Molecular Mechanisms of Epigenetics

The main epigenetic mechanisms in regulation of gene expression are discussed. The definition of epigenetics and its specific mechanisms including DNA methylation and gene imprinting, modifications of nucleosomal histones associated with silencing or activation of gene transcription, RNA interference, chromosomal silencing, and the role of mobile elements are discussed.

[1]  B. Dastugue,et al.  Coupling of Enhancer and Insulator Properties Identified in Two Retrotransposons Modulates Their Mutagenic Impact on Nearby Genes , 2002, Molecular and Cellular Biology.

[2]  Karl Henry,et al.  Rad6 plays a role in transcriptional activation through ubiquitylation of histone H2B. , 2004, Genes & development.

[3]  G. Längst,et al.  Recruitment of the Nucleolar Remodeling Complex NoRC Establishes Ribosomal DNA Silencing in Chromatin , 2004, Molecular and Cellular Biology.

[4]  J. Simon,et al.  Programming off and on states in chromatin: mechanisms of Polycomb and trithorax group complexes. , 2002, Current opinion in genetics & development.

[5]  S. Long,et al.  Extended Region of Nodulation Genes in Rhizobium meliloti 1021. II. Nucleotide Sequence, Transcription Start Sites and Protein Products. , 1987, Genetics.

[6]  V. Colot,et al.  Eukaryotic DNA methylation as an evolutionary device , 1999, BioEssays : news and reviews in molecular, cellular and developmental biology.

[7]  J. Kennison The Polycomb and trithorax group proteins of Drosophila: trans-regulators of homeotic gene function. , 1995, Annual review of genetics.

[8]  R. Jaenisch DNA methylation and imprinting: why bother? , 1997, Trends in genetics : TIG.

[9]  A. Riggs,et al.  Methylation and epigenetic fidelity , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Tony Kouzarides,et al.  Histone H3 lysine 4 methylation patterns in higher eukaryotic genes , 2004, Nature Cell Biology.

[11]  L. E. McDonald,et al.  A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[12]  A. Razin,et al.  Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line. , 1992, Genes & development.

[13]  J. Bender A Vicious Cycle RNA Silencing and DNA Methylation in Plants , 2001, Cell.

[14]  N. Tchurikov,et al.  Isolation of eukaryotic DNA fragments containing structural genes and the adjacent sequences. , 1977, Science.

[15]  F. Winston,et al.  Analysis of a Mutant Histone H3 That Perturbs the Association of Swi/Snf with Chromatin , 2004, Molecular and Cellular Biology.

[16]  Eun-Young Choi,et al.  The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'UTR. , 2004, Genes & development.

[17]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[18]  J. Workman,et al.  Function and Selectivity of Bromodomains in Anchoring Chromatin-Modifying Complexes to Promoter Nucleosomes , 2002, Cell.

[19]  N. Dhillon,et al.  Breaking through to the other side: silencers and barriers. , 2002, Current opinion in genetics & development.

[20]  R. Festenstein,et al.  Unravelling heterochromatin: competition between positive and negative factors regulates accessibility. , 2002, Trends in genetics : TIG.

[21]  Ravi S. Menon,et al.  The effects of visual object priming on brain activation before and after recognition , 2000, Current Biology.

[22]  L. Moore,et al.  The trithorax group gene osa encodes an ARID-domain protein that genetically interacts with the brahma chromatin-remodeling factor to regulate transcription. , 1999, Development.

[23]  Phillip D Zamore,et al.  Why do miRNAs live in the miRNP? , 2002, Genes & development.

[24]  C. Croce,et al.  An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[25]  R. Allshire,et al.  Hairpin RNAs and Retrotransposon LTRs Effect RNAi and Chromatin-Based Gene Silencing , 2003, Science.

[26]  E. Selker Gene silencing: repeats that count. , 1999 .

[27]  B. Kaufmann Distribution of Induced Breaks along the X-Chromosome of Drosophila Melanogaster. , 1939, Proceedings of the National Academy of Sciences of the United States of America.

[28]  W. Bender,et al.  Cross-Regulation among the Polycomb Group Genes in Drosophila melanogaster , 2004, Molecular and Cellular Biology.

[29]  Akira Ishizuka,et al.  Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. , 2004, Genes & development.

[30]  R. Allshire,et al.  Those interfering little RNAs! Silencing and eliminating chromatin. , 2004, Current opinion in genetics & development.

[31]  G. Maul,et al.  Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation. , 2003, Genes & development.

[32]  Philip Stanier,et al.  Conserved methylation imprints in the human and mouse GRB10 genes with divergent allelic expression suggests differential reading of the same mark. , 2003, Human molecular genetics.

[33]  R. Scott Hansen,et al.  Hairpin-bisulfite PCR: Assessing epigenetic methylation patterns on complementary strands of individual DNA molecules , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[34]  R. Kellum Is HP1 an RNA detector that functions both in repression and activation? , 2003, The Journal of cell biology.

[35]  R. R. Ariza,et al.  ROS1, a Repressor of Transcriptional Gene Silencing in Arabidopsis, Encodes a DNA Glycosylase/Lyase , 2002, Cell.

[36]  C. Croce,et al.  MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[37]  P. Sharp,et al.  RNAi and double-strand RNA. , 1999, Genes & development.

[38]  J. Manola,et al.  A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens. , 2004, Nucleic acids research.

[39]  Hengbin Wang,et al.  Role of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing , 2002, Science.

[40]  Xiaofeng Cao,et al.  ARGONAUTE4 Control of Locus-Specific siRNA Accumulation and DNA and Histone Methylation , 2003, Science.

[41]  R. Jirtle,et al.  Genomic imprinting: implications for human disease. , 1999, The American journal of pathology.

[42]  B. Chernov,et al.  SuUR Protein Binds to the Boundary Regions Separating Forum Domains in Drosophila melanogaster* , 2004, Journal of Biological Chemistry.

[43]  E. Li,et al.  Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting , 2004, Nature.

[44]  Long-Cheng Li,et al.  MethPrimer: designing primers for methylation PCRs , 2002, Bioinform..

[45]  R. Kingston,et al.  Requirement for Sex Comb on Midleg Protein Interactions in Drosophila Polycomb Group Repression , 2004, Genetics.

[46]  F. Ishikawa,et al.  Stable inheritance of telomere chromatin structure and function in the absence of telomeric repeats. , 2003, Genes & development.

[47]  S. Poux,et al.  Structure of a Polycomb Response Element and In Vitro Binding of Polycomb Group Complexes Containing GAGA Factor , 2000, Molecular and Cellular Biology.

[48]  B. Chernov,et al.  Gene-specific Silencing by Expression of Parallel Complementary RNA in Escherichia coli * , 2000, The Journal of Biological Chemistry.

[49]  A. Otte,et al.  Transcriptional repression mediated by the human polycomb-group protein EED involves histone deacetylation , 1999, Nature Genetics.

[50]  A. Shearn,et al.  The Direct Interaction Between ASH2, a Drosophila Trithorax Group Protein, and SKTL, a Nuclear Phosphatidylinositol 4-Phosphate 5-Kinase, Implies a Role for Phosphatidylinositol 4,5-Bisphosphate in Maintaining Transcriptionally Active Chromatin , 2004, Genetics.

[51]  Charles Kooperberg,et al.  The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. , 2004, Genes & development.

[52]  M. Matzke,et al.  HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double‐stranded RNA , 2002, The EMBO journal.

[53]  Lin He,et al.  MicroRNAs: small RNAs with a big role in gene regulation , 2004, Nature reviews genetics.

[54]  Youngchang Kim,et al.  Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. , 2003, Genes & development.

[55]  Dimitris Thanos,et al.  Deciphering the Transcriptional Histone Acetylation Code for a Human Gene , 2002, Cell.

[56]  M. Lehmann Anything else but GAGA: a nonhistone protein complex reshapes chromatin structure. , 2004, Trends in genetics : TIG.

[57]  A. Kristjuhan,et al.  Elongator interactions with nascent mRNA revealed by RNA immunoprecipitation. , 2004, Molecular cell.

[58]  Philip R. Gafken,et al.  Histone H3.3 is enriched in covalent modifications associated with active chromatin. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[59]  F. P. Villena,et al.  Genome imprinting regulated by the mouse Polycomb group protein Eed , 2003, Nature Genetics.

[60]  Laura Fanti,et al.  Heterochromatin protein 1 (HP1) is associated with induced gene expression in Drosophila euchromatin , 2003, The Journal of cell biology.

[61]  Michael Black,et al.  Role of transposable elements in heterochromatin and epigenetic control , 2004, Nature.

[62]  Victor G Corces,et al.  Polycomb and Trithorax Group Proteins Mediate the Function of a Chromatin Insulator , 1998, Cell.

[63]  D. Reinberg,et al.  Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. , 2004, Genes & development.

[64]  M. Ronaghi Pyrosequencing sheds light on DNA sequencing. , 2001, Genome research.

[65]  David I. K. Martin,et al.  Retrotransposons as epigenetic mediators of phenotypic variation in mammals , 2001, Nature Genetics.

[66]  Phillip D Zamore,et al.  RNAi: nature abhors a double-strand. , 2002, Current opinion in genetics & development.

[67]  A. Reynolds,et al.  Rational siRNA design for RNA interference , 2004, Nature Biotechnology.

[68]  C. Kanduri,et al.  An Antisense RNA Regulates the Bidirectional Silencing Property of the Kcnq1 Imprinting Control Region , 2004, Molecular and Cellular Biology.

[69]  J. C. Eissenberg,et al.  Developmental regulation of heterochromatin-mediated gene silencing in Drosophila. , 1998, Development.

[70]  K. Ekwall The RITS complex-A direct link between small RNA and heterochromatin. , 2004, Molecular cell.

[71]  R. Kingston,et al.  Stabilization of Chromatin Structure by PRC1, a Polycomb Complex , 1999, Cell.

[72]  C. Gross,et al.  The interface of sigma with core RNA polymerase is extensive, conserved, and functionally specialized. , 1999, Genes & development.

[73]  L. Pillus,et al.  Molecular Requirements for Gene Expression Mediated by Targeted Histone Acetyltransferases , 2004, Molecular and Cellular Biology.

[74]  R. Martienssen,et al.  The role of RNA interference in heterochromatic silencing , 2004, Nature.

[75]  D. Baulcombe,et al.  Crystal structure of p19--a universal suppressor of RNA silencing. , 2004, Trends in biochemical sciences.

[76]  R. Martienssen,et al.  Vernalization requires epigenetic silencing of FLC by histone methylation , 2004, Nature.

[77]  Danny Reinberg,et al.  A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. , 2004, Genes & development.

[78]  Y. Wataya,et al.  Reaction of sodium bisulfite with uracil, cytosine, and their derivatives. , 1970, Biochemistry.

[79]  S. Tilghman,et al.  CTCF maintains differential methylation at the Igf2/H19 locus , 2003, Nature Genetics.

[80]  Ira M. Hall,et al.  Regulation of Heterochromatic Silencing and Histone H3 Lysine-9 Methylation by RNAi , 2002, Science.

[81]  R. Feil,et al.  Epigenetic regulation of mammalian genomic imprinting. , 2004, Current opinion in genetics & development.

[82]  O. Niwa,et al.  Independent mechanisms involved in suppression of the moloney leukemia virus genome during differentiation of murine teratocarcinoma cells , 1983, Cell.

[83]  John M. Greally,et al.  Epigenomics: beyond CpG islands , 2004, Nature Reviews Genetics.

[84]  G. Karpen,et al.  The activation of a neocentromere in Drosophila requires proximity to an endogenous centromere. , 2001, Genetics.

[85]  R. Paro,et al.  Binding of Trithorax and Polycomb proteins to the bithorax complex: dynamic changes during early Drosophila embryogenesis , 1998, The EMBO journal.

[86]  A. Aravin,et al.  Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline , 2001, Current Biology.

[87]  Thomas Tuschl,et al.  Expanding small RNA interference , 2002, Nature Biotechnology.

[88]  S. Grewal,et al.  Heterochromatin: new possibilities for the inheritance of structure. , 2002, Current opinion in genetics & development.

[89]  Phillip D Zamore,et al.  Ancient Pathways Programmed by Small RNAs , 2002, Science.

[90]  K. Struhl,et al.  Eaf3 Regulates the Global Pattern of Histone Acetylation in Saccharomyces cerevisiae , 2004, Molecular and Cellular Biology.

[91]  Alexey G. Murzin,et al.  Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9 , 2002, Nature.

[92]  Tom Misteli,et al.  Global Nature of Dynamic Protein-Chromatin Interactions In Vivo: Three-Dimensional Genome Scanning and Dynamic Interaction Networks of Chromatin Proteins , 2004, Molecular and Cellular Biology.

[93]  Brigitte Wild,et al.  Histone Methyltransferase Activity of a Drosophila Polycomb Group Repressor Complex , 2002, Cell.

[94]  D. Beach,et al.  Polycomb CBX7 has a unifying role in cellular lifespan , 2004, Nature Cell Biology.

[95]  C. Kanduri,et al.  The nucleotides responsible for the direct physical contact between the chromatin insulator protein CTCF and the H19 imprinting control region manifest parent of origin-specific long-distance insulation and methylation-free domains. , 2003, Genes & development.

[96]  R. Kingston,et al.  Propagation of silencing; recruitment and repression of naive chromatin in trans by polycomb repressed chromatin. , 2004, Molecular cell.

[97]  V. Chandler,et al.  Chromatin conversations: mechanisms and implications of paramutation , 2004, Nature Reviews Genetics.

[98]  A. Bird DNA methylation patterns and epigenetic memory. , 2002, Genes & development.

[99]  V. Pirrotta,et al.  Polycombing the Genome: PcG, trxG, and Chromatin Silencing , 1998, Cell.

[100]  J. Bernués,et al.  The Drosophila transcription factor tramtrack (TTK) interacts with Trithorax-like (GAGA) and represses GAGA-mediated activation. , 2002, Nucleic acids research.

[101]  Ronald H. A. Plasterk,et al.  RNA Silencing: The Genome's Immune System , 2002, Science.

[102]  M. Gorovsky,et al.  Small RNAs in genome rearrangement in Tetrahymena. , 2004, Current opinion in genetics & development.

[103]  A. Riggs,et al.  Methylation dynamics, epigenetic fidelity and X chromosome structure. , 1998, Novartis Foundation symposium.

[104]  L. Wallrath,et al.  Mechanisms of HP1-mediated gene silencing in Drosophila , 2004, Development.

[105]  S. Elgin,et al.  cis-Acting Determinants of Heterochromatin Formation on Drosophila melanogaster Chromosome Four , 2004, Molecular and Cellular Biology.

[106]  Michelle T. Juarez,et al.  microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity , 2004, Nature.

[107]  Fred Winston,et al.  The Swi/Snf Chromatin Remodeling Complex Is Required for Ribosomal DNA and Telomeric Silencing in Saccharomyces cerevisiae , 2004, Molecular and Cellular Biology.

[108]  I. Grummt,et al.  The nucleolar remodeling complex NoRC mediates heterochromatin formation and silencing of ribosomal gene transcription , 2002, Nature Genetics.

[109]  A. Ciechanover,et al.  The ubiquitin‐mediated proteolytic pathway and mechanisms of energy‐dependent intracellular protein degradation , 1984, Journal of cellular biochemistry.

[110]  J. Birchler,et al.  RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. , 2002, Molecular cell.

[111]  Ueli Grossniklaus,et al.  Epigenetics: The Flowers That Come In From The Cold , 2002, Current Biology.