Functions of DNA methylation: islands, start sites, gene bodies and beyond
暂无分享,去创建一个
[1] S. Nelson,et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning , 2008, Nature.
[2] S. Henikoff,et al. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks , 2008, Nature.
[3] A. Wolffe,et al. ReCoGnizing methylated DNA , 2001, Nature Structural Biology.
[4] S. Tapscott,et al. De novo methylation of the MyoD1 CpG island during the establishment of immortal cell lines. , 1990, Proceedings of the National Academy of Sciences of the United States of America.
[5] E. Selker,et al. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. , 1997, Genes & development.
[6] G. Ast,et al. Chromatin organization marks exon-intron structure , 2009, Nature Structural &Molecular Biology.
[7] Michael Q. Zhang,et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications , 2010, Nature Biotechnology.
[8] T. Hashimshony,et al. The role of DNA methylation in setting up chromatin structure during development , 2003, Nature Genetics.
[9] M. Karin,et al. Cytosine methylation does not affect binding of transcription factor Sp1. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[10] Yi Guo,et al. An Sp1/Sp3 Binding Polymorphism Confers Methylation Protection , 2008, PLoS genetics.
[11] Vijay K. Tiwari,et al. DNA-binding factors shape the mouse methylome at distal regulatory regions , 2011, Nature.
[12] A. Klein-Szanto,et al. Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair , 2011, Cell.
[13] S. Henikoff,et al. Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis. , 2010, Genome research.
[14] J. Berg,et al. Dnmt3a is essential for hematopoietic stem cell differentiation , 2011, Nature Genetics.
[15] R. Lister,et al. Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis , 2008, Cell.
[16] C. Hsieh,et al. Dynamics of DNA methylation pattern. , 2000, Current opinion in genetics & development.
[17] Benjamin J. Raphael,et al. Integrated Genomic Analyses of Ovarian Carcinoma , 2011, Nature.
[18] Peter A. Jones,et al. Moving AHEAD with an international human epigenome project , 2008, Nature.
[19] Rudolf Jaenisch,et al. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality , 1992, Cell.
[20] S. Clark,et al. Extensive DNA methylation spanning the Rb promoter in retinoblastoma tumors. , 1997, Cancer research.
[21] Arthur D. Riggs,et al. X inactivation, differentiation, and DNA methylation. , 1975, Cytogenetics and cell genetics.
[22] K. Helin,et al. DNA methylation: TET proteins—guardians of CpG islands? , 2012, EMBO reports.
[23] Amos Tanay,et al. Constitutive Nucleosome Depletion and Ordered Factor Assembly at the GRP78 Promoter Revealed by Single Molecule Footprinting , 2006, PLoS genetics.
[24] R Holliday,et al. DNA modification mechanisms and gene activity during development , 1975, Science.
[25] Chia-Lin Wei,et al. Dynamic changes in the human methylome during differentiation. , 2010, Genome research.
[26] Peter A. Jones,et al. A decade of exploring the cancer epigenome — biological and translational implications , 2011, Nature Reviews Cancer.
[27] Zohar Yakhini,et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer , 2007, Nature Genetics.
[28] B. Migeon,et al. Methylation of the hypoxanthine phosphoribosyltransferase locus on the human X chromosome: implications for X-chromosome inactivation. , 1984, Proceedings of the National Academy of Sciences of the United States of America.
[29] Peter A. Jones,et al. H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. , 2010, Molecular cell.
[30] H. Prydz,et al. A methylated CpG island 3' in the apolipoprotein-E gene does not repress its transcription. , 1993, Human molecular genetics.
[31] T. Bestor,et al. The Colorful History of Active DNA Demethylation , 2008, Cell.
[32] Peter A. Jones,et al. Rethinking how DNA methylation patterns are maintained , 2009, Nature Reviews Genetics.
[33] P. Jones,et al. Altered chromatin structure associated with methylation-induced gene silencing in cancer cells: correlation of accessibility, methylation, MeCP2 binding and acetylation. , 2001, Nucleic acids research.
[34] N. Tommerup,et al. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene , 1999, Nature.
[35] Peter A. Jones,et al. DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter. , 2011, Human molecular genetics.
[36] G. Pfeifer,et al. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine , 2011, Proceedings of the National Academy of Sciences.
[37] W. Reik,et al. Uncovering the role of 5-hydroxymethylcytosine in the epigenome , 2011, Nature Reviews Genetics.
[38] F. Chédin,et al. ICF syndrome mutations cause a broad spectrum of biochemical defects in DNMT3B-mediated de novo DNA methylation. , 2011, Journal of molecular biology.
[39] David N. Cooper,et al. The CpG dinucleotide and human genetic disease , 1988, Human Genetics.
[40] Yi Zhang,et al. Replication-Dependent Loss of 5-Hydroxymethylcytosine in Mouse Preimplantation Embryos , 2011, Science.
[41] Juri Rappsilber,et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity , 2011, Nature.
[42] J. M. Wessels,et al. Many roads lead to Rome [blog] , 2014 .
[43] Christian Schmidl,et al. Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity. , 2009, Genome research.
[44] B. Ren,et al. Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells , 2011, PLoS genetics.
[45] J. Licht,et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. , 2010, Cancer cell.
[46] C. Walsh,et al. Cytosine methylation and the ecology of intragenomic parasites. , 1997, Trends in genetics : TIG.
[47] J. Licht,et al. DNMT3A mutations in acute myeloid leukemia , 2011, Nature Genetics.
[48] S. Gartler,et al. Comparison of transformation efficiency of human active and inactive X-chromosomal DNA , 1983, Nature.
[49] M. Pellegrini,et al. A comparative analysis of DNA methylation across human embryonic stem cell lines , 2011, Genome Biology.
[50] M. Pellegrini,et al. Relationship between nucleosome positioning and DNA methylation , 2010, Nature.
[51] G. Pfeifer,et al. Relationship between Gene Body DNA Methylation and Intragenic H3K9me3 and H3K36me3 Chromatin Marks , 2011, PloS one.
[52] D. Takai,et al. Large scale mapping of methylcytosines in CTCF-binding sites in the human H19 promoter and aberrant hypomethylation in human bladder cancer. , 2001, Human molecular genetics.
[53] S. Groshen,et al. Susceptibility of nonpromoter CpG islands to de novo methylation in normal and neoplastic cells. , 2001, Journal of the National Cancer Institute.
[54] Robert S. Illingworth,et al. CpG islands influence chromatin structure via the CpG-binding protein Cfp1 , 2010, Nature.
[55] Cassandra R. Farthing,et al. Global Mapping of DNA Methylation in Mouse Promoters Reveals Epigenetic Reprogramming of Pluripotency Genes , 2008, PLoS genetics.
[56] J. Stamatoyannopoulos,et al. DNA methylation status predicts cell type‐specific enhancer activity , 2011, The EMBO journal.
[57] G. Coetzee,et al. 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. , 1990, Science.
[58] Peter A. Jones,et al. Nucleosomes Containing Methylated DNA Stabilize DNA Methyltransferases 3A/3B and Ensure Faithful Epigenetic Inheritance , 2011, PLoS genetics.
[59] P. Laird,et al. Epigenetic stem cell signature in cancer , 2007, Nature Genetics.
[60] S. Andrews,et al. Dynamic CpG island methylation landscape in oocytes and preimplantation embryos , 2011, Nature Genetics.
[61] D. Haber,et al. DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development , 1999, Cell.
[62] J. Jiricny,et al. Genomic sequencing reveals a positive correlation between the kinetics of strand-specific DNA demethylation of the overlapping estradiol/glucocorticoid-receptor binding sites and the rate of avian vitellogenin mRNA synthesis. , 1986, Proceedings of the National Academy of Sciences of the United States of America.
[63] David R. Liu,et al. The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing , 2010, PloS one.
[64] E. Li,et al. Complete inactivation of DNMT1 leads to mitotic catastrophe in human cancer cells , 2007, Nature Genetics.
[65] Daiya Takai,et al. Comprehensive analysis of CpG islands in human chromosomes 21 and 22 , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[66] G. Prendergast,et al. Methylation-sensitive sequence-specific DNA binding by the c-Myc basic region. , 1991, Science.
[67] S. Simonsson,et al. DNA demethylation is necessary for the epigenetic reprogramming of somatic cell nuclei , 2004, Nature Cell Biology.
[68] Gangning Liang,et al. Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line , 2008, Proceedings of the National Academy of Sciences.
[69] V. Corces,et al. Enhancer function: new insights into the regulation of tissue-specific gene expression , 2011, Nature Reviews Genetics.
[70] Peter A. Jones,et al. Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island. , 2007, Cancer cell.
[71] Robert S. Illingworth,et al. Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome , 2010, PLoS genetics.
[72] W. Lam,et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells , 2005, Nature Genetics.
[73] Robert S Illingworth,et al. CpG islands – ‘A rough guide’ , 2009, FEBS letters.
[74] Tomohiro Hayakawa,et al. Maintenance of self‐renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b , 2006, Genes to cells : devoted to molecular & cellular mechanisms.
[75] R. Sandberg,et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing , 2011, Nature.
[76] M. Pellegrini,et al. Conservation and divergence of methylation patterning in plants and animals , 2010, Proceedings of the National Academy of Sciences.
[77] R. Ward,et al. Dominantly inherited constitutional epigenetic silencing of MLH1 in a cancer-affected family is linked to a single nucleotide variant within the 5'UTR. , 2011, Cancer cell.
[78] Gangning Liang,et al. Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming , 2011, Cell.
[79] M. Pellegrini,et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency , 2010, Nature.
[80] Suhua Feng,et al. 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells , 2011, Genome Biology.
[81] G. Felsenfeld,et al. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene , 2000, Nature.
[82] Stefan U Kass,et al. DNA methylation directs a time-dependent repression of transcription initiation , 1997, Current Biology.
[83] Yi Zhang,et al. Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. , 2011, Genes & development.
[84] G. Martin,et al. Methylation of the Hprt gene on the inactive X occurs after chromosome inactivation , 1987, Cell.
[85] Z. Deng,et al. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes , 2011, Nature.
[86] K. Davies,et al. Physical mapping across the fragile X: Hypermethylation and clinical expression of the fragile X syndrome , 1991, Cell.
[87] P. Laird,et al. Global and gene-specific epigenetic patterns in human bladder cancer genomes are relatively stable in vivo and in vitro over time. , 2001, Cancer research.
[88] Allen D. Delaney,et al. Conserved Role of Intragenic DNA Methylation in Regulating Alternative Promoters , 2010, Nature.
[89] P. Jones,et al. The DNA methylation paradox. , 1999, Trends in genetics : TIG.
[90] Matthew Tudor,et al. Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation , 2001, Nature Genetics.
[91] A. Bird,et al. Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability , 2011, Nature.
[92] Kelly M. McGarvey,et al. A stem cell–like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing , 2007, Nature Genetics.
[93] Peter A. Jones,et al. OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes , 2011, Proceedings of the National Academy of Sciences.
[94] U. Bunz. How Are Alkynes Scrambled? , 2005, Science.
[95] W. Reik,et al. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation , 2011, Nature.
[96] Lee E. Edsall,et al. Human DNA methylomes at base resolution show widespread epigenomic differences , 2009, Nature.
[97] W. Reik,et al. 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. , 2011, Nature communications.
[98] A. Chess,et al. Gene Body-Specific Methylation on the Active X Chromosome , 2007, Science.
[99] Yi Zhang,et al. Active DNA demethylation: many roads lead to Rome , 2010, Nature Reviews Molecular Cell Biology.
[100] C. Allis,et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA , 2007, Nature.
[101] A. Feinberg,et al. Genome-wide methylation analysis of human colon cancer reveals similar hypo- and hypermethylation at conserved tissue-specific CpG island shores , 2008, Nature Genetics.
[102] Helen M. Blau,et al. Reprogramming towards pluripotency requires AID-dependent DNA demethylation , 2010, Nature.