatocellular carcinoma: focus on polycomb group proteins. Front Med. 2013;7(2):231–41. doi: 10.1007/s11684-013-0253-7 23620257.
29. He Y, Meng XM, Huang C, Wu BM, Zhang L, Lv XW, et al. Long noncoding RNAs: Novel insights into hepatocelluar carcinoma. Cancer Lett. 2014;344(1):20–7. doi: 10.1016/j.canlet.2013.10.021 24183851.
30. Yang F, Zhang L, Huo XS, Yuan JH, Xu D, Yuan SX, et al. Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans. Hepatology. 2011;54(5):1679–89. doi: 10.1002/hep.24563 21769904.
31. Kim KH, Roberts CW. Targeting EZH2 in cancer. Nat Med. 2016;22(2):128–34. doi: 10.1038/nm.4036 26845405; PubMed Central PMCID: PMC4918227.
32. Nakagawa M, Kitabayashi I. Oncogenic roles of enhancer of zeste homolog 1/2 in hematological malignancies. Cancer Sci. 2018;109(8):2342–8. doi: 10.1111/cas.13655 29845708; PubMed Central PMCID: PMC6113435.
33. Bae WK, Kang K, Yu JH, Yoo KH, Factor VM, Kaji K, et al. The methyltransferases enhancer of zeste homolog (EZH) 1 and EZH2 control hepatocyte homeostasis and regeneration. FASEB journal: official publication of the Federation of American Societies for Experimental Biology. 2015;29(5):1653–62. doi: 10.1096/fj.14-261537 25477280; PubMed Central PMCID: PMC4415007.
34. Sakurai T, Kudo M. Molecular Link between Liver Fibrosis and Hepatocellular Carcinoma. Liver Cancer. 2013;2(3–4):365–6. doi: 10.1159/000343851 24400223; PubMed Central PMCID: PMC3881314.
35. Cui Y, Hosui A, Sun R, Shen K, Gavrilova O, Chen W, et al. Loss of signal transducer and activator of transcription 5 leads to hepatosteatosis and impaired liver regeneration. Hepatology. 2007;46(2):504–13. doi: 10.1002/hep.21713 17640041.
36. Mueller KM, Kornfeld JW, Friedbichler K, Blaas L, Egger G, Esterbauer H, et al. Impairment of hepatic growth hormone and glucocorticoid receptor signaling causes steatosis and hepatocellular carcinoma in mice. Hepatology. 2011;54(4):1398–409. doi: 10.1002/hep.24509 21725989; PubMed Central PMCID: PMC3232450.
37. Baik M, Nam YS, Piao MY, Kang HJ, Park SJ, Lee JH. Liver-specific deletion of the signal transducer and activator of transcription 5 gene aggravates fatty liver in response to a high-fat diet in mice. J Nutr Biochem. 2016;29:56–63. doi: 10.1016/j.jnutbio.2015.10.018 26895665.
38. Cordoba-Chacon J, Majumdar N, List EO, Diaz-Ruiz A, Frank SJ, Manzano A, et al. Growth Hormone Inhibits Hepatic De Novo Lipogenesis in Adult Mice. Diabetes. 2015;64(9):3093–103. doi: 10.2337/db15-0370 26015548; PubMed Central PMCID: PMC4542445.
39. Behrens A, Sibilia M, David JP, Mohle-Steinlein U, Tronche F, Schutz G, et al. Impaired postnatal hepatocyte proliferation and liver regeneration in mice lacking c-jun in the liver. EMBO J. 2002;21(7):1782–90. doi: 10.1093/emboj/21.7.1782 11927562; PubMed Central PMCID: PMC125360.
40. Laz EV, Holloway MG, Chen CS, Waxman DJ. Characterization of three growth hormone-responsive transcription factors preferentially expressed in adult female liver. Endocrinology. 2007;148(7):3327–37. doi: 10.1210/en.2006-1192 17412818; PubMed Central PMCID: PMC2585771.
41. Wauthier V, Sugathan A, Meyer RD, Dombkowski AA, Waxman DJ. Intrinsic sex differences in the early growth hormone responsiveness of sex-specific genes in mouse liver. Mol Endocrinol. 2010;24(3):667–78. doi: 10.1210/me.2009-0454 20150183; PubMed Central PMCID: PMC2840812.
42. Holloway MG, Laz EV, Waxman DJ. Codependence of growth hormone-responsive, sexually dimorphic hepatic gene expression on signal transducer and activator of transcription 5b and hepatic nuclear factor 4alpha. Mol Endocrinol. 2006;20(3):647–60. doi: 10.1210/me.2005-0328 16239260.
43. Connerney J, Lau-Corona D, Rampersaud A, Waxman DJ. Activation of Male Liver Chromatin Accessibility and STAT5-Dependent Gene Transcription by Plasma Growth Hormone Pulses. Endocrinology. 2017;158(5):1386–405. doi: 10.1210/en.2017-00060 28323953; PubMed Central PMCID: PMC6283433.
44. Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature. 2011;470(7333):279–83. Epub 2010/12/17. doi: 10.1038/nature09692 21160473.
45. Margueron R, Reinberg D. The Polycomb complex PRC2 and its mark in life. Nature. 2011;469(7330):343–9. doi: 10.1038/nature09784 21248841; PubMed Central PMCID: PMC3760771.
46. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, et al. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol. 2010;28(5):495–501. doi: 10.1038/nbt.1630 20436461; PubMed Central PMCID: PMC4840234.
47. Buettner N, Thimme R. Sexual dimorphism in hepatitis B and C and hepatocellular carcinoma. Seminars in immunopathology. 2019;41(2):203–11. Epub 2018/12/01. doi: 10.1007/s00281-018-0727-4 30498927.
48. Grindheim JM, Nicetto D, Donahue G, Zaret KS. Polycomb Repressive Complex 2 Proteins EZH1 and EZH2 Regulate Timing of Postnatal Hepatocyte Maturation and Fibrosis by Repressing Genes With Euchromatic Promoters in Mice. Gastroenterology. 2019;156(6):1834–48. Epub 2019/01/29. doi: 10.1053/j.gastro.2019.01.041 30689973; PubMed Central PMCID: PMC6599454.
49. Hlady RA, Sathyanarayan A, Thompson JJ, Zhou D, Wu Q, Pham K, et al. Integrating the Epigenome to Identify Drivers of Hepatocellular Carcinoma. Hepatology. 2019;69(2):639–52. Epub 2018/08/24. doi: 10.1002/hep.30211 30136421; PubMed Central PMCID: PMC6351162.
50. Li H, Li J, Jia S, Wu M, An J, Zheng Q, et al. miR675 upregulates long noncoding RNA H19 through activating EGR1 in human liver cancer. Oncotarget. 2015;6(31):31958–84. doi: 10.18632/oncotarget.5579 26376677; PubMed Central PMCID: PMC4741653.
51. Ling G, Sugathan A, Mazor T, Fraenkel E, Waxman DJ. Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression. Mol Cell Biol. 2010;30(23):5531–44. Epub 2010/09/30. doi: 10.1128/MCB.00601-10 20876297; PubMed Central PMCID: PMC2976433.
52. Conforto TL, Waxman DJ. Sex-specific mouse liver gene expression: genome-wide analysis of developmental changes from pre-pubertal period to young adulthood. Biol Sex Differ. 2012;3:9. doi: 10.1186/2042-6410-3-9 22475005; PubMed Central PMCID: PMC3350426.
53. Humphries C. Sex differences: Luck of the chromosomes. Nature. 2014;516(7529):S10–1. doi: 10.1038/516S10a 25470193.
54. Meyer RD, Laz EV, Su T, Waxman DJ. Male-specific hepatic Bcl6: growth hormone-induced block of transcription elongation in females and binding to target genes inversely coordinated with STAT5. Mol Endocrinol. 2009;23(11):1914–26. doi: 10.1210/me.2009-0242 19797429; PubMed Central PMCID: PMC2775936.
55. Pasini D, Malatesta M, Jung HR, Walfridsson J, Willer A, Olsson L, et al. Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes. Nucleic Acids Res. 2010;38(15):4958–69. doi: 10.1093/nar/gkq244 20385584; PubMed Central PMCID: PMC2926606.
56. Melia T, Waxman DJ. Sex-Biased lncRNAs Inversely Correlate With Sex-Opposite Gene Coexpression Networks in Diversity Outbred Mouse Liver. Endocrinology. 2019;160(5):989–1007. Epub 2019/03/07. doi: 10.1210/en.2018-00949 30840070; PubMed Central PMCID: PMC6449536.
57. Das RK, Banerjee S, Shapiro BH. Growth hormone: a newly identified developmental organizer. J Endocrinol. 2017;232(3):377–89. doi: 10.1530/JOE-16-0471 27980003; PubMed Central PMCID: PMC5241097.
58. Reizel Y, Spiro A, Sabag O, Skversky Y, Hecht M, Keshet I, et al. Gender-specific postnatal demethylation and establishment of epigenetic memory. Genes Dev. 2015;29(9):923–33. doi: 10.1101/gad.259309.115 25934504; PubMed Central PMCID: PMC4421981.
59. O'Carroll D, Erhardt S, Pagani M, Barton SC, Surani MA, Jenuwein T. The polycomb-group gene Ezh2 is required for early mouse development. Mol Cell Biol. 2001;21(13):4330–6. Epub 2001/06/08. doi: 10.1128/MCB.21.13.4330-4336.2001 11390661; PubMed Central PMCID: PMC87093.
60. Xu Z, Liu L, Pan X, Wei K, Wei M, Liu L, et al. Serum Golgi protein 73 (GP73) is a diagnostic and prognostic marker of chronic HBV liver disease. Medicine. 2015;94(12):e659. Epub 2015/03/31. doi: 10.1097/MD.0000000000000659 25816035; PubMed Central PMCID: PMC4554005.
61. Wen Y, Jeong S, Xia Q, Kong X. Role of Osteopontin in Liver Diseases. International journal of biological sciences. 2016;12(9):1121–8. Epub 2016/08/30. doi: 10.7150/ijbs.16445 27570486; PubMed Central PMCID: PMC4997056.
62. Yokoyama Y, Nimura Y, Nagino M, Bland KI, Chaudry IH. Current understanding of gender dimorphism in hepatic pathophysiology. J Surg Res. 2005;128(1):147–56. Epub 2005/06/09. doi: 10.1016/j.jss.2005.04.017 15939435.
63. Mattu S, Fornari F, Quagliata L, Perra A, Angioni MM, Petrelli A, et al. The metabolic gene HAO2 is downregulated in hepatocellular carcinoma and predicts metastasis and poor survival. J Hepatol. 2016;64(4):891–8. doi: 10.1016/j.jhep.2015.11.029 26658681.
64. Herquel B, Ouararhni K, Khetchoumian K, Ignat M, Teletin M, Mark M, et al. Transcription cofactors TRIM24, TRIM28, and TRIM33 associate to form regulatory complexes that suppress murine hepatocellular carcinoma. Proc Natl Acad Sci U S A. 2011;108(20):8212–7. doi: 10.1073/pnas.1101544108 21531907; PubMed Central PMCID: PMC3100982.
65. Jiang S, Minter LC, Stratton SA, Yang P, Abbas HA, Akdemir ZC, et al. TRIM24 suppresses development of spontaneous hepatic lipid accumulation and hepatocellular carcinoma in mice. J Hepatol. 2015;62(2):371–9. doi: 10.1016/j.jhep.2014.09.026 25281858; PubMed Central PMCID: PMC4772153.
66. Sanna L, Marchesi I, Melone MAB, Bagella L. The role of enhancer of zeste homolog 2: From viral epigenetics to the carcinogenesis of hepatocellular carcinoma. J Cell Physiol. 2018. doi: 10.1002/jcp.26545 29574790.
67. Pope C, Piekos SC, Chen L, Mishra S, Zhong XB. The role of H19, a long non-coding RNA, in mouse liver postnatal maturation. PLoS One. 2017;12(11):e0187557. doi: 10.1371/journal.pone.0187557 29099871; PubMed Central PMCID: PMC5669494.
68. Young MD, Willson TA, Wakefield MJ, Trounson E, Hilton DJ, Blewitt ME, et al. ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity. Nucleic Acids Res. 2011;39(17):7415–27. doi: 10.1093/nar/gkr416 21652639; PubMed Central PMCID: PMC3177187.
69. Healy E, Mucha M, Glancy E, Fitzpatrick DJ, Conway E, Neikes HK, et al. PRC2.1 and PRC2.2 Synergize to Coordinate H3K27 Trimethylation. Molecular cell. 2019;76(3):437–52 e6. Epub 2019/09/16. doi: 10.1016/j.molcel.2019.08.012 31521505.
70. Weisend CM, Kundert JA, Suvorova ES, Prigge JR, Schmidt EE. Cre activity in fetal albCre mouse hepatocytes: Utility for developmental studies. Genesis. 2009;47(12):789–92. doi: 10.1002/dvg.20568 19830819; PubMed Central PMCID: PMC2828742.
71. Su IH, Basavaraj A, Krutchinsky AN, Hobert O, Ullrich A, Chait BT, et al. Ezh2 controls B cell development through histone H3 methylation and Igh rearrangement. Nat Immunol. 2003;4(2):124–31. doi: 10.1038/ni876 12496962.
72. Ezhkova E, Lien WH, Stokes N, Pasolli HA, Silva JM, Fuchs E. EZH1 and EZH2 cogovern histone H3K27 trimethylation and are essential for hair follicle homeostasis and wound repair. Genes Dev. 2011;25(5):485–98. doi: 10.1101/gad.2019811 21317239; PubMed Central PMCID: PMC3049289.
73. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7(3):562–78. Epub 2012/03/03. doi: 10.1038/nprot.2012.016 22383036; PubMed Central PMCID: PMC3334321.
74. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923–30. doi: 10.1093/bioinformatics/btt656 24227677.
75. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40. doi: 10.1093/bioinformatics/btp616 19910308; PubMed Central PMCID: PMC2796818.
76. Lodato NJ, Rampersaud A, Waxman DJ. Impact of CAR Agonist Ligand TCPOBOP on Mouse Liver Chromatin Accessibility. Toxicol Sci. 2018;164(1):115–28. doi: 10.1093/toxsci/kfy070 29617930; PubMed Central PMCID: PMC6016691.
77. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9. doi: 10.1038/nmeth.1923 22388286; PubMed Central PMCID: PMC3322381.
78. Xu S, Grullon S, Ge K, Peng W. Spatial clustering for identification of ChIP-enriched regions (SICER) to map regions of histone methylation patterns in embryonic stem cells. Methods Mol Biol. 2014;1150:97–111. doi: 10.1007/978-1-4939-0512-6_5 24743992; PubMed Central PMCID: PMC4152844.
79. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137 18798982; PubMed Central PMCID: PMC2592715.
80. Shen L, Shao NY, Liu X, Maze I, Feng J, Nestler EJ. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS One. 2013;8(6):e65598. doi: 10.1371/journal.pone.0065598 23762400; PubMed Central PMCID: PMC3677880.
81. Orlando DA, Chen MW, Brown VE, Solanki S, Choi YJ, Olson ER, et al. Quantitative ChIP-Seq normalization reveals global modulation of the epigenome. Cell Rep. 2014;9(3):1163–70. doi: 10.1016/j.celrep.2014.10.018 25437568.
Článek vyšel v časopise
PLOS Genetics
2020 Číslo 5
- S diagnostikou Parkinsonovy nemoci může nově pomoci AI nástroj pro hodnocení mrkacího reflexu
- Proč při poslechu některé muziky prostě musíme tančit?
- Chůze do schodů pomáhá prodloužit život a vyhnout se srdečním chorobám
- Metamizol jako analgetikum první volby: kdy, pro koho, jak a proč?
- „Jednohubky“ z klinického výzkumu – 2024/44
Nejčtenější v tomto čísle
- The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)
- Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus
- The phosphorelay BarA/SirA activates the non-cognate regulator RcsB in Salmonella enterica
- Congenital hearing impairment associated with peripheral cochlear nerve dysmyelination in glycosylation-deficient muscular dystrophy