Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax
暂无分享,去创建一个
[1] S. Hattman,et al. [6N]METHYL ADENINE IN THE NUCLEAR DNA OF A EUCARYOTE, TETRAHYMENA PYRIFORMIS , 1973, The Journal of cell biology.
[2] H. Wieden,et al. De novo cytosine methylation in the differentiating macronucleus of the stichotrichous ciliate Stylonychia lemnae. , 2003, Nucleic acids research.
[3] J. Eeckhoute,et al. Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers , 2012, Nucleic acids research.
[4] J. Issa,et al. Decitabine in the treatment of myelodysplastic syndromes , 2010, Expert review of anticancer therapy.
[5] Tin-Lap Lee,et al. DNA methylation of cancer genome. , 2009, Birth defects research. Part C, Embryo today : reviews.
[6] S. Cross,et al. The methylated component of the Neurospora crassa genome , 2003, Nature.
[7] P. Vertino. DNA methylation in cancer , 2011 .
[8] S. Cartinhour,et al. Elimination of germ-line tandemly repeated sequences from the somatic genome of the ciliate Oxytricha fallax , 2004, Chromosoma.
[9] K. Williams,et al. Developmental precise excision of Oxytricha trifallax telomere‐bearing elements and formation of circles closed by a copy of the flanking target duplication. , 1993, The EMBO journal.
[10] M. Yao,et al. Tetrahymena thermophila JMJD3 Homolog Regulates H3K27 Methylation and Nuclear Differentiation , 2012, Eukaryotic Cell.
[11] Laura F. Landweber,et al. RNA-mediated epigenetic programming of a genome-rearrangement pathway , 2008, Nature.
[12] P. Collas,et al. Immunoprecipitation of methylated DNA. , 2009, Methods in molecular biology.
[13] Jian-Bing Fan,et al. Genome‐wide DNA methylation profiling , 2010, Wiley interdisciplinary reviews. Systems biology and medicine.
[14] J. Issa,et al. Phase II study of low‐dose decitabine in combination with imatinib mesylate in patients with accelerated or myeloid blastic phase of chronic myelogenous leukemia , 2007, Cancer.
[15] Grzegorz Rozenberg,et al. The Pathway to Detangle a Scrambled Gene , 2008, PloS one.
[16] Marie-Aline Charles,et al. Quality control and single nucleotide resolution analysis of methylated DNA immunoprecipitation products. , 2010, Analytical biochemistry.
[17] J. M. Goddard,et al. Methylated bases in DNA from Paramecium aurelia. , 1974, Biochimica et biophysica acta.
[18] R. Meehan,et al. Loss of the maintenance methyltransferase, xDnmt1, induces apoptosis in Xenopus embryos , 2001, The EMBO journal.
[19] H. Blau,et al. DNA Demethylation Dynamics , 2011, Cell.
[20] J. A. Kloetzel. COMPARTMENTALIZATION OF THE DEVELOPING MACRONUCLEUS FOLLOWING CONJUGATION IN STYLONYCHIA AND EUPLOTES , 1970, The Journal of cell biology.
[21] David H Perlman,et al. Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax , 2012, Genome Biology.
[22] M. Fraga,et al. The Polycomb group protein EZH2 directly controls DNA methylation , 2007, Nature.
[23] W. Hennig,et al. The development of the macronucleus in the ciliated protozoan Stylonychia mytilus , 1974, Chromosoma.
[24] Jorge Cortes,et al. Phase 1 study of low-dose prolonged exposure schedules of the hypomethylating agent 5-aza-2'-deoxycytidine (decitabine) in hematopoietic malignancies. , 2004, Blood.
[25] W. Schulz,et al. Causes and consequences of DNA hypomethylation in human cancer. , 2005, Biochemistry and cell biology = Biochimie et biologie cellulaire.
[26] Rudolf Jaenisch,et al. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality , 1992, Cell.
[27] R. Baur,et al. Methylated bases in the DNA of the ciliate Stylonychia mytilus. , 1981, European journal of cell biology.
[28] Peter A. Jones,et al. The fundamental role of epigenetic events in cancer , 2002, Nature Reviews Genetics.
[29] Chia-Lin Wei,et al. Dynamic changes in the human methylome during differentiation. , 2010, Genome research.
[30] J. Issa,et al. Chromatin remodeling is required for gene reactivation after decitabine-mediated DNA hypomethylation. , 2010, Cancer research.
[31] M. Yao,et al. Identification of novel chromatin-associated proteins involved in programmed genome rearrangements in Tetrahymena , 2007, Journal of Cell Science.
[32] X. Deng,et al. The epigenome and plant development. , 2011, Annual review of plant biology.
[33] D. Witherspoon,et al. Conserved features of TBE1 transposons in ciliated protozoa , 2004, Genetica.
[34] J. Walter,et al. Embryogenesis: Demethylation of the zygotic paternal genome , 2000, Nature.
[35] T. Huang,et al. Methylated DNA immunoprecipitation and microarray-based analysis: detection of DNA methylation in breast cancer cell lines. , 2009, Methods in molecular biology.
[36] D. Prescott,et al. DNA of ciliated protozoa , 1971, Chromosoma.
[37] A. Bird,et al. Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). , 2004, Nucleic acids research.
[38] R. Jaenisch,et al. Induction of Tumors in Mice by Genomic Hypomethylation , 2003, Science.
[39] T. Mikkelsen,et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells , 2008, Nature.
[40] Howard Cedar,et al. Epigenetics of haematopoietic cell development , 2011, Nature Reviews Immunology.
[41] J. Christman,et al. Inhibition of DNA methyltransferase and induction of Friend erythroleukemia cell differentiation by 5-azacytidine and 5-aza-2'-deoxycytidine. , 1982, The Journal of biological chemistry.
[42] T. Carell,et al. 5-Hydroxymethylcytosine, the sixth base of the genome. , 2011, Angewandte Chemie.
[43] David R. Liu,et al. Conversion of 5-Methylcytosine to 5- Hydroxymethylcytosine in Mammalian DNA by the MLL Partner TET1 , 2009 .
[44] William Stafford Noble,et al. The MEME Suite , 2015, Nucleic Acids Res..
[45] 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.
[46] S. Cartinhour,et al. Precise excision of telomere-bearing transposons during Oxytricha fallax macronuclear development. , 1989, Genes & development.
[47] 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.
[48] Juri Rappsilber,et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity , 2011, Nature.
[49] 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.
[50] C. Allis,et al. A Novel Chromodomain Protein, Pdd3p, Associates with Internal Eliminated Sequences during Macronuclear Development inTetrahymena thermophila , 2000, Molecular and Cellular Biology.
[51] H. Cedar,et al. De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes , 2008, Nature Structural &Molecular Biology.
[52] Sean D. Taverna,et al. RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena. , 2007, Genes & development.
[53] Julie A. Law,et al. Establishing, maintaining and modifying DNA methylation patterns in plants and animals , 2010, Nature Reviews Genetics.
[54] Rachel Jones,et al. Behavioural genetics: Worms gang up on bacteria , 2002, Nature Reviews Genetics.
[55] K. Kinzler,et al. DNA methylation and genetic instability in colorectal cancer cells. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[56] M. Muller,et al. DNA Methyltransferase 1-associated Protein (DMAP1) Is a Co-repressor That Stimulates DNA Methylation Globally and Locally at Sites of Double Strand Break Repair* , 2010, The Journal of Biological Chemistry.
[57] J. Issa,et al. Phase II study of low-dose decitabine in patients with chronic myelogenous leukemia resistant to imatinib mesylate. , 2005, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.
[58] M. Yao,et al. Pdd1p, A Novel Chromodomain-Containing Protein, Links Heterochromatin Assembly and DNA Elimination in Tetrahymena , 1996, Cell.
[59] D. Haber,et al. DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development , 1999, Cell.
[60] J. Magdalena,et al. Methyl DNA immunoprecipitation. , 2009, Methods in molecular biology.
[61] David R. Liu,et al. The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing , 2010, PloS one.
[62] J. Herman,et al. A systematic profile of DNA methylation in human cancer cell lines. , 2003, Cancer research.
[63] E. Selker,et al. dim‐2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora , 2001, The EMBO journal.
[64] 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.
[65] P. Rae,et al. Macronuclear DNA of the hypotrichous ciliate Oxytricha fallax. , 1978, Proceedings of the National Academy of Sciences of the United States of America.
[66] Yi Zhang,et al. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification , 2010, Nature.
[67] J. Ballesta,et al. Proteins P1, P2, and P0, components of the eukaryotic ribosome stalk. New structural and functional aspects. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.
[68] S. Adl,et al. Timing of Life Cycle Morphogenesis in Synchronous Samples of Sterkiella histriomuscorum. II. The Sexual Pathway , 2000, The Journal of eukaryotic microbiology.
[69] D. Ammermann. RELEASE OF DNA BREAKDOWN PRODUCTS INTO THE CULTURE MEDIUM OF STYLONYCHIA MYTILUS EXCONJUGANTS (PROTOZOA, CILIATA) DURING THE DESTRUCTION OF THE POLYTENE CHROMOSOMES , 1969, The Journal of cell biology.
[70] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[71] M. Frommer,et al. CpG islands in vertebrate genomes. , 1987, Journal of molecular biology.
[72] R. Weksberg,et al. Assessment of methylation level prediction accuracy in methyl-DNA immunoprecipitation and sodium bisulfite based microarray platforms , 2011, Epigenetics.
[73] Esteban Ballestar,et al. Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. , 2008, BioTechniques.
[74] M. Pellegrini,et al. Conservation and divergence of methylation patterning in plants and animals , 2010, Proceedings of the National Academy of Sciences.
[75] B. Spear,et al. Polytene chromosomes of Oxytricha: Biochemical and morphological changes during macronuclear development in a ciliated protozoan , 1976, Chromosoma.
[76] Dirk Schübeler,et al. Methylated DNA immunoprecipitation (MeDIP). , 2009, Methods in molecular biology.
[77] C. Boulesteix,et al. 5-Methylcytosine and 5-Hydroxymethylcytosine Spatiotemporal Profiles in the Mouse Zygote , 2012, PloS one.
[78] A. Bird. DNA methylation patterns and epigenetic memory. , 2002, Genes & development.
[79] Yi Zhang,et al. Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. , 2011, Genes & development.
[80] A. Niveleau,et al. Monitoring of urinary excretion of modified nucleosides in cancer patients using a set of six monoclonal antibodies. , 1992, Cancer letters.
[81] A. Cassidy,et al. Hypomethylation of retrotransposable elements correlates with genomic instability in non‐small cell lung cancer , 2009, International journal of cancer.
[82] D. Prescott,et al. DNA of ciliated protozoa: DNA sequence diminution during macronuclear development of oxytricha , 1976, Cell.
[83] E. Ballestar,et al. Discovery of epigenetically silenced genes by methylated DNA immunoprecipitation in colon cancer cells. , 2007, Cancer research.
[84] D. Zilberman,et al. Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation , 2010, Science.
[85] D. Ang,et al. Mobile elements bounded by C4A4 telomeric repeats in oxytricha fallax , 1985, Cell.
[86] Colin A. Johnson,et al. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex , 1998, Nature.
[87] H. Cedar,et al. G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis , 2006, Nature Cell Biology.
[88] Thomas D. Schmittgen,et al. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.
[89] W. Reik,et al. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation , 2011, Nature.
[90] S. Sanyal,et al. Bacterial ribosome requires multiple L12 dimers for efficient initiation and elongation of protein synthesis involving IF2 and EF-G , 2011, Nucleic acids research.
[91] A. Mégarbané,et al. Heterochromatic Genes Undergo Epigenetic Changes and Escape Silencing in Immunodeficiency, Centromeric Instability, Facial Anomalies (ICF) Syndrome , 2011, PloS one.
[92] K. Ghoshal,et al. 5-Aza-Deoxycytidine Induces Selective Degradation of DNA Methyltransferase 1 by a Proteasomal Pathway That Requires the KEN Box, Bromo-Adjacent Homology Domain, and Nuclear Localization Signal , 2005, Molecular and Cellular Biology.
[93] W. Reik,et al. 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. , 2011, Nature communications.
[94] Yi Zhang,et al. Active DNA demethylation: many roads lead to Rome , 2010, Nature Reviews Molecular Cell Biology.
[95] S. Baylin,et al. DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci , 2000, Nature Genetics.
[96] Zuhong Lu,et al. Identification of methylated regions with peak search based on Poisson model from massively parallel methylated DNA immunoprecipitation‐sequencing data , 2010, Electrophoresis.