Genome-wide approaches to studying chromatin modifications

[1]  R. Durbin,et al.  Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P

, 2022 .

[2]  Istvan Albert,et al.  GeneTrack - a genomic data processing and visualization framework , 2008, Bioinform..

[3]  Ruiqiang Li,et al.  SOAP: short oligonucleotide alignment program , 2008, Bioinform..

[4]  Michael Q. Zhang,et al.  Using quality scores and longer reads improves accuracy of Solexa read mapping , 2008, BMC Bioinformatics.

[5]  Haruhiko Koseki,et al.  Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells , 2007, Nature Cell Biology.

[6]  Z. Xuan,et al.  Genome-wide in situ exon capture for selective resequencing , 2007, Nature Genetics.

[7]  Response: Mapping Nucleosome Positions Using ChIP-Seq Data , 2007, Cell.

[8]  Philipp Bucher,et al.  ChIP-Seq Data Reveal Nucleosome Architecture of Human Promoters , 2007, Cell.

[9]  Steven Henikoff,et al.  Genome-wide analysis of DNA methylation patterns , 2007, Development.

[10]  Ronald W. Davis,et al.  A high-resolution atlas of nucleosome occupancy in yeast , 2007, Nature Genetics.

[11]  Xiaole Shirley Liu,et al.  Getting Started in Tiling Microarray Analysis , 2007, PLoS Comput. Biol..

[12]  Li Zhang,et al.  Genome-Wide Profiling of DNA Methylation Reveals a Class of Normally Methylated CpG Island Promoters , 2007, PLoS genetics.

[13]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[14]  William Stafford Noble,et al.  Nucleosome positioning signals in genomic DNA. , 2007, Genome research.

[15]  Jane M J Lin,et al.  Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome , 2007, PLoS genetics.

[16]  R. Young,et al.  A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells , 2007, Cell.

[17]  Howard Y. Chang,et al.  Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.

[18]  C. Jin,et al.  Nucleosome stability mediated by histone variants H3.3 and H2A.Z. , 2007, Genes & development.

[19]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[20]  Allen D. Delaney,et al.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing , 2007, Nature Methods.

[21]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[22]  V. Iyer,et al.  FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. , 2007, Genome research.

[23]  Shane C. Dillon,et al.  The landscape of histone modifications across 1% of the human genome in five human cell lines. , 2007, Genome research.

[24]  S. Grewal,et al.  Transcription and RNA interference in the formation of heterochromatin , 2007, Nature.

[25]  A. Feinberg.  Phenotypic plasticity and the epigenetics of human disease , 2007, Nature.

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

[27]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[28]  Thomas Lengauer,et al.  CpG Island Mapping by Epigenome Prediction , 2007, PLoS Comput. Biol..

[29]  Mark Ptashne,et al.  On the use of the word ‘epigenetic’ , 2007, Current Biology.

[30]  Philippe Collas,et al.  Q2ChIP, a Quick and Quantitative Chromatin Immunoprecipitation Assay, Unravels Epigenetic Dynamics of Developmentally Regulated Genes in Human Carcinoma Cells , 2007, Stem cells.

[31]  M. Esteller.  Cancer epigenomics: DNA methylomes and histone-modification maps , 2007, Nature Reviews Genetics.

[32]  I. Albert,et al.  Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome , 2007, Nature.

[33]  S. Henikoff,et al.  Histone Replacement Marks the Boundaries of cis-Regulatory Domains , 2007, Science.

[34]  Michael B. Stadler,et al.  Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome , 2007, Nature Genetics.

[35]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[36]  Bing Li,et al.  The Role of Chromatin during Transcription , 2007, Cell.

[37]  C. Allis,et al.  Epigenetics: A Landscape Takes Shape , 2007, Cell.

[38]  E. Lander,et al.  The Mammalian Epigenome , 2007, Cell.

[39]  T. Kouzarides.  Chromatin Modifications and Their Function , 2007, Cell.

[40]  T. Cremer,et al.  Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions , 2007, Nature Reviews Genetics.

[41]  Jun S. Song,et al.  High-throughput mapping of the chromatin structure of human promoters , 2007, Nature Biotechnology.

[42]  Keji Zhao,et al.  Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. , 2006, Genome research.

[43]  C. Jin,et al.  Nucleosome stability mediated by histone variants H 3 . 3 and H 2 , 2007 .

[44]  S. Henikoff,et al.  Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription , 2007, Nature Genetics.

[45]  Steven M. Johnson,et al.  Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. , 2006, Genome research.

[46]  B. Steensel,et al.  Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C) , 2006, Nature Genetics.

[47]  K. Sandhu,et al.  Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions , 2006, Nature Genetics.

[48]  J. Rogers,et al.  DNA methylation profiling of human chromosomes 6, 20 and 22 , 2006, Nature Genetics.

[49]  Suresh Cuddapah,et al.  The genomic landscape of histone modifications in human T cells , 2006, Proceedings of the National Academy of Sciences.

[50]  C. Nusbaum,et al.  Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. , 2006, Genome research.

[51]  M. Pellegrini,et al.  Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis , 2006, Cell.

[52]  Michael Q. Zhang,et al.  Bioinformatics Original Paper Predicting Methylation Status of Cpg Islands in the Human Brain , 2022 .

[53]  I. Albert,et al.  Nucleosome positions predicted through comparative genomics , 2006, Nature Genetics.

[54]  Tae Hoon Kim,et al.  Genome-wide analysis of protein-DNA interactions. , 2006, Annual review of genomics and human genetics.

[55]  Irene K. Moore,et al.  A genomic code for nucleosome positioning , 2006, Nature.

[56]  Clifford A. Meyer,et al.  Model-based analysis of tiling-arrays for ChIP-chip , 2006, Proceedings of the National Academy of Sciences.

[57]  L. Gaudreau,et al.  Reuniting the contrasting functions of H2A.Z. , 2006, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[58]  J. Lieb,et al.  Cell Cycle–Specified Fluctuation of Nucleosome Occupancy at Gene Promoters , 2006, PLoS genetics.

[59]  Kenny Q. Ye,et al.  Comparative isoschizomer profiling of cytosine methylation: the HELP assay. , 2006, Genome research.

[60]  Michael Q. Zhang,et al.  Computational prediction of methylation status in human genomic sequences. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[61]  T. Wolfsberg,et al.  DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays , 2006, Nature Methods.

[62]  Henriette O'Geen,et al.  Suz12 binds to silenced regions of the genome in a cell-type-specific manner. , 2006, Genome research.

[63]  B. Turner,et al.  Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations , 2006, Nature Genetics.

[64]  J. Zeitlinger,et al.  Polycomb complexes repress developmental regulators in murine embryonic stem cells , 2006, Nature.

[65]  Megan F. Cole,et al.  Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells , 2006, Cell.

[66]  James A. Cuff,et al.  A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells , 2006, Cell.

[67]  Alberto Riva,et al.  START: an automated tool for serial analysis of chromatin occupancy data , 2006, Bioinform..

[68]  Wei Jiang,et al.  High-throughput DNA methylation profiling using universal bead arrays. , 2006, Genome research.

[69]  M. Fraga,et al.  The Polycomb group protein EZH2 directly controls DNA methylation , 2006, Nature.

[70]  I. Simon,et al.  Evidence for an instructive mechanism of de novo methylation in cancer cells , 2006, Nature Genetics.

[71]  Thomas Lengauer,et al.  CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure , 2006, PLoS genetics.

[72]  Z. Weng,et al.  A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome , 2006, Cell.

[73]  Michael Q. Zhang,et al.  Large-scale structure of genomic methylation patterns. , 2005, Genome research.

[74]  M. Daly,et al.  Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). , 2005, Genome research.

[75]  J. Workman,et al.  Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[76]  Mathieu Blanchette,et al.  Variant Histone H2A.Z Is Globally Localized to the Promoters of Inactive Yeast Genes and Regulates Nucleosome Positioning , 2005, PLoS biology.

[77]  S. Schreiber,et al.  Histone Variant H2A.Z Marks the 5′ Ends of Both Active and Inactive Genes in Euchromatin , 2005, Cell.

[78]  B. Cairns,et al.  Genome-Wide Dynamics of Htz1, a Histone H2A Variant that Poises Repressed/Basal Promoters for Activation through Histone Loss , 2005, Cell.

[79]  A. Gnirke,et al.  Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis , 2005, Nucleic acids research.

[80]  Wing Hung Wong,et al.  TileMap: create chromosomal map of tiling array hybridizations , 2005, Bioinform..

[81]  S. Henikoff,et al.  Genome-scale profiling of histone H3.3 replacement patterns , 2005, Nature Genetics.

[82]  N. Friedman,et al.  Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae , 2005, PLoS biology.

[83]  Megan F. Cole,et al.  Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast , 2005, Cell.

[84]  Leah Barrera,et al.  A high-resolution map of active promoters in the human genome , 2005, Nature.

[85]  Lani F. Wu,et al.  Genome-Scale Identification of Nucleosome Positions in S. cerevisiae , 2005, Science.

[86]  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.

[87]  T. Sugiyama,et al.  Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome , 2005, Nature Genetics.

[88]  R. Flavell,et al.  Interchromosomal associations between alternatively expressed loci , 2005, Nature.

[89]  Keji Zhao,et al.  Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. , 2005, Genes & development.

[90]  Martin Radolf,et al.  The profile of repeat‐associated histone lysine methylation states in the mouse epigenome , 2005, The EMBO journal.

[91]  Eric S. Lander,et al.  Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse , 2005, Cell.

[92]  J. Ecker,et al.  Applications of DNA tiling arrays for whole-genome analysis. , 2005, Genomics.

[93]  Gail Mandel,et al.  Defining the CREB Regulon A Genome-Wide Analysis of Transcription Factor Regulatory Regions , 2004, Cell.

[94]  Antony V. Cox,et al.  Open access, freely available online PLoS BIOLOGY DNA Methylation Profiling of the Human Major Histocompatibility Complex: A Pilot Study , 2022 .

[95]  I. Gut,et al.  De novo quantitative bisulfite sequencing using the pyrosequencing technology. , 2004, Analytical biochemistry.

[96]  Richard A Flavell,et al.  Long-range intrachromosomal interactions in the T helper type 2 cytokine locus , 2004, Nature Immunology.

[97]  Nick Gilbert,et al.  Chromatin Architecture of the Human Genome Gene-Rich Domains Are Enriched in Open Chromatin Fibers , 2004, Cell.

[98]  S. Schreiber,et al.  Global nucleosome occupancy in yeast , 2004, Genome Biology.

[99]  J. Lieb,et al.  Evidence for nucleosome depletion at active regulatory regions genome-wide , 2004, Nature Genetics.

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

[101]  David Landsman,et al.  High-resolution genome-wide mapping of histone modifications , 2004, Nature Biotechnology.

[102]  J. Minna,et al.  Global survey of chromatin accessibility using DNA microarrays. , 2004, Genome research.

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

[104]  Alice Young,et al.  Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[105]  M. Grunstein,et al.  Genomewide histone acetylation microarrays. , 2003, Methods.

[106]  Patrick O. Brown,et al.  Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[107]  S. Cross,et al.  The methylated component of the Neurospora crassa genome , 2003, Nature.

[108]  Hiten D. Madhani,et al.  Conserved Histone Variant H2A.Z Protects Euchromatin from the Ectopic Spread of Silent Heterochromatin , 2003, Cell.

[109]  Kevin Struhl,et al.  Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. , 2003, Molecular cell.

[110]  S. Schreiber,et al.  Signaling Network Model of Chromatin , 2002, Cell.

[111]  Ira M. Hall,et al.  Establishment and Maintenance of a Heterochromatin Domain , 2002, Science.

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

[113]  A. Sakurada,et al.  A microarray-based method for detecting methylated loci , 2002, Journal of Human Genetics.

[114]  Arkady B. Khodursky,et al.  Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[115]  Stuart L. Schreiber,et al.  Methylation of histone H3 Lys 4 in coding regions of active genes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[116]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[117]  Ioannis Xenarios,et al.  Microarray Deacetylation Maps Determine Genome-Wide Functions for Yeast Histone Deacetylases , 2002, Cell.

[118]  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.

[119]  Thomas D. Otto,et al.  Tumour class prediction and discovery by microarray-based DNA methylation analysis , 2002 .

[120]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[121]  Fabian Model,et al.  Tumour class prediction and discovery by microarray-based DNA methylation analysis. , 2001, Nucleic acids research.

[122]  P. Jeffrey,et al.  Regulation of Heterochromatic Silencing and Histone H 3 Lysine-9 Methylation by RNAi , 2002 .

[123]  Huidong Shi,et al.  Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. , 2002, Genome research.

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

[125]  C. M. Chen,et al.  Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. , 2001, Cancer research.

[126]  E. Selker,et al.  A histone H3 methyltransferase controls DNA methylation in Neurospora crassa , 2001, Nature.

[127]  K. Luger,et al.  Crystal structure of a nucleosome core particle containing the variant histone H2A.Z , 2000, Nature Structural Biology.

[128]  A. Wolffe,et al.  DNA methylation in health and disease , 2000, Nature Reviews Genetics.

[129]  B M Turner,et al.  Histone acetylation and an epigenetic code. , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[130]  Michael Q. Zhang,et al.  Large-scale human promoter mapping using CpG islands , 2000, Nature Genetics.

[131]  Shirley M. Tilghman,et al.  CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus , 2000, Nature.

[132]  P. Laird,et al.  MethyLight: a high-throughput assay to measure DNA methylation. , 2000, Nucleic acids research.

[133]  S. Elgin,et al.  The HP1 protein family: getting a grip on chromatin. , 2000, Current opinion in genetics & development.

[134]  J. Herman,et al.  DNA hypermethylation in tumorigenesis: epigenetics joins genetics. , 2000, Trends in genetics : TIG.

[135]  S. Henikoff,et al.  Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase , 2000, Nature Biotechnology.

[136]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[137]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[138]  A. West,et al.  The Protein CTCF Is Required for the Enhancer Blocking Activity of Vertebrate Insulators , 1999, Cell.

[139]  Nancy Kleckner,et al.  Cohesins Bind to Preferential Sites along Yeast Chromosome III, with Differential Regulation along Arms versus the Centric Region , 1999, Cell.

[140]  A. Bird,et al.  DNA methylation and chromatin modification. , 1999, Current opinion in genetics & development.

[141]  Peter A. Jones,et al.  Cancer-epigenetics comes of age , 1999, Nature Genetics.

[142]  A. Wolffe,et al.  Chromatin disruption and modification. , 1999, Nucleic acids research.

[143]  S Holmberg,et al.  Nucleosome structure of the yeast CHA1 promoter: analysis of activation‐dependent chromatin remodeling of an RNA‐polymerase‐II‐transcribed gene in TBP and RNA pol II mutants defective in vivo in response to acidic activators , 1998, The EMBO journal.

[144]  J. Herman,et al.  Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[145]  D. Lohr,et al.  GAL4/GAL80-dependent Nucleosome Disruption/Deposition on the Upstream Regions of the Yeast GAL1-10 and GAL80 Genes (*) , 1995, The Journal of Biological Chemistry.

[146]  Renato Paro,et al.  Mapping polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin , 1993, Cell.

[147]  A. Bird,et al.  Effects of DNA methylation on DNA-binding proteins and gene expression. , 1993, Current opinion in genetics & development.

[148]  C. Allis,et al.  Chromatin condensation: does histone H1 dephosphorylation play a role? , 1992, Trends in biochemical sciences.

[149]  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.

[150]  W. Hörz,et al.  A functional role for nucleosomes in the repression of a yeast promoter. , 1991, The EMBO journal.

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

[152]  H. Drew,et al.  Sequence periodicities in chicken nucleosome core DNA. , 1986, Journal of molecular biology.

[153]  A. Bird,et al.  Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis. , 1978, Journal of molecular biology.