Литература

Ahmad K. and Henikoff S. 2002. The histone variant H3.3 marks ac­tive chromatin by replication-independent nucleosome assembly. Mol. Cell 9: 1191-1200.

Allfrey V.G., Faulkner R., and Mirsky A.E. 1964. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl Acad. Sci. 51: 786-794.

Almeida R. and Allshire R.C. 2005. RNA silencing and genome regulation. Trends Cell Biol. 15: 251-258.

Aparicio O.M., Billington B.L., and Gottschling D.E. 1991. Modi­fiers of position effect are shared between telomeric and silent mating-type loci in S cerevisiae. Cell 66: 1279-1287.

Avery O.T., Macleod C.M., and McCarty M. 1944. Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Induction of transformation by a desoxy­ribonucleic acid fraction isolated from pneumococcus Type III. J. Exp. Med. 79: 137-158.

Avner R and Heard E. 2001. X-chromosome inactivation: Counting, choice and initiation. Nat. Rev. Genet. 2: 59-67.

Bannister A.J. and Kouzarides T. 2005. Reversing histone methyla­tion. Nature 436: 1103-1106.

Bannister A. J., Zegerman R, Partridge J.E, Miska E.A., Thomas J.O., Allshire R.C, and Kouzarides T. 2001. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410: 120-124.

Barton S.C., Surani M.A., and Norris M.L. 1984. Role of paternal and maternal genomes in mouse development. Nature 311: 374-376.

Bastow R., Mylne J.S., Lister C, Lippman Z., Martienssen R.A., and Dean C. 2004. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427: 164-167.

Baxter J., Sauer S., Peters A., John R., Williams R., Caparros M.L., Amey K., Otte A., Jenuwein T, Merkenschlager M., and Fisher A. G. 2004. Histone hypomethylation is an indicator of epigenetic plasticity in quiescent lymphocytes. EMBO J. 23: 4462-4472. Berger S.L. 2002. Histone modifications in transcriptional regulation. Curr. Opin. Genet. Dev. 12: 142-148.

Bernard P., Maure J.E, Partridge J.F., Genier S., Javerzat J.P., and Allshire R.C. 2001. Requirement of heterochromatin for cohesion at centromeres. Science 294: 2539-2542.

Bernstein B.E., Kamal M., Lindblad-Toh K., Bekiranov S., Bailey D. K., Huebert D.J., McMahon S., Karlsson E.K., Kulbokas E. J., III, Gitigeras T.R., et al. 2005. Genomic maps and com­parative analysis of histone modifications in human and mouse. Cell 120: 169-181.

Bernstein B.E., Mikkelsen T.S., Xie X., Kamal M., Huebert D.J., Cuff J., Fry B., Meissner A., Wemig M., Plath K., et al. 2006. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315-326.

Bernstein E. and Allis C.D. 2005. RNA meets chromatin. Genes Dev. 19: 1635-1655.

Bird A.P. 1986. CpG-rich islands and the function of DNA methyla­tion. Nature 321: 209-213.

Birky C.W., Jr. 2001. The inheritance of genes in mitochondria and chloroplasts: Laws, mechanisms, and models. Annu. Rev. Genet. 35: 125-148.

Bolland D.J., Wood A.L., Johnston CM., Bunting S.F., Morgan G., Chakalova L., Fraser P.J., and Corcoran A.E. 2004. Antisense inter-genic transcription in V(D)J recombination. Nat. Immunol. 5: 630-637.

Bourc’his D. and Bestor T.H. 2004. Meiotic catastrophe and ret- rotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431: 96-99.

Boyer L.A., Plath K., Zeitlinger J., Brambrink T., Medeiros L.A., Lee T.I., Levine S.S., Wemig M., Tajonar A., Ray M.K., et al. 2006 Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441: 349-353.

Bracken A.P, Dietrich N., Pasini D., Hansen K.H., and Helin K. 2006. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 20: 1123-1136. Braig M., Lee S.. Loddenkemper C, Rudolph C, Peters A.H., Schlegelberger B., Stein H., Dorken B., Jenuwein T., and Schmitt C. A. 2005. Oncogene-induced senescence as an initial barrier in lymphoma development. Nature 436: 660-665.

Brownell J.E., Zhou J., Ranalli T., Kobayashi R., Edmondson D. G., Roth S.Y., and Allis C.D. 1996. Tetrahymena histone acetyltrans-ferase A: A homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84: 843-851.

Caims B.R. 2005. Chromatin remodeling complexes: Strength in diversity, precision through specialization. Curr. Opin. Genet. Dev. 15: 185-190.

Campbell K.H., McWhir J., Ritchie W.A., and Wilmut 1.1996. Sheep cloned by nuclear transfer from a cultured cell line. Nature 380: 64-66.

Cao R., Wang L., Wang H., Xia L., Erdjument-Bromage H., Tempst P., Jones R.S.,and Zhang Y. 2002. Role ofhistone H3 lysine 27 methy­lation in Polycomb-group silencing. Science 298: 1039-1043.

Cavalli G. and Paro R. 1999. Epigenetic inheritance of active chro­matin after removal of the main transactivator. Science 286: 955-958.

Chakalova L., Debrand E., Mitchell J.A., Osbome C.S., and Fraser P. 2005. Replication and transcription: Shaping the landscape of the genome. Nat. Rev. Genet. 6: 669-677.

Chalker D.L. and Yao M.C. 2001. Nongenic, bidirectional transcrip­tion precedes and may promote developmental DNA deletion in Tetrahymena thermophila. Genes Dev. 15: 1287-1298.

Chan S.W., Zilberman D., Xie Z., Johansen L.K., Carrington J.C., and Jacobsen S.E.2004. RNA silencing genes control de novo DNA methylation. Science 303: 1336.

Chen R.Z., Pettersson U., Beard C., Jackson-Grusby L., and Jaenisch R. 1998. DNA hypomethylation leads to elevated mutation rates. Nature 395: 89-93.

Cheng D., Yadav N., King R.W., Swanson M.S., Weinstein E.J., and Bedford M.T. 2004. Small molecule regulators of protein arginine methyltransferases. J. Biol. Chem. 279: 23892-23899.

Cheng J.C., Yoo C.B., Weisenberger D.J., Chuang J., Wozniak C., Liang G., Marquez V.E., Greer S., Omtoft T.F., Thykjaer T., and Jones P.A. 2004. Preferential response of cancer cells to zebularine. Cancer Cell 6: 151-158.

Cho K.S., Elizondo L.I., and Boerkoel C.F. 2004. Advances in chromatin remodeling and human disease. Curr. Opin. Genet. Dev. 14: 308-315.

Chuikov S., Kurash J.K., Wilson J.R., Xiao B., Justin N., Ivanov G.S., McKinney K., Tempst P., Prives C., Gamblin S.J.. et al. Regulation of p53 activity through lysine methylation. Nature 432: 353-360.

Clark-Adams C.D., Noms D., Osley M.A., Fassler J.S., and Winston F. 1988. Changes in histone gene dosage alter transcription in yeast. Genes Dev. 2: 150-159.

Cohen F.E. and Prusiner S.B. 1998. Pathologic conformations of prion proteins. Annu. Rev. Biochem. 67: 793-819.

Cosgrove M.S., Boeke J.D., and Wolberger C. 2004. Regulated nu- cleosome mobility and the histone code. Nat. Struct. Mol. Biol. 11: 1037-1043.

Cremer T. and Cremer C. 2001. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2: 292-301.

Daujat S., Zeissler U., Waldmann T., Happel N., and Schneider R. 2005. HP1 binds specifically to Lys26-methylated histone H1.4, whereas simultaneous Ser27 phosphorylation blocks HPl bind­ing. /. Biol. Chem. 280: 38090-38095.

Dellino G.I., Schwartz Y.B., Farkas G., McCabe D.. Elgin S.C.. and Pirrotta V. 2004. Polycomb silencing blocks transcription initiation. Mol. Cell 13: 887-893.

Dhalluin C, Carlson J.E., Zeng L., He C., Aggarwal A.K., and Zhou M.M. 1999. Structure and ligand of a histone acetyltransferase bromodomain. Nature 399: 491-496.

Di Croce L. 2005. Chromatin modifying activity of leukaemia associated fusion proteins. Hum. Mol. Genet. 14 Spec. No. 1: R77-R84.

Dou Y. and Gorovsky M.A. 2000. Phosphorylation of linker histone HI regulates gene expression in vivo by creating a charge patch. Mol. Cell 6: 225-231.

Fan Y, Nikitina T., Zhao J., Fleury T.J., Bhattacharyya R., Bouhas- sira E.E., Stein A., Woodcock C.L., and Skoultchi A.I. 2005.

Histone HI depletion in mammals alters global chromatin structure but causes specific changes in gene regulation. Cell 123: 1199-1212.

Feinberg A.P. 2004. The epigenetics of cancer etiology. Semin. Cancer Biol 14: 427-432.

Feinberg A. P. and Tycko B. 2004. The history of cancer epigenetics Nat. Rev. Cancer 4: 143-153.

Feinberg A.P. and Vogelstein B. 1983. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301: 89-92.

Felsenfeld G. and Groudine M. 2003. Controlling the double helix. Nature 421: 448-453.

Fischle W., Wang Y., and Allis C.D. 2003a. Binary switches and modification cassettes in histone biology and beyond. Nature 425: 475-479.

Fischle W., Wang Y., and Allis C.D. 2003b Histone and chromatin cross-talk. Curr. Opin. Cell Biol. 15: 172-183.

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. 2005. Regulation of HP 1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438: 1116-1122.

Fisher A.G. and Merkenschlager M. 2002. Gene silencing, cell fate and nuclear organisation. Curr. Opin. Genet. Dev. 12: 193-197.

Fodor B.D., Kubicek S., Yonezawa M., O’Sullivan R.J., Sengupta R., Perez-Burgos L., Opravil S., Mechtler K., Schotta G., and Jenuwein T. 2006. Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells. Genes Dev. 20: 1557-1562.

Fraga M.F., Ballestar E., Paz M.E., Ropero S., Setien F. Ballestar M.L., Heine-Suner D., Cigudosa J.C., Urioste M., Benitez J., et al. 2005. Epigenetic differences arise during the lifetime of monozygotic twins. Proc. Natl. Acad. Sci. 102: 10604-10609.

Francis N.J., Kingston R.E., and Woodcock C.L. 2004. Chromatin compaction by a polycomb group protein complex. Science 306: 1574-1577.

Fukagawa T, Nogami M., Yoshikawa M., Ikeno M., Okazaki T., Takami Y., Nakayama T., and Oshimura M. 2004. Dicer is essen­tial for formation of the heterochromatin structure in vertebrate cells. Nat. Cell Biol. 6: 784-791.

Garcia-Manero G. and Issa J.P. 2005. Histone deacetylase inhibitors: A review of their clinical status as antineoplastic agents. Cancer Invest. 23: 635-642.

Gilbert N., Boyle S., Fiegler H., Woodfine K., Carter N.P., and Bickmore W.A. 2004 Chromatin architecture of the human genome: Generich domains are enriched in open chromatin fibers. Cell 118: 555-566.

Gilfillan G.D., Dahlsveen I.K., and Becker P.B. 2004. Lifting a chromosome: Dosage compensation in Drosophila melanogaster. FEBSLett. 567: 8-14.

Goll M.G., Kirpekar E., Maggert K.A., Yoder J.A., Hsieh C.L., Zhang X., Golic K.G., Jacobsen S.E., and Bestor T.H. 2006. Methylation of tRNAAsp by the DNA methyltransferase ho­molog Dnmt2. Science 311: 395-398.

Gonzalo S. and Blasco M.A. 2005. Role of Rb family in the epigenetic definition of chromatin Cell Cycle 4: 752-755.

Gottschling D.E., Aparicio O.M., Billington B.L., and Zakian V.A. 1990. Position effect at S. cerevisiae telomeres: Reversible repres­sion of Pol II transcription. Cell 63: 751-762.

Grant P.A., Duggan L., Cote J., Roberts S.M., Brownell I.E., Candau R., Ohba R., Owen-Hughes T., Allis CD., Winston E, et al. 1997. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: Characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 11: 1640-1650.

Greiner D., BonaldiT., Eskeland R., RoemerE., and ImhofA. 2005. Identification of a specific inhibitor of the histone methyltrans­ferase SU(VAR)3-9. Nat. Chem. Biol. 1: 143-145.

Grewal S.I. and Klar A.J. 1996. Chromosomal inheritance of epi­genetic states in fission yeast during mitosis and meiosis. Cell 86: 95-101.

Grozinger C.M. and Schreiber S.L. 2002. Deacetylase enzymes: Biological functions and the use of small molecule inhibitors. Chem. Biol. 9: 3-16.

Guarente L. and Picard E 2005. Calorie restriction — The SIR2 connection. Cell 120: 473-482.

Hall I.M., Shankaranarayana G.D., Noma K., Ayoub N., Cohen A., and Grewal S.L. 2002. Establishment and maintenance of a heterochromatin domain. Science 297: 2232-2237.

Hanahan D. and Weinberg R.A. 2000. The hallmarks of cancer. Cell 100: 57-70.

Harvey A.C. and Downs J .A. 2004. What functions do linker histones provide? Mol. Microbiol. 53: 771-775.

Hassan A.H., Prochasson P., Neely K.E., Galasinski S.C., Chandy M., Carrozza M.J., and Workman J.L. 2002. Function and se­lectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111: 369-379.

Heard E. 2005. Delving into the diversity of facultative heterochro­matin: The epigenetics of the inactive X chromosome. Curr. Opin. Genet. Dev. 15: 482-489.

Henikoff S. 2005. Histone modifications: Combinatorial complex­ity or cumulative simplicity? Proc. Natl. Acad. Sci. 102: 5308- , 5309.

Henikoff S. and Ahmad K. 2005. Assembly of vanant histones into chromatin. Annu Rev. Cell Dev. Biol. 21: 133-153.

Herr A.J., Jensen M.B., DalmayT., and Baulcombe D.C. 2005. RNA polymerase IV directs silencing of endogenous DNA. Science 308: 118-120.

Hirota T., Lipp J.J., Toh B.H., and Peters J.M. 2005. Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin. Nature 438: 1176-1180.

Hochedlinger K., Blelloch R., Brennan C, Yamada Y, Kim M., Chin L., and Jaenisch R. 2004. Reprogramming of a melanoma genome by nuclear transplantation. Genes Dev. 18: 1875-1885.

Holbert M.A. and Marmorstein R. 2005. Structure and activity of enzymes that remove histone modifications. Curr. Opin. Struct. Biol. 15: 673-680. Holliday R. 1994. Epigenetics: An overview. Dev. Genet. 15: 453-457.

Ishii K.J. and Akira S. 2005. TLR ignores methylated RNA? Im­munity 23: 111-113.

Jackson J.P., Lindroth A.M., CaoX., and Jacobsen S.E. 2002. Con­trol of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556-560.

Jacobson R.H., Ladumer A.G., King D.S. andTjian R. 2000. Struc­ture and function of a human TAFII250 double bromodomain module. Science. 288: 1422-1425.

Jaenisch R. and Bird A. 2003. Epigenetic regulation of gene expres­sion: How the genome integrates intrinsic and environmental signals. Nat. Genet, (suppl.) 33: 245-254.

Janicki S.M., Tsukamoto T., Salghetti S.E., Tansey W.P., Sachidanan- dam R., Prasanth K.V., Ried T., Shav-Tal Y., Bertrand E., Singer R.H., and Spector D.L. 2004. From silencing to gene expression: Real-time analysis in single cells. Cell 116: 683-698.

Jeddeloh J.A., Stokes..L., and Richards E.J. 1999. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat. Genet. 22: 94-97.

Jenuwein T. and Allis C.D. 2001. Translating the histone code. Sci­ence 293: 1074-1080.

Jones RA. and Martienssen R. 2005. A blueprint for a Human Epigenome Project: The AACR Human Epigenome Workshop. Cancer Res. 65: 11241-11246.

Kanellopoulou C, Muljo S.A., Kung A.L., Ganesan S., Drapkin R., Jenuwein T., Livingston D.M., and Rajewsky K. 2005. Dicer- deficient mouse embryonic stem cells are defective in differentia­tion and centromeric silencing. Genes Dev. 19: 489-501.

Kayne P.S., Kim U.J., Han M., Mullen J.R., Yoshizaki E, and Grunstein M. 1988. Extremely conserved histone H4 N terminus is dispensable for growth but essential for repressing the silent mating loci in yeast. Cell 55: 27- 39.

Khochbin S. 2001. Histone HI diversity: Bridging regulatory signals to linker histone function. Gene 271: 1-12.

Khorasanizadeh S. 2004. The nucleosome: From genomic organiza­tion to genomic regulation. Cell 116: 259-272.

Kim J., Daniel J., Espejo A., Lake A., Krishna M., Xia L., Zhang Y., and Bedford M.X. 2006. Tudor, MBT and chromo domains gauge the degree of lysine methylation. EMBO Rep. 4: 397-403.

Kimmins S. and Sassone-Corsi P. 2005. Chromatin remodeling and epigenetic features of germ cells. Nature 434: 583-589.

KlarAJ. 1998. Propagating epigenetic states through meiosis: Where Mendel’s gene is more than a DNA moiety. Trends Genet. 14: 299-301.

KlarAJ. 2004. An epigenetic hypothesis for human brain laterality, handedness, and psychosis development. Cold Spring Harbor Symp. Quant. Biol. 69: 499-506.

Knoepfler P.S., ZhangX.-Y., Cheng R.E., Gafken P.R., McMahon S.B., and Eisenman R.N 2006. Myc influences global chromatin structure. EMBO J. 25: 2723-2734.

Komberg R.D. 1974. Chromatin structure: A repeating unit of his­tones and DNA. Science 184: 868-871.

Lachner M., O’Sullivan R.J., and Jenuwein T 2003. An epigenetic road map for histone lysine methylation. J. Cell Sci. 116: 2117-2124.

Lachner M., Sengupta R., Schotta G., and Jenuwein T. 2004. Trilo­gies of histone lysine methylation as epigenetic landmarks of the eukaryotic genome. Cold Spring Harbor Symp. Quant. Biol. 69: 209-218.

Lachner M., O’Carroll D., Rea S., Mechtler K., and Jenuwein T. 2001 Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410: 116-120.

Langst G. and Becker P.B. 2004. Nucleosome remodeling: One mecha­nism, many phenomena? Biochim. Biophys. Acta 1677: 58-63.

Lee D.Y., Teyssier C, Strahl B.D., and Stallcup M.R. 2005. Role of protein methylation in regulation of transcription. Endocr. Rev. 26: 147-170.

Lee T.L, 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., et al. 2006. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125: 301-313.

LengauerC., KinzlerK.W., and Vogelstein B. 1998. Genetic instabili­ties in human cancers. Nature 396: 643-649.

Li E., Bestor T.H., and Jaenisch R. 1992. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69: 915-926.

Lippman Z., Gendrel A.V., Black M., Vaughn M.W., Dedhia N., McCombie W.R., Lavine K., Mittal V., May B., Kasschau K.D., et al. 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.

Litt M.D., Simpson M., Gaszner M., Allis C.D., and Felsenfeld G. 2001. Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus. Science 293: 2453-2455.

Luger K., Mader A.W., Richmond R.K., Sargent D.F., and Richmond T.J. 1997. Crystal structure of the nucleosome core particle at 2.8 E resolution. Nature 389: 251-260.

Lund A.H. and van Lohuizen M. 2004. Polycomb complexes and silencing mechanisms. Curr. Opin. Cell Biol. 16: 239-246.

Lyko F. 2001. DNA methylation learns to fly. Trends Genet. 17: 169- 172.

Maher E.R. 2005. Imprinting and assisted reproductive technology. Hum. Mol. Genet 14 Spec. No. 1: R133-R138.

Maison C., Bailly D., Peters A.H., Quivy J.P., Roche D., Taddei A., Lachner M., Jenuwein T., and Almouzni G. 2002. Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component. Nat. Genet. 30: 329-334.

Marks P. A. and Jiang X. 2005. Histone deacetylase inhibitors in pro­grammed cell death and cancer therapy. Cell Cycle 4: 549-551.

Martens J.H., O’Sullivan R.J., Braunschweig U., Opravil S., Radolf M , Steinlein P., and Jenuwein T. 2005. The profile of repeat- associated histone lysine methylation states in the mouse epig­enome. EMBO J. 24: 800-812.

Maurer-Stroh S., Dickens N.J., Hughes-Davies L., Kouzarides T., Eisenhaber R., and Ponting C.P. 2003. The Tudor domain ‘Royal Family’: Tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends Biochem. Sci. 28: 69-74.

MayerW., Niveleau A., Walter J., Fundele R., and HaafT. 2000. Dem- ethylation of the zygotic paternal genome. Nature 403: 501-502.

McClintock B. 1951. Chromosome organization and genic expres­sion. Cold Spring Harbor Symp. Quant. Biol. 16: 13-47.

McGarvey K., Fahmer J., Green E., Martens J., Jenuwein T., and Baylin S.B. 2006. Silenced tumor suppressor genes reactivated by DNA demethylation do not return to a fully euchromatic chromatin state. Cancer Res. 66: 3541-3549.

McGrath J. and Solter D. 1984. Completion of mouse embryogenesis re­quires both the maternal and paternal genomes. Cell 37: 179-183.

Metzger E., Wissmann M., Yin N., Muller J.M., Schneider R., Pe­ters A.H., Gunther T, Buettner R., and Schule R. 2005. LSD1 demethylates repressive histone marks to promote androgen- receptor-dependent transcription. Nature 437: 436-439.

Meyer B.J., McDonel P., Csankovszki G., and Ralston E. 2004. Sex and X-chromosome-wide repression in Caenorhabditis elegans. Cold Spring Harbor Symp. Quant. Biol. 69: 71-79.

Misteli T. 2004. Spatial positioning; a new dimension in genome function. Cell 119: 153-156.

Mito Y., Henikoff J.G., and Henikoff S. 2005. Genome-scale pro­filing of histone H3.3 replacement patterns. Nat. Genet. 37: 1090-1097.

Mizuguchi G, Shen X., Landry J., Wu W.H., Sen S., and Wu C. 2004 ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303: 343-348.

Mochizuki K., Fine N.A., Fujisawa T., and Gorovsky M.A. 2002. Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena. Cell 110: 689-699.

Mohrmann L. and Verrijzer C.P. 2005. Composition and functional specificity of SWI2/SNF2 class chromatin remodeling com­plexes. Biochim. Biophys. Acta 1681: 59-73.

Morgan H.D., Santos F, Green K., Dean W., and Reik W. 2005. Epigenetic reprogramming in mammals. Hum. Mol. Genet. 14 Spec. No. 1: R47-R58.

Motamedi M.R., Verdel A., Colmenares S.U., Gerber S.A., Gygi S.R, and Moazed D. 2004. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119: 789-802.

Muller H.J. 1930. Types of visible variations induced by X-rays in Drosophila. J. Genet. 22: 299-334.

Nakayama J., Rice J.C., Strahl B.D., Allis C.D., and Grewal S.I. 2001. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292: 110-113.

Narita M., Nunez S., Heard E., Narita M., Lin A.W., Hearn S.A., Spector D.L., Hannon G.J., and Lowe S.W. 2003. Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence. Cell 113: 703-716.

Narlikar G.J., Fan H.Y., and Kingston R.E. 2002. Cooperation between complexes that regulate chromatin structure and tran­scription. Cell 108: 475-487.

Nowak S.J. and Corces V.G. 2004. Phosphorylation of histone H3: A balancing act between chromosome condensation and tran­scriptional activation. Trends Genet. 20: 214-220.

Orphanides C., LeRoy G., Chang C.H., Luse D.S., and Reinberg D. 1998. FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 92: 105-116.

Pal-Bhadra M., Leibovitch B.A., Gandhi S.G., Rao M., Bhadra U., Birchler J.A., and Elgin S.C. 2004. Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303: 669-672.

Paro R. and Hogness D.S. 1991. The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila. Proc. Natl. Acad. Sci. 88: 263-267.

Petersen-Mahrt S. 2005. DNA deamination in immunity. Immunol. Rev. 203: 80-97.

Pirrotta V. 1998. Polycombingthe genome: PcG, trxG, and chromatin silencing. Cell 93: 333-336.

Pontier D., Yahubyan G., Vega D., Bulski A., Saez-Vasquez J., Hakimi M.A., Lerbs-Mache S., Colot V., and Lagrange T. 2005. Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev. 19: 2030-2040.

Ratcliff R., Harrison B.D., and Baulcombe D.C. 1997. A similarity between viral defense and gene silencing in plants. Science 276: 1558-1560.

Razin A. and Riggs A.D. 1980. DNA methylation and gene function. Science 210: 604-610.

Rea S., Eisenhaber E., O’Carroll D., Strahl B.D., Sun Z.W., Schmid M., Opravil S., Mechtler K., Ponting C.P., Allis C.D., and Jenuwein T 2000. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406: 593-599.

Reinberg D., Chuikov S., Famham P., Karachentsev D., Kirmizis A., Kuzmichev A., Margueron R., Nishioka K., Preissner T.S., Sarma K., et al. 2004. Steps toward understanding the inheritance of repressive methyl-lysine marks in histones. Cold Spring Harbor Symp. Quant. Biol. 69: 171-182.

Reinhart B.J. and Bartel D.P. 2002. Small RNAs correspond to cen­tromere heterochromatic repeats. Science 297: 1831.

Rme J. 2005. Cell biology. Twists in the tale of the aging yeast. Sci­ence 310: 1124-1125.

Ringrose L. and Paro R. 2004 Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet. 38: 413-443.

Ringrose L., Ehret H., and Paro R. 2004. Distinct contributions of histone H3 lysine 9 and 27 methylation to locus-specific stability of polycomb complexes. Mol. Cell 16: 641-653.

Robertson K.D. 2005. DNA methylation and human disease. Nat. Rev. Genet. 6: 597-610.

RoloffT.C. and Nuber U.A. 2005. Chromatin, epigenetics and stem cells. Eur. J. Cell Biol. 84: 123-135.

Roth S.Y., Denu J.M., and Allis C.D. 2001. Histone acetyltrans- ferases. Annu. Rev. Biochem. 70: 81-120.

Sanchez-Eisner T., Gou D., Kremmer E., and Sauer F. 2006. Non­coding RNAs of trithorax response elements recruit Drosophila Ashl to ultrabithorax. Science 311: 1118-1123.

Santos-Rosa H., Schneider R., Bannister A. J., Sherriff J., Bernstein B. E., Emre N.C., Schreiber S.L., Mellor J., and Kouzarides T. 2002. Active genes are tri-methylated at K4 of histone H3. Nature 419: 407-411.

Sarma K. and Reinberg D. 2005. Histone variants meet their match. Nat. Rev. Mol. Cell Biol. 6: 139-149.

Scaffidi P., Gordon L., and Misteli T. 2005. The cell nucleus and aging: Tantalizing clues and hopeful promises. PLoS. Biol. 3: e395.

Schalch T., Duda S., Sargent D.E, and Richmond T.J. 2005. X-ray structure of a tetranucleosome and its implications for the chro­matin fibre. Nature 436: 138-141.

Schmitt S., Prestel M., and Paro R. 2005. Intergenic transcription through a polycomb group response element counteracts silenc­ing. Genes Dev. 19: 697-708.

Schneider R., Bannister A. J., and Kouzarides T. 2002. Unsafe SETs: Histone lysine methyltransferases and cancer. Trends Biochem. Sci. 27: 396-402.

Schreiber S.L. and Bernstein B.E. 2002. Signaling network model of chromatin. Cell 111: 771-778.

Schwartz B.E. and Ahmad K. 2005. Transcnptional activation trig­gers deposition and removal of the histone variant H3.3. Genes Dev. 19: 804-814.

Schwartz Y.B., Kahn T.G., and Pirrotta V. 2005. Characteristic low density and shear sensitivity of cross-linked chromatin containing polycomb complexes. Mol. Cell Biol. 25: 432-439.

Sekinger E.A., Moqtaderi Z., and Struhl K. 2005. Intrinsic histone- DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell 18: 735-748.

Seligson D.B., Horvath S., Shi T., Yu H., Tze S., Grunstein M., and Kurdistani S.K. 2005. Global histone modification patterns pre­dict risk of prostate cancer recurrence. Nature 435: 1262-1266.

ShenX., Mizuguchi G., Hamiche A., and Wu C. 2000. A chromatin remodeling complex involved in transcription and DNA process­ing. Nature 406: 541-544

Shi Y., Lan E., Matson C, Mulligan P., Whetstine J.R., Cole P.A., Casero R.A., and Shi Y. 2004. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119: 941-953.

Shorter J. and Lindquist S. 2005. Prions as adaptive conduits of memory and inheritance. Nat. Rev. Genet. 6: 435-450.

Sims R.J., III, Belotserkovskaya R., and Reinberg D. 2004. Elonga­tion by RNA polymerase II : The short and long of it. Genes Dev. 18: 2437-2468.

Smith C.L. and Peterson C.L. 2005. ATP-dependent chromatin remodeling. Curr. Top. Dev. Biol. 65: 115-148.

Squazzo S.L., O’Geen H., Komashko V.M., Krig S.R., Jin V.X., Jang S.W., Margueron R., Reinberg D., Green R., and Famham RJ. 2006 Suzl2 binds to silenced regions on the genome in a cell- type-specific manner. Genome Res. 16: 890-900.

Sterner D.E. and Berger S.L. 2000. Acetylation of histones and transcription-related factors. Microbiol. Mol. Biol. Rev. 64: 435- 459.

Strahl B.D. and Allis C.D. 2000. The language of covalent histone modifications. Nature 403: 41-45.

Strahl B.D., Ohba R., Cook R.G., and Allis C.D. 1999. Methylation of histone H3 at lysine 4 is highly conserved and correlates with transcriptionally active nuclei in Tetrahymena. Proc. Natl. Acad. Sci. 96: 14967-14972.

Su G.H., Sohn T.A., Ryu B., and Kern S.E. 2000. A novel histone deacetylase inhibitor identified by high-throughput transcription­al screening of a compound library. Cancer Res. 60: 3137-3142.

Sung S. and Amasino R.M. 2004. Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 427: 159-164.

Surani M.A., Barton S.C, and Norris M.X. 1984. Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature 308: 548-550.

Tagami H., Ray-Gallet D., Almouzni G., and Nakatani Y. 2004 Histone H3.1 and H3.3 complexes mediate nucleosome as­sembly pathways dependent or independent of DNA synthesis. Cell 116: 51-61.

Tamaru H. and Selker E.V. 2001. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414: 277-283.

Tanaka E.M. 2003. Regeneration: If they can do it, why can’t we? Cell 113: 559-562.

Thomas J.O. 1999. Histone HI: Location and role. Curr. Opin. Cell Biol. 11: 312-317.

Tsukada Y., Fang J., Erdjument-Bromage H., Warren M.E., Borch- ers C.H., Tempst P., and Zhang Y. 2006. Histone demethylation by a family of JmjC domain-containing proteins. Nature 439: 811-816

TsukiyamaT., Daniel C., Tamkun J., and Wu C. 1995. ISWI, amember of the SWI2/SNF2 ATPase family, encodes the 140 kDa sub­unit of the nucleosome remodeling factor Cell 83: 1021-1026.

Turner B.M. 2000. Histone acetylation and an epigenetic code. Bio Essays 22: 836-845.

Valk-Lingbeek M.E., Bruggeman S.W., and van Lohuizen M. 2004. Stem cells and cancer; the polycomb connection. Cell 118: 409-418

van Attikum H. and Gasser S.M. 2005. The histone code at DNA breaks: A guide to repair? Nat. Rev. Mol. Cell Biol. 6: 757-765.

van der Heijden G.W., Dieker J.W., DerijckA.A., Muller S., Berden J.H , Braat D.D., van der Vlag J., and de Boer P. 2005. Asymmetry in histone H3 variants and lysine methylation between paternal and maternal chromatin of the early mouse zygote. Mech. Dev. 122: 1008-1022.

Vaquero A., Loyola A., and Reinberg D. 2003. The constantly changing face of chromatin. Sci. Aging Knowledge Environ. 2003: RE4.

Varga-Weisz P.D., Wilm M., Bonte E., Dumas K., Mann M., and Becker P.B. 1997. Chromatin-remodeling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 388: 598-602

Verdel A., Jia S., Gerber S., Sugiyama T., Gygi S., Grewal S.L, and Moazed D. 2004. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303: 672-676.

Vidanes C.M., Bonilla C.Y., and Toczyski D.P. 2005. Complicated tails: Histone modifications and the DNA damage response. Cell 121: 973-976.

Vignali M., Hassan A.H., Neely K.E., and Workman J.L.. 2000. ATP-dependent chromatin-remodeling complexes. Mol. Cell. Biol. 20: 1899-1910.

Vire E., Brenner C., Deplus R., Blanchon L., Fraga M., Didelot C. , Morey L., Van E.A., Bernard D., Vanderwinden J.M., et al. 2005. The Polycomb group protein EZH2 directly controls DNA methylation Nature 439: 861-874.

Volpe T.A., Kidner C., Hall I.M., Teng C., Grewal S.L, and Mar- tienssen R.A. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297: 1833-1837.

Waddington C.H. 1957. The strategy of the genes. MacMillan, New York.

Wade P.A., Gegonne A., Jones P.L., Ballestar E., Aubry E., and Wolffe A.P. 1999. Mi-2 complex couples DNA methylation to chromatin remodeling and histone deacetylation. Nat. Genet. 23: 62-66.

Walsh C.P., Chaillet J .R., and Bestor T.H. 1998. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 20: 116-117.

Watanabe Y., Yokobayashi S., Yamamoto M., and Nurse P. 2001. Premeiotic S phase is linked to reductional chromosome segregation and recombination. Nature 409: 359-363.

Watson J.D. 2003. Celebrating the genetic jubilee: A conversation with James D. Watson. Interviewed by John Rennie. Sci. Am. 288: 66-69.

Wei Y., Yu L., Bowen J., Gorovsky M.A., and Allis C.D. 1999. Phos­phorylation of histone H3 is required for proper chromosome condensation and segregation. Cell 97: 99-109.

Whetstine J.R., Nottke A., Lan R., Huarte M., Smolikov S., Chen Z., Spooner E., Li E., Zhang G., Colaiacovo M., and Shi Y. 2006. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125: 467-481.

Wolffe A.P. and Matzke M.A. 1999. Epigenetics: Regulation through repression. Science 286: 481-486.

Wysocka J., Swigut T., Milne T.A., Dou Y., Zhang X., Burlingame A.L., Roeder R.G., Brivanlou A.H., and Allis C.D. 2005. WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121: 859-872.

Yan Q., Huang J., Fan T., Zhu H., and Muegge K. 2003. Lsh, a modulator of CpG methylation. is crucial for normal histone methylation. EMBO J. 22: 5154-5162.

Yu B., Yang Z., Li J., Minakhina S., Yang M., Padgett R.W., Steward R., and Chen X. 2005. Methylation as a crucial step in plant micro RNA biogenesis. Science 307: 932-935.

Zhang Y. and Reinberg D. 2001. Transcription regulation by histone methylation: Interplay between different covalent modifications of the core histone tails. Genes Dev. 15: 2343-2360.

Zhang Y., LeRoy G., Seeiig H.R, Lane W.S., and Reinberg D. 1998. The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities. Cell 95: 279-289.