Decoding liver injury: A regulatory role for histone modifications

International Journal of Biochemistry and Cell Biology

Volumn 67, Issue , 2015, Pages 188-193

  Tian, Wenfang ^a   Xu, Yong ^a  

^a NANJING MEDICAL UNIVERSITY   (China)

Author keywords

Epigenetics; Histone acetylation; Histone methylation; Liver injury; Transcriptional regulation

Indexed keywords

ALCOHOL; DNA; HISTONE; HISTONE DEACETYLASE INHIBITOR; REACTIVE OXYGEN METABOLITE; TRANSCRIPTOME; TRICHOSTATIN A; UNTRANSLATED RNA; CHROMATIN;

ALCOHOL LIVER DISEASE; ARTICLE; DNA HISTONE INTERACTION; ENZYME ACTIVITY; EPIGENETICS; HISTONE ACETYLATION; HISTONE METHYLATION; HISTONE MODIFICATION; HUMAN; LIVER DISEASE; LIVER FIBROSIS; LIVER INJURY; LIVER REGENERATION; NONALCOHOLIC FATTY LIVER; NONHUMAN; ACETYLATION; ALCOHOL LIVER CIRRHOSIS; CHEMISTRY; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; FATTY LIVER; GENETIC EPIGENESIS; GENETIC TRANSCRIPTION; GENETICS; LIVER; METABOLISM; METHYLATION; PATHOLOGY; PROTEIN PROCESSING;

ACETYLATION; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; EPIGENESIS, GENETIC; FATTY LIVER; HISTONES; HUMANS; LIVER; LIVER CIRRHOSIS, ALCOHOLIC; LIVER REGENERATION; METHYLATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; RNA, UNTRANSLATED; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84940894834     PISSN: 13572725     EISSN: 18785875     Source Type: Journal    
DOI: 10.1016/j.biocel.2015.03.009     Document Type: Review

References (66)

1. W.K. Bae, K. Kang, J.H. Yu, K.H. Yoo, V.M. Factor, K. Kaji, and et al. The methyltransferases enhancer of zeste homolog (EZH) 1 and EZH2 control hepatocyte homeostasis and regeneration FASEB J Off Publ Fed Am Soc Exp Biol 2014
2. F. Bardag-Gorce, B.A. French, M. Joyce, M. Baires, R.O. Montgomery, J. Li, and et al. Histone acetyltransferase p300 modulates gene expression in an epigenetic manner at high blood alcohol levels Exp Mol Pathol 82 2007 197 202
3. M.T. Bedford Arginine methylation at a glance J Cell Sci 120 2007 4243 4246
4. D.A. Brenner, T. Waterboer, S.K. Choi, J.N. Lindquist, B. Stefanovic, E. Burchardt, and et al. New aspects of hepatic fibrosis J Hepatol 32 2000 32 38
5. J. Bricambert, J. Miranda, F. Benhamed, J. Girard, C. Postic, and R. Dentin Salt-inducible kinase 2 links transcriptional coactivator p300 phosphorylation to the prevention of ChREBP-dependent hepatic steatosis in mice J Clin Investig 120 2010 4316 4331
6. J.E. Brownell, J. Zhou, T. Ranalli, R. Kobayashi, D.G. Edmondson, S.Y. Roth, and et al. Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation Cell 84 1996 843 851
7. M. Bysani, O. Wallerman, S. Bornelov, K. Zatloukal, J. Komorowski, and C. Wadelius ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer BMC Med Genomics 6 2013 50
8. R. Cao, and Y. Zhang The functions of E(Z)/EZH2-mediated methylation of lysine 27 in histone H3 Curr Opin Genet Dev 14 2004 155 164
9. Y. Cao, Y. Xue, L. Xue, X. Jiang, X. Wang, Z. Zhang, and et al. Hepatic menin recruits SIRT1 to control liver steatosis through histone deacetylation J Hepatol 59 2013 1299 1306
10. D. Cassiman, and T. Roskams Beauty is in the eye of the beholder: emerging concepts and pitfalls in hepatic stellate cell research J Hepatol 37 2002 527 535
11. M. Choudhury, P.H. Park, D. Jackson, and S.D. Shukla Evidence for the role of oxidative stress in the acetylation of histone H3 by ethanol in rat hepatocytes Alcohol 44 2010 531 540
12. R. Dentin, F. Benhamed, I. Hainault, V. Fauveau, F. Foufelle, J.R. Dyck, and et al. Liver-specific inhibition of ChREBP improves hepatic steatosis and insulin resistance in ob/ob mice Diabetes 55 2006 2159 2170
13. F. Esfandiari, V. Medici, D.H. Wong, S. Jose, M. Dolatshahi, E. Quinlivan, and et al. Epigenetic regulation of hepatic endoplasmic reticulum stress pathways in the ethanol-fed cystathionine beta synthase-deficient mouse Hepatology 51 2010 932 941
14. M. Esteller Epigenetics in cancer N Engl J Med 358 2008 1148 1159
15. F. Fang, D. Chen, L. Yu, X. Dai, Y. Yang, W. Tian, and et al. Proinflammatory stimuli engage Brahma related gene 1 and Brahma in endothelial injury Circul Res 113 2013 986 996
16. A.P. Feinberg Phenotypic plasticity and the epigenetics of human disease Nature 447 2007 433 440
17. W. Fischle, F. Dequiedt, M.J. Hendzel, M.G. Guenther, M.A. Lazar, W. Voelter, and et al. Enzymatic activity associated with class II HDACs is dependent on a multiprotein complex containing HDAC3 and SMRT/N-CoR Mol Cell 9 2002 45 57
18. F. Fuks, P.J. Hurd, R. Deplus, and T. Kouzarides The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase Nucleic Acids Res 31 2003 2305 2312
19. B. Gao, and R. Bataller Alcoholic liver disease: pathogenesis and new therapeutic targets Gastroenterology 141 2011 1572 1585
20. A. Ghezzi, H.R. Krishnan, L. Lew, F.J. Prado 3rd, D.S. Ong, and N.S. Atkinson Alcohol-induced histone acetylation reveals a gene network involved in alcohol tolerance PLoS Genet 9 2013 e1003986
21. A.K. Ghosh, S. Bhattacharyya, G. Lakos, S.J. Chen, Y. Mori, and J. Varga Disruption of transforming growth factor beta signaling and profibrotic responses in normal skin fibroblasts by peroxisome proliferator-activated receptor gamma Arthritis Rheumat 50 2004 1305 1318
22. Z.D. Goodman Grading and staging systems for inflammation and fibrosis in chronic liver diseases J Hepatol 47 2007 598 607
23. T. Gustot, A. Lemmers, C. Moreno, N. Nagy, E. Quertinmont, C. Nicaise, and et al. Differential liver sensitization to toll-like receptor pathways in mice with alcoholic fatty liver Hepatology 43 2006 989 1000
24. S. Imai From heterochromatin islands to the NAD World: a hierarchical view of aging through the functions of mammalian Sirt1 and systemic NAD biosynthesis Biochim Biophys Acta 1790 2009 997 1004
25. T.T. James, A.R. Aroor, R.W. Lim, and S.D. Shukla Histone H3 phosphorylation (Ser10, Ser28) and phosphoacetylation (K9S10) are differentially associated with gene expression in liver of rats treated in vivo with acute ethanol J Pharmacol Exp Therap 340 2012 237 247
26. J. Jin, P. Iakova, Y. Jiang, E.E. Medrano, and N.A. Timchenko The reduction of SIRT1 in livers of old mice leads to impaired body homeostasis and to inhibition of liver proliferation Hepatology 54 2011 989 998
27. N. Kaplowitz Liver biology and pathobiology Hepatology 43 2006 S235 S238
28. S.F. Kendrick, G. O'Boyle, J. Mann, M. Zeybel, J. Palmer, D.E. Jones, and et al. Acetate, the key modulator of inflammatory responses in acute alcoholic hepatitis Hepatology 51 2010 1988 1997
29. I. Kirpich, S. Ghare, J. Zhang, L. Gobejishvili, G. Kharebava, S.J. Barve, and et al. Binge alcohol-induced microvesicular liver steatosis and injury are associated with down-regulation of hepatic Hdac 1, 7, 9, 10, 11 and up-regulation of Hdac 3 Alcohol Clin Exp Res 36 2012 1578 1586
30. I. Kirpich, J. Zhang, L. Gobejishvili, G. Kharebava, D. Barker, S. Ghare, and et al. Binge ethanol-induced HDAC3 down-regulates Cpt1alpha expression leading to hepatic steatosis and injury Alcohol Clin Exp Res 37 2013 1920 1929
31. T. Kisseleva, and D.A. Brenner The phenotypic fate and functional role for bone marrow-derived stem cells in liver fibrosis J Hepatol 56 2012 965 972
32. A. Koteish, S. Yang, H. Lin, X. Huang, and A.M. Diehl Chronic ethanol exposure potentiates lipopolysaccharide liver injury despite inhibiting Jun N-terminal kinase and caspase 3 activation J Biol Chem 277 2002 13037 13044
33. M. Lachner, R.J. O'Sullivan, and T. Jenuwein An epigenetic road map for histone lysine methylation J Cell Sci 116 2003 2117 2124
34. J. Lee, S. Seok, P. Yu, K. Kim, Z. Smith, M. Rivas-Astroza, and et al. Genomic analysis of hepatic farnesoid X receptor binding sites reveals altered binding in obesity and direct gene repression by farnesoid X receptor in mice Hepatology 56 2012 108 117
35. C. Liu, X. Chen, L. Yang, T. Kisseleva, D.A. Brenner, and E. Seki Transcriptional repression of the transforming growth factor beta (TGF-beta) Pseudoreceptor BMP and activin membrane-bound inhibitor (BAMBI) by Nuclear Factor kappaB (NF-kappaB) p50 enhances TGF-beta signaling in hepatic stellate cells J Biol Chem 289 2014 7082 7091
36. J. Mann, D.C. Chu, A. Maxwell, F. Oakley, N.L. Zhu, H. Tsukamoto, and et al. MeCP2 controls an epigenetic pathway that promotes myofibroblast transdifferentiation and fibrosis Gastroenterology 138 2010 705 714 14 e1-4
37. I. Mannaerts, N. Eysackers, O.O. Onyema, K. Van Beneden, S. Valente, A. Mai, and et al. Class II HDAC inhibition hampers hepatic stellate cell activation by induction of microRNA-29 PLoS One 8 2013 e55786
38. A. Masamune, K. Kikuta, M. Satoh, Y. Sakai, A. Satoh, and T. Shimosegawa Ligands of peroxisome proliferator-activated receptor-gamma block activation of pancreatic stellate cells J Biol Chem 277 2002 141 147
39. K.B. Morshead, D.N. Ciccone, S.D. Taverna, C.D. Allis, and M.A. Oettinger Antigen receptor loci poised for V(D)J rearrangement are broadly associated with BRG1 and flanked by peaks of histone H3 dimethylated at lysine 4 Proc Natl Acad Sci USA 100 2003 11577 11582
40. S.K. Murphy, H. Yang, C.A. Moylan, H. Pang, A. Dellinger, M.F. Abdelmalek, and et al. Relationship between methylome and transcriptome in patients with nonalcoholic fatty liver disease Gastroenterology 145 2013 1076 1087
41. J. Oliva, J. Dedes, J. Li, S.W. French, and F. Bardag-Gorce Epigenetics of proteasome inhibition in the liver of rats fed ethanol chronically World J Gastroenterol WJG 15 2009 705 712
42. A. Page, P.P. Paoli, S.J. Hill, R. Howarth, R. Wu, S.M. Kweon, and et al. Alcohol directly stimulates epigenetic modifications in hepatic stellate cells J Hepatol 62 2015 388 397
43. M. Pal-Bhadra, U. Bhadra, D.E. Jackson, L. Mamatha, P.H. Park, and S.D. Shukla Distinct methylation patterns in histone H3 at Lys-4 and Lys-9 correlate with up- & down-regulation of genes by ethanol in hepatocytes Life Sci 81 2007 979 987
44. R.R. Pannem, C. Dorn, C. Hellerbrand, and R. Massoumi Cylindromatosis gene CYLD regulates hepatocyte growth factor expression in hepatic stellate cells through interaction with histone deacetylase 7 Hepatology 60 2014 1066 1081
45. P.H. Park, R.W. Lim, and S.D. Shukla Involvement of histone acetyltransferase (HAT) in ethanol-induced acetylation of histone H3 in hepatocytes: potential mechanism for gene expression Am J Physiol Gastroint Liver Physiol 289 2005 G1124 G1136
46. M. Pinzani Hepatic stellate (ITO) cells: expanding roles for a liver-specific pericyte J Hepatol 22 1995 700 706
47. L. Qin, and Y.P. Han Epigenetic repression of matrix metalloproteinases in myofibroblastic hepatic stellate cells through histone deacetylases 4: implication in tissue fibrosis Am J Pathol 177 2010 1915 1928
48. J. Schneider, P. Bajwa, F.C. Johnson, S.R. Bhaumik, and A. Shilatifard Rtt109 is required for proper H3K56 acetylation: a chromatin mark associated with the elongating RNA polymerase II J Biol Chem 281 2006 37270 37274
49. Z. Sun, R.A. Miller, R.T. Patel, J. Chen, R. Dhir, H. Wang, and et al. Hepatic Hdac3 promotes gluconeogenesis by repressing lipid synthesis and sequestration Nature Med 18 2012 934 942
50. Z. Tang, W.Y. Chen, M. Shimada, U.T. Nguyen, J. Kim, X.J. Sun, and et al. SET1 and p300 act synergistically, through coupled histone modifications, in transcriptional activation by p53 Cell 154 2013 297 310
51. C. Thoma, C.P. Day, and M.I. Trenell Lifestyle interventions for the treatment of non-alcoholic fatty liver disease in adults: a systematic review J Hepatol 56 2012 255 266
52. W. Tian, C. Hao, Z. Fan, X. Weng, H. Qin, X. Wu, and et al. Myocardin related transcription factor A programs epigenetic activation of hepatic stellate cells J Hepatol 62 2015 165 174
53. W. Tian, H. Xu, F. Fang, Q. Chen, Y. Xu, and A. Shen Brahma-related gene 1 bridges epigenetic regulation of proinflammatory cytokine production to steatohepatitis in mice Hepatology 58 2013 576 588
54. C.L. Wilson, J. Mann, M. Walsh, M.J. Perrugoria, F. Oakley, M.C. Wright, and et al. Quiescent hepatic stellate cells functionally contribute to the hepatic innate immune response via TLR3 PLoS One 9 2014 e83391
55. J. Xia, Y. Zhou, H. Ji, Y. Wang, Q. Wu, J. Bao, and et al. Loss of histone deacetylases 1 and 2 in hepatocytes impairs murine liver regeneration through Ki67 depletion Hepatology 58 2013 2089 2098
56. H. Xu, X. Wu, H. Qin, W. Tian, J. Chen, L. Sun, and et al. Myocardin-related transcription factor a epigenetically regulates renal fibrosis in diabetic nephropathy J Am Soc Nephrol JASN 2014
57. Y. Xu, S.R. Farmer, and B.D. Smith Peroxisome proliferator-activated receptor gamma interacts with CIITA x RFX5 complex to repress type I collagen gene expression J Biol Chem 282 2007 26046 26056
58. M.D. Yang, Y.M. Chiang, R. Higashiyama, K. Asahina, D.A. Mann, J. Mann, and et al. Rosmarinic acid and baicalin epigenetically derepress peroxisomal proliferator-activated receptor gamma in hepatic stellate cells for their antifibrotic effect Hepatology 55 2012 1271 1281
59. X.J. Yang The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases Nucleic Acids Res 32 2004 959 976
60. X.J. Yang, and E. Seto The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men Nat Rev Mol Cell Biol 9 2008 206 218
61. Y. Yang, X. Cheng, W. Tian, B. Zhou, X. Wu, H. Xu, and et al. MRTF-A steers an epigenetic complex to activate endothelin-induced pro-inflammatory transcription in vascular smooth muscle cells Nucleic Acids Res 42 2014 10460 10472
62. S. Yavrom, L. Chen, S. Xiong, J. Wang, R.A. Rippe, and H. Tsukamoto Peroxisome proliferator-activated receptor gamma suppresses proximal alpha1(I) collagen promoter via inhibition of p300-facilitated NF-I binding to DNA in hepatic stellate cells J Biol Chem 280 2005 40650 40659
63. L. Yu, X. Weng, P. Liang, X. Dai, X. Wu, H. Xu, and et al. MRTF-A mediates LPS-induced pro-inflammatory transcription by interacting with the COMPASS complex J Cell Sci 127 2014 4645 4657
64. M. Zeybel, T. Hardy, Y.K. Wong, J.C. Mathers, C.R. Fox, A. Gackowska, and et al. Multigenerational epigenetic adaptation of the hepatic wound-healing response Nat Med 18 2012 1369 1377
65. T. Zhang, and W.L. Kraus SIRT1-dependent regulation of chromatin and transcription: linking NAD(+) metabolism and signaling to the control of cellular functions Biochim Biophys Acta 1804 2010 1666 1675
66. N.L. Zhu, J. Wang, and H. Tsukamoto The Necdin-Wnt pathway causes epigenetic peroxisome proliferator-activated receptor gamma repression in hepatic stellate cells J Biol Chem 285 2010 30463 30471