Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax

[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]  S. Cartinhour,et al.  Elimination of germ-line tandemly repeated sequences from the somatic genome of the ciliate Oxytricha fallax , 2004, Chromosoma.

[8]  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.

[9]  M. Yao,et al.  Tetrahymena thermophila JMJD3 Homolog Regulates H3K27 Methylation and Nuclear Differentiation , 2012, Eukaryotic Cell.

[10]  Laura F. Landweber,et al.  RNA-mediated epigenetic programming of a genome-rearrangement pathway , 2008, Nature.

[11]  P. Collas,et al.  Immunoprecipitation of methylated DNA. , 2009, Methods in molecular biology.

[12]  Jian-Bing Fan,et al.  Genome‐wide DNA methylation profiling , 2010, Wiley interdisciplinary reviews. Systems biology and medicine.

[13]  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.

[14]  Grzegorz Rozenberg,et al.  The Pathway to Detangle a Scrambled Gene , 2008, PloS one.

[15]  Marie-Aline Charles,et al.  Quality control and single nucleotide resolution analysis of methylated DNA immunoprecipitation products. , 2010, Analytical biochemistry.

[16]  J. M. Goddard,et al.  Methylated bases in DNA from Paramecium aurelia. , 1974, Biochimica et biophysica acta.

[17]  R. Meehan,et al.  Loss of the maintenance methyltransferase, xDnmt1, induces apoptosis in Xenopus embryos , 2001, The EMBO journal.

[18]  H. Blau,et al.  DNA Demethylation Dynamics , 2011, Cell.

[19]  J. A. Kloetzel COMPARTMENTALIZATION OF THE DEVELOPING MACRONUCLEUS FOLLOWING CONJUGATION IN STYLONYCHIA AND EUPLOTES , 1970, The Journal of cell biology.

[20]  M. Fraga,et al.  The Polycomb group protein EZH2 directly controls DNA methylation , 2007, Nature.

[21]  W. Hennig,et al.  The development of the macronucleus in the ciliated protozoan Stylonychia mytilus , 1974, Chromosoma.

[22]  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.

[23]  W. Schulz,et al.  Causes and consequences of DNA hypomethylation in human cancer. , 2005, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[24]  Rudolf Jaenisch,et al.  Targeted mutation of the DNA methyltransferase gene results in embryonic lethality , 1992, Cell.

[25]  R. Baur,et al.  Methylated bases in the DNA of the ciliate Stylonychia mytilus. , 1981, European journal of cell biology.

[26]  Peter A. Jones,et al.  The fundamental role of epigenetic events in cancer , 2002, Nature Reviews Genetics.

[27]  Chia-Lin Wei,et al.  Dynamic changes in the human methylome during differentiation. , 2010, Genome research.

[28]  J. Issa,et al.  Chromatin remodeling is required for gene reactivation after decitabine-mediated DNA hypomethylation. , 2010, Cancer research.

[29]  M. Yao,et al.  Identification of novel chromatin-associated proteins involved in programmed genome rearrangements in Tetrahymena , 2007, Journal of Cell Science.

[30]  X. Deng,et al.  The epigenome and plant development. , 2011, Annual review of plant biology.

[31]  D. Witherspoon,et al.  Conserved features of TBE1 transposons in ciliated protozoa , 2004, Genetica.

[32]  J. Walter,et al.  Embryogenesis: Demethylation of the zygotic paternal genome , 2000, Nature.

[33]  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.

[34]  D. Prescott,et al.  DNA of ciliated protozoa , 1971, Chromosoma.

[35]  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.

[36]  R. Jaenisch,et al.  Induction of Tumors in Mice by Genomic Hypomethylation , 2003, Science.

[37]  T. Mikkelsen,et al.  Genome-scale DNA methylation maps of pluripotent and differentiated cells , 2008, Nature.

[38]  Howard Cedar,et al.  Epigenetics of haematopoietic cell development , 2011, Nature Reviews Immunology.

[39]  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.

[40]  T. Carell,et al.  5-Hydroxymethylcytosine, the sixth base of the genome. , 2011, Angewandte Chemie.

[41]  David R. Liu,et al.  Conversion of 5-Methylcytosine to 5- Hydroxymethylcytosine in Mammalian DNA by the MLL Partner TET1 , 2009 .

[42]  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.

[43]  S. Cartinhour,et al.  Precise excision of telomere-bearing transposons during Oxytricha fallax macronuclear development. , 1989, Genes & development.

[44]  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.

[45]  Juri Rappsilber,et al.  TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity , 2011, Nature.

[46]  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.

[47]  C. Allis,et al.  A Novel Chromodomain Protein, Pdd3p, Associates with Internal Eliminated Sequences during Macronuclear Development inTetrahymena thermophila , 2000, Molecular and Cellular Biology.

[48]  H. Cedar,et al.  De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes , 2008, Nature Structural &Molecular Biology.

[49]  Sean D. Taverna,et al.  RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena. , 2007, Genes & development.

[50]  Julie A. Law,et al.  Establishing, maintaining and modifying DNA methylation patterns in plants and animals , 2010, Nature Reviews Genetics.

[51]  Rachel Jones,et al.  Behavioural genetics: Worms gang up on bacteria , 2002, Nature Reviews Genetics.

[52]  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.

[53]  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.

[54]  David H Perlman,et al.  Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax , 2012, Genome Biology.

[55]  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.

[56]  M. Yao,et al.  Pdd1p, A Novel Chromodomain-Containing Protein, Links Heterochromatin Assembly and DNA Elimination in Tetrahymena , 1996, Cell.

[57]  D. Haber,et al.  DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development , 1999, Cell.

[58]  J. Magdalena,et al.  Methyl DNA immunoprecipitation. , 2009, Methods in molecular biology.

[59]  David R. Liu,et al.  The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing , 2010, PloS one.

[60]  J. Herman,et al.  A systematic profile of DNA methylation in human cancer cell lines. , 2003, Cancer research.

[61]  E. Selker,et al.  dim‐2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora , 2001, The EMBO journal.

[62]  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.

[63]  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.

[64]  Yi Zhang,et al.  Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification , 2010, Nature.

[65]  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.

[66]  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.

[67]  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.

[68]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[69]  M. Frommer,et al.  CpG islands in vertebrate genomes. , 1987, Journal of molecular biology.

[70]  R. Weksberg,et al.  Assessment of methylation level prediction accuracy in methyl-DNA immunoprecipitation and sodium bisulfite based microarray platforms , 2011, Epigenetics.

[71]  Esteban Ballestar,et al.  Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. , 2008, BioTechniques.

[72]  M. Pellegrini,et al.  Conservation and divergence of methylation patterning in plants and animals , 2010, Proceedings of the National Academy of Sciences.

[73]  B. Spear,et al.  Polytene chromosomes of Oxytricha: Biochemical and morphological changes during macronuclear development in a ciliated protozoan , 1976, Chromosoma.

[74]  Dirk Schübeler,et al.  Methylated DNA immunoprecipitation (MeDIP). , 2009, Methods in molecular biology.

[75]  C. Boulesteix,et al.  5-Methylcytosine and 5-Hydroxymethylcytosine Spatiotemporal Profiles in the Mouse Zygote , 2012, PloS one.

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

[77]  Yi Zhang,et al.  Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. , 2011, Genes & development.

[78]  A. Niveleau,et al.  Monitoring of urinary excretion of modified nucleosides in cancer patients using a set of six monoclonal antibodies. , 1992, Cancer letters.

[79]  A. Cassidy,et al.  Hypomethylation of retrotransposable elements correlates with genomic instability in non‐small cell lung cancer , 2009, International journal of cancer.

[80]  D. Prescott,et al.  DNA of ciliated protozoa: DNA sequence diminution during macronuclear development of oxytricha , 1976, Cell.

[81]  E. Ballestar,et al.  Discovery of epigenetically silenced genes by methylated DNA immunoprecipitation in colon cancer cells. , 2007, Cancer research.

[82]  D. Zilberman,et al.  Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation , 2010, Science.

[83]  D. Ang,et al.  Mobile elements bounded by C4A4 telomeric repeats in oxytricha fallax , 1985, Cell.

[84]  Colin A. Johnson,et al.  Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex , 1998, Nature.

[85]  H. Cedar,et al.  G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis , 2006, Nature Cell Biology.

[86]  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.

[87]  W. Reik,et al.  Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation , 2011, Nature.

[88]  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.

[89]  A. Mégarbané,et al.  Heterochromatic Genes Undergo Epigenetic Changes and Escape Silencing in Immunodeficiency, Centromeric Instability, Facial Anomalies (ICF) Syndrome , 2011, PloS one.

[90]  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.

[91]  W. Reik,et al.  5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. , 2011, Nature communications.

[92]  Yi Zhang,et al.  Active DNA demethylation: many roads lead to Rome , 2010, Nature Reviews Molecular Cell Biology.

[93]  S. Baylin,et al.  DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci , 2000, Nature Genetics.

[94]  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.