Innovation in gene regulation: The case of chromatin computation

Journal of Theoretical Biology

Volumn 265, Issue 1, 2010, Pages 27-44

  Prohaska, Sonja J ^a,b   Stadler, Peter F ^a,b,c,d,e   Krakauer, David C ^b  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b SANTA FE INSTITUTE   (United States)

^c MAX PLANCK INSTITUTE FOR MATHEMATICS IN THE SCIENCES   (Germany)

^d FRAUNHOFER INSTITUTE FOR CELL THERAPY AND IMMUNOLOGY   (Germany)

^e UNIVERSITY OF VIENNA   (Austria)

Author keywords

Chromatin; Evolution; Gene regulation

Indexed keywords

BASIC PROTEIN; CHROMOSOMAL ARCHITECTURAL PROTEIN; CHROMOSOME PROTEIN; DNA; UNCLASSIFIED DRUG;

BIOCHEMISTRY; CHROMOSOME; EUKARYOTE; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; PROTEIN;

ACETYLATION; ARTICLE; CHROMATIN; CHROMATIN STRUCTURE; CHROMOSOME VARIANT; DEACETYLATION; DEMETHYLATION; EPIGENETICS; EUKARYOTIC CELL; EVOLUTION; GENE CONTROL; GENE FUNCTION; GENE LOCUS; GENOME; HYPOTHESIS; INHERITANCE; MEMORY; METHYLATION; MOLECULAR DYNAMICS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DEPHOSPHORYLATION; PROTEIN DOMAIN; PROTEIN PHOSPHORYLATION; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; UBIQUITINATION;

EUKARYOTA;

EID: 77953621315     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.03.011     Document Type: Article

References (194)

1. Adams-Cioaba M.A., Min J. Structure and function of histone methylation binding proteins. Biochem. Cell Biol. 2009, 87:93-105.
2. Ahmad K., Henikoff S. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell 2002, 9:1191-1200.
3. Amaral P.P., Mattick J.S. Noncoding RNA in development. Mamm. Genome 2008, 19:454-492.
4. Andreeva A., Howorth D., Chandonia J.-M., Brenner S.E., Hubbard T.J.P., Chothia C., Murzin A.G. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 2008, 36:D419-D425.
5. Arenas A.F., Gutierrez Escobar A.J., Gómez-Marin J.E. Evolutionary origin of the protozoan parasites histone-like proteins (HU). In Silico Biol. 2007, 8:2.
6. Armstrong J.A. Negotiating the nucleosome: factors that allow RNA polymerase II to elongate through chromatin. Biochem. Cell Biol. 2007, 85:426-434.
7. Azam T.A., Ishihama A. Twelve species of the nucleoid-associated protein from Escherichia coli sequence recognition specificity and DNA binding affinity. J. Biol. Chem. 1999, 274:33105-33113.
8. Bühler M., Verdel A., Moazed D. Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell 2006, 125:873-886.
9. Bailey K.A., Pereira S.L., Widom J., Reeve J.N. Archaeal histone selection of nucleosome positioning sequences and the procaryotic origin of histone-dependent genome evolution. J. Mol. Biol. 2000, 303:25-34.
10. Bailey K.A., Marc F., Sandman K., Reeve J.N. Both DNA and histone fold sequences contribute to archaeal nucleosome stability. J. Biol. Chem. 2002, 277:9293-9301.
11. Bailey-Serres J., Sorenson R., Juntawong P. Getting the message across: cytoplasmic ribonucleoprotein complexes. Trends Plant Sci. 2009, 14:443-453.
12. Barrett A.J., Rawlings N.D. Evolutionary lines of cysteine peptidases. Biol. Chem. 2001, 382:727-733.
13. Basu A., Rose K.L., Zhang J., Beavis R.C., Ueberheide B., Garcia B.A., Chait B., Zhao Y., Hunt D.F., Segal E., Allis C.D., Hake S.B. Proteome-wide prediction of acetylation substrates. Proc. Natl. Acad. Sci. USA 2009, 106:13785-13790.
14. Becerra A., Delaye L., Islas S., Lazcano A. The very early stages of biological evolution and the nature of the Last Common Ancestor of the three major cell domains. Annu. Rev. Ecol. Evol. Syst. 2007, 38:361-379.
15. Beck H.C., Nielsen E.C., Matthiesen R., Jensen L.H., Sehested M., Finn P., Grauslund M., Hansen A.M., Jensen O.N. Quantitative proteomic analysis of post-translational modifications of human histones. Mol. Cell. Proteomics 2006, 5:1314-1325.
16. Bedford M.T., Clarke S.G. Protein arginine methylation in mammals: Who, what, and why. Mol. Cell 2009, 33:1-13.
17. Bedford M.T., Richard S. Arginine methylation an emerging regulator of protein function. Mol. Cell 2005, 18:263-272.
18. Bell S.D., Botting C.H., Wardleworth B.N., Jackson S.P., White M.F. The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science 2002, 296:148-151.
19. Benecke A. Chromatin code local non-equilibrium dynamics, and the emergence of transcription regulatory programs. Eur. Phys. J. E Soft Matter 2006, 19:353-366.
20. Benson L.J., Gu Y., Yakovleva T., Tong K., Barrows C., Strack C.L., Cook R.G., Mizzen C.A., Annunziato A.T. Modifications of H3 and H4 during chromatin replication nucleosome assembly and histone exchange. J. Biol. Chem. 2006, 281:9287-9396.
21. Besant P.G., Attwood P.V. Detection of a mammalian histone H4 kinase that has yeast histidine kinase-like enzymic activity. Int. J. Biochem. Cell Biol. 2000, 32:243-253.
22. Besant P.G., Attwood P.V. Detection and analysis of protein histidine phosphorylation. Mol. Cell. Biochem. 2009, 329:93-106.
23. Bhaumik S.R., Smith E., Shilatifard A. Covalent modifications of histones during development and disease pathogenesis. Nat. Struct. Mol. Biol. 2007, 14:1008-1016.
24. Bonn S., Furlong E.E. cis-regulatory networks during development: a view of Drosophila. Curr. Opin. Genet. Dev. 2008, 18:513-520.
25. Boussau B., Blanquart S., Neculea A., Lartillot N., Gouy M. Parallel adaptations to high temperatures in the Archaean Eon. Nature 2008, 456:942-946.
26. Brown D.T. Histone variants: Are they functionally heterogeneous?. Genome Biol. 2001, 2.
27. Brown R.S. Zinc finger proteins: getting a grip on RNA. Curr. Opin. Struct. Biol. 2005, 15:94-98.
28. Broyles S.S., Pettijohn D.E. Interaction of the Escherichia coli HU protein with DNA. Evidence for formation of nucleosome-like structures with altered DNA helical pitch. J. Mol. Biol. 1986, 187:47-60.
29. Buck S.W., Gallo C.M., Smith J.S. Diversity in the Sir2 family of protein deacetylases. J. Leukoc. Biol. 2004, 75:939-950.
30. Chan S.W. Inputs and outputs for chromatin-targeted RNAi. Trends Plant Sci. 2008, 13:383-389.
31. Cheng X., Collins R.E., Zhang X. Structural and sequence motifs of protein (histone) methylation enzymes. Annu. Rev. Biophys. Biomol. Struct. 2005, 34:267-294.
32. Chomsky N. On certain formal properties of grammars. Inf. Control 1959, 2:137-167.
33. Cirillo L.A., Lin F.R., Cuesta I., Friedman D., Jarnik M., Zaret K.S. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol. Cell 2002, 9:279-289.
34. Claret L., Rouviere-Yaniv J. Variation in HU composition during growth of Escherichia coli: the heterodimer is required for long term survival. J. Mol. Biol. 1997, 273:93-104.
35. Cozzone A.J. Bacterial tyrosine kinases: novel targets for antibacterial therapy?. Trends Microbiol. 2009, 17:536-543.
36. Cubonová L., Sandman K., Hallam S.J., Delong E.F., Reeve J.N. Histones in crenarchaea. J. Bacteriol. 2005, 187:5482-5485.
37. Cuthbert G., Daujat S., Snowden A.W., Erdjument-Bromage H., Hagiwara T., Yamada M., Schneider R., Gregory P.D., Tempst P., Bannister A.J., Kouzarides T. Histone deimination antagonizes arginine methylation. Cell 2004, 118:545-553.
38. Dai J., Higgins J.M.G. Haspin: a mitotic histone kinase required for metaphase chromosome alignment. Cell Cycle 2005, 4:665-668.
39. Dame R.T., Noom M., Wuite G.J.L. Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature 2006, 444:387-390.
40. de la Cruz X., Lois S., Sánchez-Molina S., Martínez-Balbás M.A. Do protein motifs read the histone code?. Bioessays 2005, 27:164-175.
41. Di Giulio M. The origin of genes could be polyphyletic. Gene 2008, 426:39-46.
42. Dillon S.C., Zhang X., Trievel R.C., Cheng X. The SET-domain protein superfamily: protein lysine methyltransferases. Genome Biol. 2005, 6:227.
43. Dion M.F., Altschuler S.J., Wu L.F., Rando O.J. Genomic characterization reveals a simple histone H4 acetylation code. Proc. Natl. Acad. Sci. USA 2005, 102:5501-5506.
44. Dri A.M., Rouviere-Yaniv J., Moreau P.L. Inhibition of cell division in hupA/hupB mutant bacteria lacking HU protein. J. Bacteriol. 1991, 173:2852-2863.
45. Eichler J., Adams M.W. Posttranslational protein modification in Archaea. Microbiol. Mol. Biol. Rev. 2005, 69:393-425.
46. Eigen M. Selforganization of matter and the evolution of macromolecules. Naturwiss. 1971, 58:465-523.
47. Eigen M., McCaskill J., Schuster P. The molecular quasispecies. Adv. Chem. Phys. 1989, 75:149-263.
48. Eissenberg J.C. Molecular biology of the chromo domain: an ancient chromatin module comes of age. Gene 2001, 275:19-29.
49. Escargueil A.E., Soares D.G., Salvador M., Larsen A.K., Henriques J.A. What histone code for DNA repair?. Mutat. Res. 2008, 658:259-270.
50. Esteller M., Herman J.G. Cancer as an epigenetic disease: DNA methylation and chromatin alterations in human tumours. J. Pathol. 2002, 196:1-7.
51. Ferl R.J., Manak M.S., Reyes M.F. The 14-3-3s. Genome Biol. 2002, 3:7.
52. Fischle W., Wang Y., Allis C.D. Binary switches and modification cassettes in histone biology and beyond. Nature 2003, 425:475-479.
53. Forneris F., Binda C., Vanoni M.A., Battaglioli E., Mattevi A. Human histone demethylase LSD1 reads the histone code. J. Biol. Chem. 2005, 280:41360-41365.
54. Forterre P. The origin of DNA genomes and DNA replication proteins. Curr. Opin. Microbiol. 2002, 5:525-532.
55. Forterre P. Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain. Proc. Natl. Acad. Sci. USA 2006, 103:3669-3674.
56. Freitag M., Selker E.U. Controlling DNA methylation: many roads to one modification. Curr. Opin. Genet. Dev. 2005, 15:191-199.
57. Freitas M.A., Sklenar A.R., Parthun M.R. Application of mass spectrometry to the identification and quantification of histone post-translational modifications. J. Cell. Biochem. 2004, 92:691-700.
58. Frenkiel-Krispin I., Ben-Avraham D., Englander J., Shimoni E., Wolf S.G., Minsky A. Nucleoid restructuring in stationary-state bacteria. Mol. Microbiol. 2004, 51:395-405.
59. Frye R.A. Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem. Biophys. Res. Commun. 2000, 273:793-798.
60. Garcia B.A., Hake S.B., Diaz R.L., Kauer M., Morris S.A., Recht J., Shabanowitz J., Mishra N., Strahl B.D., Allis C.D., Hunt D.F. Organismal differences in post-translational modifications in histones H3 and H4. J. Biol. Chem. 2007, 282:7641-7655.
61. Glansdorff N., Xu Y., Labedan B. The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol. Direct 2008, 3:29.
62. Grayling R.A., Sandman K., Reeve J.N. Histones and chromatin structure in hyperthermophilic Archaea. FEMS Microbiol. Rev. 1996, 18:203-213.
63. Gregoretti I.V., Lee Y.M., Goodson H.V. Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis. J. Mol. Biol. 2004, 338:17-31.
64. Grieshaber N.A., Fischer E.R., Mead D.J., Dooley C.A., Hackstadt T. Chlamydial histone-DNA interactions are disrupted by a metabolite in the methylerythritol phosphate pathway of isoprenoid biosynthesis. Proc. Natl. Acad. Sci. USA 2004, 101:7451-7456.
65. Guo L., Feng Y., Zhang Z., Yao H., Luo Y., Wang J., Huang L. Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea. Nucleic Acids Res. 2008, 36:1129-1137.
66. Hake S.B., Allis C.D. Histone H3 variants and their potential role in indexing mammalian genomes: the "H3 barcode hypothesis". Proc. Natl. Acad. Sci. USA 2006, 103:6428-6435.
67. Hall I.M., Shankaranarayana G.D., Noma K., Ayoub N., Cohen A., Grewal S.I. Establishment and maintenance of a heterochromatin domain. Science 2002, 297:2232-2237.
68. Hall T.M. Multiple modes of RNA recognition by zinc finger proteins. Curr. Opin. Struct. Biol. 2005, 15:367-373.
69. Hammet A., Magill C., Heierhorst J., Jackson S.P. Rad9 BRCT domain interaction with phosphorylated H2AX regulates the G1 checkpoint in budding yeast. EMBO Rep. 2007, 8:851-857.
70. Healy S., Heightman T.D., Hohmann L., Schriemer D., Gravel R.A. Nonenzymatic biotinylation of histone H2A. Protein Sci. 2009, 18:314-328.
71. Hekimoglu B., Ringrose L. Non-coding RNAs in polycomb/trithorax regulation. RNA Biol. 2009, 6:129-137.
72. Henikoff S. Histone modifications: combinatorial complexity or cumulative simplicity?. Proc. Natl. Acad. Sci. USA 2005, 102:5308-5309.
73. Henikoff S. Nucleosome destabilization in the epigenetic regulation of gene expression. Nat. Rev. Genet. 2008, 9:15-26.
74. Hochstrasser M. Evolution and function of ubiquitin-like protein-conjugation systems. Nat. Cell Biol. 2000, 2:E153-E157.
75. Hochstrasser M. Origin and function of ubiquitin-like proteins. Nature 2009, 458:422-429.
76. Istrail S., De-Leon S.B., Davidson E.H. The regulatory genome and the computer. Dev. Biol. 2007, 310:187-195.
77. Iyer L.M., Anantharaman V., Wolf M.Y., Aravind L. Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes. Int. J. Parasitol. 2008, 38:1-31.
78. Izawa S., Inoue Y. Post-transcriptional regulation of gene expression in yeast under ethanol stress. Biotechnol. Appl. Biochem. 2009, 53:93-99.
79. Izban M.G., Luse D.S. Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates. J. Biol. Chem. 1992, 267:13647-13655.
80. Jelinska C., Conroy M.J., Craven C.J., Hounslow A.M., Bullough P.A., Waltho J.P., Taylor G.L., White M.F. Obligate heterodimerization of the archaeal Alba2 protein with Alba1 provides a mechanism for control of DNA packaging. Structure 2005, 13:963-971.
81. Jiang C., Pugh B.F. Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 2009, 10:161-172.
82. Jin J., Cai Y., Li B., Conaway R.C., Workman J.L., Conaway J.W., Kusch T. In and out: histone variant exchange in chromatin. Trends Biochem. Sci. 2005, 30:680-687.
83. Kamakaka R.T., Biggins S. Histone variants: Deviants?. Genes Dev. 2005, 19:295-310.
84. Kasinsky H.E., Lewis J.D., Dacks J.B., Ausió J. Origin of H1 linker histones. FASEB J. 2001, 15:34-42.
85. Kennely P.J. Protein kinases and protein phosphatases in prokaryotes: a genomic perspective. FEMS Microbiol. Lett. 2002, 206:1-8.
86. Kennely P.J. Archaeal protein kinases and protein phosphatases: insights from genomics and biochemistry. Biochem. J. 2003, 370:373-389.
87. Khalil A.M., Guttman M., Huarte M., Garber M., Raj A.M., Rivea Morales D., Thomas K., Presser A., Bernstein B.E., van Oudenaarden A., Regev A., Lander E.S., Rinn J.L. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 2009, 106:11675-11680.
88. Klenov M.S., Lavrov S.A., Stolyarenko A.D., Ryazansky S.S., Aravin A.A., Tuschl T., Gvozdev V.A. Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline. Nucleic Acids Res. 2007, 35:5430-5438.
89. Koonin E.V., Martin W. On the origin of genomes and cells within inorganic compartments. Trends Genet. 2005, 21:647-654.
90. Kothapalli N., Camporeale G., Kueh A., Chew Y.C., Oommen A.M., Griffin J.B., Zempleni J. Biological functions of biotinylated histones. J. Nutr. Biochem. 2005, 16:446-448.
91. Koutroubas G., Merika M., Thanos D. Bypassing the requirements for epigenetic modifications in gene transcription by increasing enhancer strength. Mol. Cell. Biol. 2008, 28:926-938.
92. Kuang F.L., Luo Z., Scharff M.D. H3 trimethyl K9 and H3 acetyl K9 chromatin modifications are associated with class switch recombination. Proc. Natl. Acad. Sci. USA 2009, 106:5288-5293.
93. Kurth H.M., Mochizuki K. Non-coding RNA: a bridge between small RNA and DNA. RNA Biol. 2009, 6:138-140.
94. Leeb M., Steffen P.A., Wutz A. X chromosome inactivation sparked by non-coding RNA. RNA Biol. 2009, 6:94-99.
95. Lesne A. The chromatin regulatory code: beyond a histone code. Eur. Phys. J. E Soft Matter 2006, 19:375-377.
96. Levine M., Davidson E.H. Gene regulatory networks for development. Proc. Natl. Acad. Sci. USA 2005, 102:4936-4942.
97. Li B., Carey M., Workman J.L. The role of chromatin during transcription. Cell 2007, 128:707-719.
98. Liu Y., Taverna S.D., Muratore T.L., Shabanowitz J., Hunt D.F., Allis C.D. RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena. Genes Dev. 2007, 21:1530-1545.
99. Lomvardas S., Thanos D. Opening chromatin. Mol. Cell 2002, 9:209-211.
100. Long K.S., Poehlsgaard J., Kehrenberg C., Schwarz S., Vester B. The Cfr rRNA methyltransferase confers resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A antibiotics. Antimicrob. Agents Chemother. 2006, 50:2500-2505.
101. Lowary P.T., Widom J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 1998, 276:19-42.
102. Lozada-Chávez I., Chandra Janga S., Collado-Vides J. Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res. 2006, 34:3434-3445.
103. Lucchini S., Rowley G., Goldberg M.D., Hurd D., Harrison M., Hinton J.C.D. H-NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathogens 2006, 2:e81.
104. Luijsterburg M.S., White M.F., van Driel R., Dame R.T. The major architects of chromatin: architectural proteins in bacteria archaea and eukaryotes. Crit. Rev. Biochem. Mol. Biol. 2008, 43:393-418.
105. Malik H.S., Henikoff S. Phylogenomics of the nucleosome. Nat. Struct. Biol. 2003, 10:882-891.
106. Marc F., Sandman K., Lurz R., Reeve J.N. Archaeal histone tetramerization determines DNA affinity and the direction of DNA supercoiling. J. Biol. Chem. 2002, 277:30879-30886.
107. Marsh V.L., Peak-Chew S.Y., Bell S.D. Sir2 and the acetyltransferase, Pat, regulate the archaeal chromatin protein, Alba. J. Biol. Chem. 2005, 280:21122-21128.
108. Martens C., Vandepoele K., Van de Peer Y. Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species. Proc. Natl. Acad. Sci. USA 2008, 105:3427-3432.
109. Mat W.K., Xue H., Wong J.T. The genomics of LUCA. Front Biosci. 2008, 13:5605-5613.
110. Mattick J.S. A new paradigm for developmental biology. J. Exp. Biol. 2007, 210:1526-1547.
111. Mattick J.S., Amaral P.P., Dinger M.E., Mercer T.R., Mehler M.F. RNA regulation of epigenetic processes. Bioessays 2009, 31:51-59.
112. Matzke M., Kanno T., Daxinger L., Huettel B., Matzke A.J. RNA-mediated chromatin-based silencing in plants. Curr. Opin. Cell. Biol. 2009, 21:367-376.
113. Mersfelder E.L., Parthun M.R. The tale beyond the tail: histone core domain modifications and the regulation of chromatin structure. Nucleic Acids Res. 2006, 34:2653-2662.
114. Moazed D. Small RNAs in transcriptional gene silencing and genome defence. Nature 2009, 457:413-420.
115. Moreno Díaz de la Espina S., Alverca E., Cuadrado A., Franca S. Organization of the genome and gene expression in a nuclear environment lacking histones and nucleosomes: the amazing dinoflagellates. Eur. J. Cell Biol. 2005, 84:137-149.
116. Morgan H.D., Santos F., Green K., Dean W., Reik W. Epigenetic reprogramming in mammals. Hum. Mol. Genet. 2005, 14(Spec No 1):47-58.
117. Morrison D.K. The 14-3-3 proteins: integrators of diverse signaling cues that impact cell fate and cancer development. Trends Cell Biol. 2009, 19:16-23.
118. Mujtaba S., Zeng L., Zhou M.M. Structure and acetyl-lysine recognition of the bromodomain. Oncogene 2007, 26:5521-5527.
119. Murata M., Azuma Y., Miura K., Rahman M.A., Matsutani M., Aoyama M., Suzuki H., Sugi K., Shirai M. Chlamydial SET domain protein functions as a histone methyltransferase. Microbiology 2007, 153:585-592.
120. Nelson C.J., Santos-Rosa H., Kouzarides T. Proline isomerization of histone H3 regulates lysine methylation and gene expression. Cell 2006, 126:905-916.
121. Nemeth M.J., Lowrey C.H. An erythroid-specific chromatin opening element increases beta-globin gene expression from integrated retroviral gene transfer vectors. Gene Ther. Mol. Biol. 2004, 8:475-486.
122. Ng R.K., Gurdon J.B. Epigenetic inheritance of cell differentiation status. Cell Cycle 2008, 7:1173-1777.
123. Nijman S.M., Luna-Vargas M.P., Velds A., Brummelkamp T.R., Dirac A.M., Sixma T.K., Bernards R. A genomic and functional inventory of deubiquitinating enzymes. Cell 2005, 123:773-786.
124. Noom M.C., Hol F.J.H., Laurens N., While M.F., Dame R.T., Wuite G.J.L. Unravelling the role of Alba in the organization of the archaeal nucleoid. Biophys. J. 2009, 96(Suppl. 1):61a. (Poster Abstract).
125. Norris V. Poly-(R)-3-hydroxybutyrate and the pioneering work of Rosetta Natoli Reusch. Cell Mol. Biol. 2005, 51:629-634.
126. Orfaniotou F., Tzamalis P., Thanassoulas A., Stefanidi E., Zees A., Boutou E., Vlassi M., Nounesis G., Vorgias C.E. The stability of the archaeal HU histone-like DNA-binding protein from Thermoplasma volcanium. Extremophiles 2009, 13:1-10.
127. Pandey R., Müller A., Napoli C.A., Selinger D.A., Pikaard C.S., Richards E.J., Bender J., Mount D.W., Jorgensen R.A. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res. 2002, 30:5036-5055.
128. Pandey R.R., Mondal T., Mohammad F., Enroth S., Redrup L., Komorowski J., Nagano T., Mancini-Dinardo D., Kanduri C. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell 2008, 32:232-246.
129. Pélissier T., Wassenegger M. A DNA target of 30bp is sufficient for RNA-directed DNA methylation. RNA 2000, 6:55-65.
130. Perez J.C., Latifi T., Groisman E.A. Overcoming H-NS-mediated transcriptional silencing of horizontally acquired genes by the PhoP and SlyA proteins in Salmonella enterica. J. Biol. Chem. 2008, 283:10773-10783.
131. Pérez-Martín J., de Lorenzo V. Clues and consequences of DNA bending in transcription. Annu. Rev. Microbiol. 1997, 51:593-628.
132. Pinson V., Takahashi M., Rouviere-Yaniv J. Differential binding of the escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA. J. Mol. Biol. 1999, 267:485-497.
133. Poole A.M., Logan D.T. Modern mRNA proofreading and repair: clues that the last universal ancestor possessed an RNA genome?. Mol. Biol. Evol. 2005, 22:1444-1455.
134. Probst A.V., Dunleavy E., Almouzni G. Epigenetic inheritance during the cell cycle. Nat. Rev. Mol. Cell Biol. 2009, 10:192-206.
135. Prohaska, S.J., P.F., Stadler, P.F., 2007. A story of growing confusion: genes and their regulation. In: Mondaini, R.P., Dilão, R. (Eds.), BIOMAT-2007: International Symposium on Mathematical and Computational Biology. World Scientific, Singapore, pp. 325-345 (Armação dos Búzios, RJ, Brazil, 24-29 November 2008).
136. Rando O.J., Ahmad K. Rules and regulation in the primary structure of chromatin. Curr. Opin. Cell. Biol. 2007, 19:250-256.
137. Reeve J.N., Bailey K.A., Li W.T., Marc F., Sandman K., Soares D.J. Archaeal histones: structures, stability and DNA binding. Biochem. Soc. Trans. 2004, 32:227-230.
138. Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 2007, 447:425-432.
139. Rinn J.L., Kertesz M., Wang J.K., Squazzo S.L., Xu X., Brugmann S.A., Goodnough L.H., Helms J.A., Farnham P.J., Segal E., Chang H.Y. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007, 29:1311-1323.
140. Rodríguez-Trelles F., Rosa Tarrío R., Ayala F.J. Origins and evolution of spliceosomal introns. Annu. Rev. Genet. 2006, 40:47-76.
141. Roh T.Y., Cuddapah S., Zhao K. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev. 2005, 19:542-552.
142. Rundlett S.E., Carmen A.A., Kobayashi R., Bavykin S., Turner B.M., Grunstein M. HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc. Natl. Acad. Sci. USA 1996, 93:14503-14508.
143. Ryan M.P., Jones R., Morse R.H. SWI-SNF complex participation in transcriptional activation at a step subsequent to activator binding. Mol. Cell. Biol. 1998, 18:1774-1782.
144. Sanchez-Elsner T., Gou D., Kremmer E., Sauer F. Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. Science 2006, 311:1118-1123.
145. Sandman K., Grayling R.A., Dobrinski B., Lurz R., Reeve J.A. Growth-phase-dependent synthesis of histones in the archaeon Methanothermus fervidus. Proc. Natl. Acad. Sci. USA 1994, 91:12624-12628.
146. Sandman K., Pereira S.L., Reeve J.N. Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome. Cell. Mol. Life Sci. 1998, 54:1350-1364.
147. Sandman K., Reeve J.N. Structure and functional relationships of archaeal and eukaryal histones and nucleosomes. Arch. Microbiol. 2000, 173:165-169.
148. Schübeler D., Francastel C., Cimbora D.M., Reik A., Martin D.I., Groudine M. Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human beta-globin locus. Genes Dev. 2000, 14:940-950.
149. Schubert H.L., Blumenthal R.M., Cheng X. Many paths to methyltransfer: a chronicle of convergence. Trends Biochem. Sci. 2003, 28:329-335.
150. Schuettengruber B., Chourrout D., Vervoort M., Leblanc B., Cavalli G. Genome regulation by polycomb and trithorax proteins. Cell 2007, 128:735-745.
151. Schwartz Y.B., Pirrotta V. Polycomb complexes and epigenetic states. Curr. Opin. Cell. Biol. 2008, 20:266-273.
152. Sedighi M., Sengupta A.M. Epigenetic chromatin silencing: bistability and front propagation. Phys. Biol. 2007, 4:246-255.
153. Segal E., Widom J. What controls nucleosome positions?. Trends Genet. 2009, 25:225-343.
154. Shi Y., Berg J.M. Specific DNA-RNA hybrid binding by zinc finger proteins. Science 1995, 268:282-284.
155. Shi Y., Lan F., Matson C., Mulligan P., Whetstine J.R., Cole P.A., Casero R.A., Shi Y. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 2004, 119:941-953.
156. Siegel T.N., Hekstra D.R., Kemp L.E., Figueiredo L.M., Lowell J.E., Fenyo D., Wang X., Dewell S., Cross G.A. Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei. Genes Dev. 2009, 23:1063-1076.
157. Singh S.K., Choudhury S.R., Roy S., Sengupta D.N. Sequential, structural, and phylogenetic study of BRCT module in plants. J. Biomol. Struct. Dyn. 2008, 26:235-245.
158. Slesarev A.I., Belova G.I., Kozyavkin S.A., Lake J.A. Evidence for an early prokaryotic origin of histones H2A and H4 prior to the emergence of eukaryotes. Nucleic Acids Res. 1998, 26:427-430.
159. Smith J.S., Brachmann C.B., Celic I., Kenna M.A., Muhammad S., Starai V.J., Avalos J.L., Escalante-Semerena J.C., Grubmeyer C., Wolberger C., Boeke J.D. A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family. Proc. Natl. Acad. Sci. USA 2000, 97:6658-6663.
160. Starai V.J., Escalante-Semerena J.C. Identification of the protein acetyltransferase (Pat) enzyme that acetylates acetyl-CoA synthetase in Salmonella enterica. J. Mol. Biol. 2004, 340:1005-1012.
161. Sun W., Xu X., Pavlova M., Edwards A.M., Joachimiak A., Savchenko A., Christendat D. The crystal structure of a novel SAM-dependent methyltransferase PH1915 from Pyrococcus horikoshii. Protein Sci. 2005, 14:3121-3128.
162. Talbert P.B., Henikoff S. Chromatin-based transcriptional punctuation. Genes Dev. 2009, 23:1037-1041.
163. Tan E., Besant P.G., Zu X.L., Turck C.W., Bogoyevitch M.A., Lim S.G., Attwood P.V., Yeoh G.C. Histone H4 histidine kinase displays the expression pattern of a liver oncodevelopmental marker. Carcinogenesis 2004, 25:2083-2088.
164. Tariq M., Paszkowski J. DNA and histone methylation in plants. Trends Genet. 2004, 20:244-251.
165. Taunton J., Hassig C.A., Schreiber S.L. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 1996, 272:408-411.
166. Taverna S.D., Li H., Ruthenburg A.J., Allis C.D., Patel D.J. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 2007, 14:1025-1040.
167. Taylor B.L. An alternative strategy for adaptation in bacterial behavior. J. Bacteriol. 2004, 186:3671-3673.
168. Taylor W.R. Transcription and translation in an RNA world. Philos. Trans. R. Soc. B 2006, 361:1751-1760.
169. Thanbichler M., Wang S.C., Shapiro L. The bacterial nucleoid: a highly organized and dynamic structure. J. Cell. Biochem. 2005, 96:506-521.
170. Thatcher T.H., Gorovsky M.A. Phylogenetic analysis of the core histones H2A, H2B, H3, and H4. Nucleic Acids Res. 1994, 22:174-179.
171. Torres-Padilla M.E., Parfitt D.E., Kouzarides T., Zernicka-Goetz M. Histone arginine methylation regulates pluripotency in the early mouse embryo. Nature 2007, 445:214-218.
172. Travers A., Muskhelishvili G. Bacterial chromatin. Curr. Opin. Genet. Dev. 2005, 15:507-514.
173. Trewick S.C., McLaughlin P.J., Allshire R.C. Methylation: lost in hydroxylation?. EMBO Rep. 2005, 6:315-320.
174. Triana O., Galanti N., Olea N., Hellman U., Wernstedt C., Lujan H., Medina C., Toro G.C. Chromatin and histones from Giardia lamblia: a new puzzle in primitive eukaryotes. J. Cell. Biochem. 2001, 82:573-582.
175. Tsukada Y., Fang J., Erdjument-Bromage H., Warren M.E., Borchers C.H., Tempst P., Zhang Y. Histone demethylation by a family of JmjC domain-containing proteins. Nature 2006, 439:811-816.
176. Verdel A., Vavasseur A., Le Gorrec M., Touat-Todeschini L. Common themes in siRNA-mediated epigenetic silencing pathways. Int. J. Dev. Biol. 2009, 53:245-257.
177. Vetting M.W., Magnet S., Nieves E., Roderick S.L., Blanchard J.S. A bacterial acetyltransferase capable of regioselective N-acetylation of antibiotics and histones. Chem. Biol. 2004, 11:565-573.
178. Vilkaitis G., Suetake I., Klimasauskas S., Tajima S. Processive methylation of hemimethylated CpG sites by mouse Dnmt1 DNA methyltransferase. J. Biol. Chem. 2005, 280:64-72.
179. Wang H., Zhai L., Xu J., Joo H.-Y., Jackson S., Erdjument-Bromage H., Tempst P., Xiong Y., Zhang Y. Histone H3 and H4 ubiquitylation by the CUL4-DDB-ROC1 ubiquitin ligase facilitates cellular response to DNA damage. Mol. Cell 2006, 22:383-394.
180. Wang Y., Wysocka J., Sayegh J., Lee Y.H., Perlin J.R., Leonelli L., Sonbuchner L.S., McDonald C.H., Cook R.G., Dou Y., Roeder R.G., Clarke S., Stallcup M.R., Allis C.D., Coonrod S.A. Human PAD4 regulates histone arginine methylation levels via demethylimination. Science 2004, 306:279-283.
181. Wardleworth B.N., Russell R.J., Bell S.D., Taylor G.L., White M.F. Structure of alba: an archaeal chromatin protein modulated by acetylation. EMBO J. 2002, 21:4654-4662.
182. Washietl S., Machné R., Goldman N. Evolutionary footprints of nucleosome positions in yeast. Trends Genet. 2008, 24:583-587.
183. Weake V.M., Workman J.L. Histone ubiquitination: triggering gene activity. Mol. Cell 2008, 28:653-663.
184. Wenkert D., Allis C.D. Timing of the appearance of macronuclear-specific histone variant hv1 and gene expression in developing new macronuclei of Tetrahymena thermophila. J. Cell. Biol. 1984, 98:2107-2117.
185. White M.F., Bell S.D. Holding it together: chromatin in the archaea. Trends Genet. 2002, 18:621-626.
186. Wilson D., Pethica R., Zhou Y., Talbot C., Vogel C., Madera M., Chothia C., Gough J. SUPERFAMILY-comparative genomics, datamining and sophisticated visualisation. Nucleic Acids Res. 2009, 37:D380-D386.
187. Wolf Y.I., Koonin E.V. On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biol. Direct 2007, 2:14.
188. Wong J.T.Y., New D.C., Wong J.C.W., Hung V.K.L. Histone-like proteins of the dinoflagellate Crypthecodinium cohnii have homologies to bacterial DNA-binding proteins. Eukaryotic Cell 2003, 2:646-650.
189. Xu C., Cui G., Botuyan M.V., Mer G. Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S. Structure 2008, 16:1740-1750.
190. Yang J., Medvedev S., Yu J., Schultz R.M., Hecht N.B. Deletion of the DNA/RNA-binding protein MSY2 leads to post-meiotic arrest. Mol. Cell. Endocrinol. 2006, 250:20-24.
191. Yoon H.S., Hackett J.D., Pinto G., Bhattacharya D. The single, ancient origin of chromist plastids. Proc. Natl. Acad. Sci. USA 2002, 99:15507-15512.
192. Zhang L., Eugeni E.E., Parthun M.R., Freitas M.A. Identification of novel histone post-translational modifications by peptide mass fingerprinting. Chromosoma 2003, 112:77-86.
193. Zhang L., Jones K., Gong F. The molecular basis of chromatin dynamics during nucleotide excision repair. Biochem. Cell Biol. 2009, 87:265-272.
194. Zhou W., Wang X., Rosenfeld M.G. Histone H2A ubiquitination in transcriptional regulation and DNA damage repair. Int. J. Biochem. Cell Biol. 2009, 41:12-15.