Histone modification patterns and epigenetic codes

Biochimica et Biophysica Acta - General Subjects

Volumn 1790, Issue 9, 2009, Pages 863-868

  Lennartsson, Andreas ^a   Ekwall, Karl ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Cancer; Cell differentiation; Chromatin; Epigenetic; Histone code; Histone modification

Indexed keywords

BIOLOGICAL MARKER; DNA; HETEROCHROMATIN PROTEIN 1; HISTONE; HISTONE DEACETYLASE; HISTONE DEACETYLASE INHIBITOR; HISTONE H2A; HISTONE H2B; HISTONE H3; HISTONE H4; VALPROIC ACID;

ACETYLATION; AMINO TERMINAL SEQUENCE; ANTINEOPLASTIC ACTIVITY; BIOLOGICAL MODEL; BREAST CANCER; CANCER CELL; CELL DIFFERENTIATION; CELL MATURATION; CHROMATIN; COLORECTAL CANCER; DNA MICROARRAY; DNA SEQUENCE; EPIGENETICS; GENE CLUSTER; GENE EXPRESSION REGULATION; GENE MAPPING; GENE THERAPY; GENE TRANSFER; GENETIC CODE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HISTONE MODIFICATION; HUMAN; LIVER CARCINOGENESIS; LUNG NON SMALL CELL CANCER; NONHUMAN; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; PROGNOSIS; PROMOTER REGION; PROSTATE CANCER; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; REVIEW; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SPECIES COMPARISON; STOMACH ADENOCARCINOMA;

ANIMALS; CELL DIFFERENTIATION; EPIGENESIS, GENETIC; HISTONES; HUMANS; NEOPLASMS;

EUKARYOTA;

EID: 68349135058     PISSN: 03044165     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbagen.2008.12.006     Document Type: Review

References (64)

1. Grunstein M. Histones as regulators of genes. Sci. Am. 267 (1992) 68-74B
2. Strahl B.D., and Allis C.D. The language of covalent histone modifications. Nature 403 (2000) 41-45
3. Turner B.M. Histone acetylation and an epigenetic code. BioEssays 22 (2000) 836-845
4. Zhang L., Eugeni E.E., Parthun M.R., and Freitas M.A. Identification of novel histone post-translational modifications by peptide mass fingerprinting. Chromosoma 112 (2003) 77-86
5. Bird A. Perceptions of epigenetics. Nature 447 (2007) 396-398
6. Kouskouti A., and Talianidis I. Histone modifications defining active genes persist after transcriptional and mitotic inactivation. EMBO J. 24 (2005) 347-357
7. Valls E., Sanchez-Molina S., and Martinez-Balbas M.A. Role of histone modifications in marking and activating genes through mitosis. J. Biol. Chem. 280 (2005) 42592-42600
8. Xin L., Zhou G.L., Song W., Wu X.S., Wei G.H., Hao D.L., Lv X., Liu D.P., and Liang C.C. Exploring cellular memory molecules marking competent and active transcriptions. BMC Mol. Biol. 8 (2007) 31
9. Chen E.S., Zhang K., Nicolas E., Cam H.P., Zofall M., and Grewal S.I. Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 451 (2008) 734-737
10. Garcia B.A., Shabanowitz J., and Hunt D.F. Characterization of histones and their post-translational modifications by mass spectrometry. Curr. Opin. Chem. Biol. 11 (2007) 66-73
11. van Leeuwen F., and van Steensel B. Histone modifications: from genome-wide maps to functional insights. Genome Biol. 6 (2005) 113
12. Wang Z., Zang C., Rosenfeld J.A., Schones D.E., Barski A., Cuddapah S., Cui K., Roh T.Y., Peng W., Zhang M.Q., and Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40 (2008) 897-903
13. Kurdistani S.K., Tavazoie S., and Grunstein M. Mapping global histone acetylation patterns to gene expression. Cell 117 (2004) 721-733
14. Liu C.L., Kaplan T., Kim M., Buratowski S., Schreiber S.L., Friedman N., and Rando O.J. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol. 3 (2005) e328
15. Raisner R.M., Hartley P.D., Meneghini M.D., Bao M.Z., Liu C.L., Schreiber S.L., Rando O.J., and Madhani H.D. Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell 123 (2005) 233-248
16. Wyrick J.J., and Parra M.A. The role of histone H2A and H2B post-translational modifications in transcription: a genomic perspective. Biochim. Biophys. Acta 1789 (2009) 37-44
17. Lee J.H., Hart S.R., and Skalnik D.G. Histone deacetylase activity is required for embryonic stem cell differentiation. Genesis 38 (2004) 32-38
18. De Felice L., Tatarelli C., Mascolo M.G., Gregorj C., Agostini F., Fiorini R., Gelmetti V., Pascale S., Padula F., Petrucci M.T., Arcese W., and Nervi C. Histone deacetylase inhibitor valproic acid enhances the cytokine-induced expansion of human hematopoietic stem cells. Cancer Res. 65 (2005) 1505-1513
19. Snykers S., Vanhaecke T., De Becker A., Papeleu P., Vinken M., Van Riet I., and Rogiers V. Chromatin remodeling agent trichostatin A: a key-factor in the hepatic differentiation of human mesenchymal stem cells derived of adult bone marrow. BMC Dev. Biol. 7 (2007) 24
20. Munster P.N., Troso-Sandoval T., Rosen N., Rifkind R., Marks P.A., and Richon V.M. The histone deacetylase inhibitor suberoylanilide hydroxamic acid induces differentiation of human breast cancer cells. Cancer Res. 61 (2001) 8492-8497
21. Minucci S., Nervi C., Lo Coco F., and Pelicci P.G. Histone deacetylases: a common molecular target for differentiation treatment of acute myeloid leukemias. Oncogene 20 (2001) 3110-3115
22. Levenson J.M., and Sweatt J.D. Epigenetic mechanisms: a common theme in vertebrate and invertebrate memory formation. Cell Mol. Life Sci. 63 (2006) 1009-1016
23. Meshorer E., Yellajoshula D., George E., Scambler P.J., Brown D.T., and Misteli T. Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev. Cell 10 (2006) 105-116
24. Lee T.I., Jenner R.G., Boyer L.A., Guenther M.G., Levine S.S., Kumar R.M., Chevalier B., Johnstone S.E., Cole M.F., Isono K., Koseki H., Fuchikami T., Abe K., Murray H.L., Zucker J.P., Yuan B., Bell G.W., Herbolsheimer E., Hannett N.M., Sun K., Odom D.T., Otte A.P., Volkert T.L., Bartel D.P., Melton D.A., Gifford D.K., Jaenisch R., and Young R.A. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125 (2006) 301-313
25. Bracken A.P., Dietrich N., Pasini D., Hansen K.H., and Helin K. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 20 (2006) 1123-1136
26. Boyer L.A., Plath K., Zeitlinger J., Brambrink T., Medeiros L.A., Lee T.I., Levine S.S., Wernig M., Tajonar A., Ray M.K., Bell G.W., Otte A.P., Vidal M., Gifford D.K., Young R.A., and Jaenisch R. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441 (2006) 349-353
27. Sanders S.L., Portoso M., Mata J., Bahler J., Allshire R.C., and Kouzarides T. Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage. Cell 119 (2004) 603-614
28. Biron V.L., McManus K.J., Hu N., Hendzel M.J., and Underhill D.A. Distinct dynamics and distribution of histone methyl-lysine derivatives in mouse development. Dev. Biol. 276 (2004) 337-351
29. Bernstein B.E., Mikkelsen T.S., Xie X., Kamal M., Huebert D.J., Cuff J., Fry B., Meissner A., Wernig M., Plath K., Jaenisch R., Wagschal A., Feil R., Schreiber S.L., and Lander E.S. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125 (2006) 315-326
30. Kimura H., Tada M., Nakatsuji N., and Tada T. Histone code modifications on pluripotential nuclei of reprogrammed somatic cells. Mol. Cell. Biol. 24 (2004) 5710-5720
31. McGarvey K.M., Fahrner J.A., Greene E., Martens J., Jenuwein T., and Baylin S.B. Silenced tumor suppressor genes reactivated by DNA demethylation do not return to a fully euchromatic chromatin state. Cancer Res. 66 (2006) 3541-3549
32. Fischle W., Tseng B.S., Dormann H.L., Ueberheide B.M., Garcia B.A., Shabanowitz J., Hunt D.F., Funabiki H., and Allis C.D. Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438 (2005) 1116-1122
33. Frederiks F., Tzouros M., Oudgenoeg G., van Welsem T., Fornerod M., Krijgsveld J., and van Leeuwen F. Nonprocessive methylation by Dot1 leads to functional redundancy of histone H3K79 methylation states. Nat. Struct. Mol. Biol. 15 (2008) 550-557
34. McGinty R.K., Kim J., Chatterjee C., Roeder R.G., and Muir T.W. Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation. Nature 453 (2008) 812-816
35. Turner B.M. Simplifying a complex code. Nat. Struct. Mol. Biol. 15 (2008) 542-544
36. Wiencke J.K., Zheng S., Morrison Z., and Yeh R.F. Differentially expressed genes are marked by histone 3 lysine 9 trimethylation in human cancer cells. Oncogene 27 (2008) 2412-2421
37. Vakoc C.R., Mandat S.A., Olenchock B.A., and Blobel G.A. Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin. Mol. Cell 19 (2005) 381-391
38. Peedicayil J. The role of epigenetics in mental disorders. Indian J. Med. Res. 126 (2007) 105-111
39. Waggoner D. Mechanisms of disease: epigenesis. Semin. Pediatr. Neurol. 14 (2007) 7-14
40. Ralph S.A., and Scherf A. The epigenetic control of antigenic variation in Plasmodium falciparum. Curr. Opin. Microbiol. 8 (2005) 434-440
41. Feinberg A.P., Ohlsson R., and Henikoff S. The epigenetic progenitor origin of human cancer. Nat. Rev. Genet. 7 (2006) 21-33
42. Ohm J.E., McGarvey K.M., Yu X., Cheng L., Schuebel K.E., Cope L., Mohammad H.P., Chen W., Daniel V.C., Yu W., Berman D.M., Jenuwein T., Pruitt K., Sharkis S.J., Watkins D.N., Herman J.G., and Baylin S.B. A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat. Genet. 39 (2007) 237-242
43. Fahrner J.A., Eguchi S., Herman J.G., and Baylin S.B. Dependence of histone modifications and gene expression on DNA hypermethylation in cancer. Cancer Res. 62 (2002) 7213-7218
44. Nguyen C.T., Weisenberger D.J., Velicescu M., Gonzales F.A., Lin J.C., Liang G., and Jones P.A. Histone H3-lysine 9 methylation is associated with aberrant gene silencing in cancer cells and is rapidly reversed by 5-aza-2′-deoxycytidine. Cancer Res. 62 (2002) 6456-6461
45. Kondo Y., Shen L., and Issa J.P. Critical role of histone methylation in tumor suppressor gene silencing in colorectal cancer. Mol. Cell. Biol. 23 (2003) 206-215
46. Park Y.S., Jin M.Y., Kim Y.J., Yook J.H., Kim B.S., and Jang S.J. The global histone modification pattern correlates with cancer recurrence and overall survival in gastric adenocarcinoma. Ann. Surg. Oncol. 15 (2008) 1968-1976
47. Seligson D.B., Horvath S., Shi T., Yu H., Tze S., Grunstein M., and Kurdistani S.K. Global histone modification patterns predict risk of prostate cancer recurrence. Nature 435 (2005) 1262-1266
48. Mohamed M.A., Greif P.A., Diamond J., Sharaf O., Maxwell P., Montironi R., Young R.A., and Hamilton P.W. Epigenetic events, remodelling enzymes and their relationship to chromatin organization in prostatic intraepithelial neoplasia and prostatic adenocarcinoma. BJU Int. 99 (2007) 908-915
49. Fraga M.F., Ballestar E., Villar-Garea A., Boix-Chornet M., Espada J., Schotta G., Bonaldi T., Haydon C., Ropero S., Petrie K., Iyer N.G., Perez-Rosado A., Calvo E., Lopez J.A., Cano A., Calasanz M.J., Colomer D., Piris M.A., Ahn N., Imhof A., Caldas C., Jenuwein T., and Esteller M. Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat. Genet. 37 (2005) 391-400
50. Shogren-Knaak M., Ishii H., Sun J.M., Pazin M.J., Davie J.R., and Peterson C.L. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311 (2006) 844-847
51. Wiren M., Silverstein R.A., Sinha I., Walfridsson J., Lee H.M., Laurenson P., Pillus L., Robyr D., Grunstein M., and Ekwall K. Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast. EMBO J. 24 (2005) 2906-2918
52. Bell O., Wirbelauer C., Hild M., Scharf A.N., Schwaiger M., MacAlpine D.M., Zilbermann F., van Leeuwen F., Bell S.P., Imhof A., Garza D., Peters A.H., and Schubeler D. Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila. EMBO J. 26 (2007) 4974-4984
53. Akhtar A., and Becker P.B. Activation of transcription through histone H4 acetylation by MOF, an acetyltransferase essential for dosage compensation in Drosophila. Mol. Cell 5 (2000) 367-375
54. Tryndyak V.P., Kovalchuk O., and Pogribny I.P. Loss of DNA methylation and histone H4 lysine 20 trimethylation in human breast cancer cells is associated with aberrant expression of DNA methyltransferase 1, Suv4-20h2 histone methyltransferase and methyl-binding proteins. Cancer Biol. Ther. 5 (2006) 65-70
55. Pogribny I.P., Ross S.A., Tryndyak V.P., Pogribna M., Poirier L.A., and Karpinets T.V. Histone H3 lysine 9 and H4 lysine 20 trimethylation and the expression of Suv4-20h2 and Suv-39h1 histone methyltransferases in hepatocarcinogenesis induced by methyl deficiency in rats. Carcinogenesis 27 (2006) 1180-1186
56. Gupta A., Guerin-Peyrou T.G., Sharma G.G., Park C., Agarwal M., Ganju R.K., Pandita S., Choi K., Sukumar S., Pandita R.K., Ludwig T., and Pandita T.K. The mammalian ortholog of Drosophila MOF that acetylates histone H4 lysine 16 is essential for embryogenesis and oncogenesis. Mol. Cell. Biol. 28 (2008) 397-409
57. Barlesi F., Giaccone G., Gallegos-Ruiz M.I., Loundou A., Span S.W., Lefesvre P., Kruyt F.A., and Rodriguez J.A. Global histone modifications predict prognosis of resected non small-cell lung cancer. J. Clin. Oncol. 25 (2007) 4358-4364
58. Kleer C.G., Cao Q., Varambally S., Shen R., Ota I., Tomlins S.A., Ghosh D., Sewalt R.G., Otte A.P., Hayes D.F., Sabel M.S., Livant D., Weiss S.J., Rubin M.A., and Chinnaiyan A.M. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 11606-11611
59. Yu J., Yu J., Rhodes D.R., Tomlins S.A., Cao X., Chen G., Mehra R., Wang X., Ghosh D., Shah R.B., Varambally S., Pienta K.J., and Chinnaiyan A.M. A polycomb repression signature in metastatic prostate cancer predicts cancer outcome. Cancer Res. 67 (2007) 10657-10663
60. Guenther M.G., Levine S.S., Boyer L.A., Jaenisch R., and Young R.A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130 (2007) 77-88
61. Schubeler D., MacAlpine D.M., Scalzo D., Wirbelauer C., Kooperberg C., van Leeuwen F., Gottschling D.E., O L.P., Neill, Turner B.M., Delrow J., Bell S.P., and Groudine M. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 18 (2004) 1263-1271
62. Ekwall K. Genome-wide analysis of HDAC function. Trends Genet. 21 (2005) 608-615
63. Marchion D., and Munster P. Development of histone deacetylase inhibitors for cancer treatment. Expert Rev. Anticancer Ther. 7 (2007) 583-598
64. Bug G., Schwarz K., Schoch C., Kampfmann M., Henschler R., Hoelzer D., Ottmann O.G., and Ruthardt M. Effect of histone deacetylase inhibitor valproic acid on progenitor cells of acute myeloid leukemia. Haematologica 92 (2007) 542-545