N 6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

[1]  L. Aravind,et al.  DNA Methylation on N6-Adenine in C. elegans , 2015, Cell.

[2]  Tao Pan,et al.  High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing. , 2015, Angewandte Chemie.

[3]  Gideon Rechavi,et al.  Gene expression regulation mediated through reversible m6A RNA methylation , 2014, Nature Reviews Genetics.

[4]  D. Zilberman,et al.  Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes , 2014, Cell.

[5]  Wesley R. Legant,et al.  Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells , 2014, Cell.

[6]  Zachary D. Smith,et al.  DNA methylation: roles in mammalian development , 2013, Nature Reviews Genetics.

[7]  Gideon Rechavi,et al.  Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing , 2013, Nature Protocols.

[8]  Tyson A. Clark,et al.  Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing , 2012, Nature Biotechnology.

[9]  Richard J. Roberts,et al.  The methylomes of six bacteria , 2012, Nucleic acids research.

[10]  B. Pugh,et al.  ChIP‐exo Method for Identifying Genomic Location of DNA‐Binding Proteins with Near‐Single‐Nucleotide Accuracy , 2012, Current protocols in molecular biology.

[11]  O. Elemento,et al.  Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons , 2012, Cell.

[12]  Peter A. Jones Functions of DNA methylation: islands, start sites, gene bodies and beyond , 2012, Nature Reviews Genetics.

[13]  M. Kupiec,et al.  Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq , 2012, Nature.

[14]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[15]  Chengqi Yi,et al.  N6-Methyladenosine in Nuclear RNA is a Major Substrate of the Obesity-Associated FTO , 2011, Nature chemical biology.

[16]  Wen-Hsiung Li,et al.  Coordinated histone modifications are associated with gene expression variation within and between species. , 2011, Genome research.

[17]  B. Mueller‐Roeber,et al.  AN OPTIMIZED METHOD FOR THE ISOLATION OF NUCLEI FROM CHLAMYDOMONAS REINHARDTII (CHLOROPHYCEAE) 1 , 2011, Journal of phycology.

[18]  M. Pellegrini,et al.  Relationship between nucleosome positioning and DNA methylation , 2010, Nature.

[19]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

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

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

[22]  Robert E. Jinkerson,et al.  Genetic Engineering of Algae for Enhanced Biofuel Production , 2010, Eukaryotic Cell.

[23]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[24]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[25]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[26]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[27]  Ovidiu Ruecker,et al.  Strategies to facilitate transgene expression in Chlamydomonas reinhardtii , 2009, Planta.

[28]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[29]  R. Lister,et al.  Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis , 2008, Cell.

[30]  Y. Matsui,et al.  Epigenetic events in mammalian germ-cell development: reprogramming and beyond , 2008, Nature Reviews Genetics.

[31]  Lucy Shapiro,et al.  A DNA methylation ratchet governs progression through a bacterial cell cycle , 2007, Proceedings of the National Academy of Sciences.

[32]  Sara L. Zimmer,et al.  The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions , 2007, Science.

[33]  Adrian Bird,et al.  Perceptions of epigenetics , 2007, Nature.

[34]  D. Wion,et al.  N6-methyl-adenine: an epigenetic signal for DNA–protein interactions , 2006, Nature Reviews Microbiology.

[35]  François Berger,et al.  N6-methyladenine: the other methylated base of DNA. , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[36]  M. Schroda,et al.  Analysis of Chromatin Structure in the Control Regions of the Chlamydomonas HSP70A and RBCS2 Genes , 2005, Plant Molecular Biology.

[37]  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.

[38]  D. M. Krylov,et al.  Genome-Wide Annotation and Expression Profiling of Cell Cycle Regulatory Genes in Chlamydomonas reinhardtii1[w] , 2005, Plant Physiology.

[39]  D. Low,et al.  Roles of DNA Adenine Methylation in Regulating Bacterial Gene Expression and Virulence , 2001, Infection and Immunity.

[40]  W. Mages,et al.  A link between DNA methylation and epigenetic silencing in transgenic Volvox carteri. , 2001, Nucleic acids research.

[41]  H. Cerutti,et al.  Epigenetic silencing of a foreign gene in nuclear transformants of Chlamydomonas. , 1997, The Plant cell.

[42]  J. Rogers,et al.  Comparison of the effects of N6-methyldeoxyadenosine and N5-methyldeoxycytosine on transcription from nuclear gene promoters in barley. , 1995, The Plant journal : for cell and molecular biology.

[43]  Nancy Kleckner,et al.  SeqA: A negative modulator of replication initiation in E. coli , 1994, Cell.

[44]  J. V. Van Etten,et al.  Characterization of Chlorella virus PBCV-1 CviAII restriction and modification system. , 1992, Nucleic acids research.

[45]  W. Messer,et al.  Timing and targeting: The biological functions of Dam methylation in E. coli , 1988, Cell.

[46]  N. Sternberg Evidence that adenine methylation influences DNA-protein interactions in Escherichia coli , 1985, Journal of bacteriology.

[47]  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.

[48]  S. Hattman,et al.  Comparative study of DNA methylation in three unicellular eucaryotes , 1978, Journal of bacteriology.

[49]  P. V. von Hippel,et al.  Effects of methylation on the stability of nucleic acid conformations. Studies at the polymer level. , 1978, The Journal of biological chemistry.

[50]  G. Vovis,et al.  Complementary action of restriction enzymes endo R-DpnI and Endo R-DpnII on bacteriophage f1 DNA. , 1977, Journal of molecular biology.

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

[52]  L. Aravind,et al.  Natural history of eukaryotic DNA methylation systems. , 2011, Progress in molecular biology and translational science.

[53]  F. Dilworth,et al.  Analysis of epigenetic modifications of chromatin at specific gene loci by native chromatin immunoprecipitation of nucleosomes isolated using hydroxyapatite chromatography , 2008, Nature Protocols.

[54]  M. Ehrlich,et al.  Chapter 10 Naturally Occurring Modified Nucleosides in DNA , 1990 .

[55]  P. Crain,et al.  Preparation and enzymatic hydrolysis of DNA and RNA for mass spectrometry. , 1990, Methods in enzymology.