Literature DB >> 19273618

Finding the fifth base: genome-wide sequencing of cytosine methylation.

Ryan Lister1, Joseph R Ecker.   

Abstract

Complete sequences of myriad eukaryotic genomes, including several human genomes, are now available, and recent dramatic developments in DNA sequencing technology are opening the floodgates to vast volumes of sequence data. Yet, despite knowing for several decades that a significant proportion of cytosines in the genomes of plants and animals are present in the form of methylcytosine, until very recently the precise locations of these modified bases have never been accurately mapped throughout a eukaryotic genome. Advanced "next-generation" DNA sequencing technologies are now enabling the global mapping of this epigenetic modification at single-base resolution, providing new insights into the regulation and dynamics of DNA methylation in genomes.

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Year:  2009        PMID: 19273618      PMCID: PMC3807530          DOI: 10.1101/gr.083451.108

Source DB:  PubMed          Journal:  Genome Res        ISSN: 1088-9051            Impact factor:   9.043


  72 in total

1.  Comprehensive high-throughput arrays for relative methylation (CHARM).

Authors:  Rafael A Irizarry; Christine Ladd-Acosta; Benilton Carvalho; Hao Wu; Sheri A Brandenburg; Jeffrey A Jeddeloh; Bo Wen; Andrew P Feinberg
Journal:  Genome Res       Date:  2008-03-03       Impact factor: 9.043

2.  Fixing the front end.

Authors:  Ken Garber
Journal:  Nat Biotechnol       Date:  2008-10       Impact factor: 54.908

Review 3.  Next-generation DNA sequencing methods.

Authors:  Elaine R Mardis
Journal:  Annu Rev Genomics Hum Genet       Date:  2008       Impact factor: 8.929

4.  Evidence for an instructive mechanism of de novo methylation in cancer cells.

Authors:  Ilana Keshet; Yeshayahu Schlesinger; Shlomit Farkash; Eyal Rand; Merav Hecht; Eran Segal; Eli Pikarski; Richard A Young; Alain Niveleau; Howard Cedar; Itamar Simon
Journal:  Nat Genet       Date:  2006-02       Impact factor: 38.330

5.  Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation.

Authors:  Da Jia; Renata Z Jurkowska; Xing Zhang; Albert Jeltsch; Xiaodong Cheng
Journal:  Nature       Date:  2007-08-22       Impact factor: 49.962

6.  A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

Authors:  Thomas A Down; Vardhman K Rakyan; Daniel J Turner; Paul Flicek; Heng Li; Eugene Kulesha; Stefan Gräf; Nathan Johnson; Javier Herrero; Eleni M Tomazou; Natalie P Thorne; Liselotte Bäckdahl; Marlis Herberth; Kevin L Howe; David K Jackson; Marcos M Miretti; John C Marioni; Ewan Birney; Tim J P Hubbard; Richard Durbin; Simon Tavaré; Stephan Beck
Journal:  Nat Biotechnol       Date:  2008-07       Impact factor: 54.908

7.  ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase.

Authors:  Zhizhong Gong; Teresa Morales-Ruiz; Rafael R Ariza; Teresa Roldán-Arjona; Lisa David; Jian Kang Zhu
Journal:  Cell       Date:  2002-12-13       Impact factor: 41.582

Review 8.  The methylome: approaches for global DNA methylation profiling.

Authors:  Stephan Beck; Vardhman K Rakyan
Journal:  Trends Genet       Date:  2008-03-05       Impact factor: 11.639

9.  Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells.

Authors:  Madeleine P Ball; Jin Billy Li; Yuan Gao; Je-Hyuk Lee; Emily M LeProust; In-Hyun Park; Bin Xie; George Q Daley; George M Church
Journal:  Nat Biotechnol       Date:  2009-03-29       Impact factor: 54.908

10.  DNA methylation profiling of human chromosomes 6, 20 and 22.

Authors:  Florian Eckhardt; Joern Lewin; Rene Cortese; Vardhman K Rakyan; John Attwood; Matthias Burger; John Burton; Tony V Cox; Rob Davies; Thomas A Down; Carolina Haefliger; Roger Horton; Kevin Howe; David K Jackson; Jan Kunde; Christoph Koenig; Jennifer Liddle; David Niblett; Thomas Otto; Roger Pettett; Stefanie Seemann; Christian Thompson; Tony West; Jane Rogers; Alex Olek; Kurt Berlin; Stephan Beck
Journal:  Nat Genet       Date:  2006-10-29       Impact factor: 38.330

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  146 in total

1.  Identification of epigenetic DNA modifications with a protein nanopore.

Authors:  Emma V B Wallace; David Stoddart; Andrew J Heron; Ellina Mikhailova; Giovanni Maglia; Timothy J Donohoe; Hagan Bayley
Journal:  Chem Commun (Camb)       Date:  2010-10-06       Impact factor: 6.222

Review 2.  DNA methylation topology: potential of a chromatin landmark for epigenetic drug toxicology.

Authors:  Jian Tajbakhsh
Journal:  Epigenomics       Date:  2011-12       Impact factor: 4.778

Review 3.  Proteomic investigation of epigenetics in neuropsychiatric disorders: a missing link between genetics and behavior?

Authors:  Mariana D Plazas-Mayorca; Kent E Vrana
Journal:  J Proteome Res       Date:  2010-09-09       Impact factor: 4.466

Review 4.  Conservation and divergence in eukaryotic DNA methylation.

Authors:  Tzuu-Fen Lee; Jixian Zhai; Blake C Meyers
Journal:  Proc Natl Acad Sci U S A       Date:  2010-05-10       Impact factor: 11.205

5.  Conservation and divergence of DNA methylation in eukaryotes: new insights from single base-resolution DNA methylomes.

Authors:  Zhixi Su; Leng Han; Zhongming Zhao
Journal:  Epigenetics       Date:  2011-02-01       Impact factor: 4.528

Review 6.  Integrative systems biology: an attempt to describe a simple weed.

Authors:  Louisa M Liberman; Rosangela Sozzani; Philip N Benfey
Journal:  Curr Opin Plant Biol       Date:  2012-01-23       Impact factor: 7.834

7.  A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences.

Authors:  Evgenia N Nikolova; Robyn L Stanfield; H Jane Dyson; Peter E Wright
Journal:  Biochemistry       Date:  2020-05-12       Impact factor: 3.162

8.  Locus- and cell type-specific epigenetic switching during cellular differentiation in mammals.

Authors:  Ying-Tao Zhao; Maria Fasolino; Zhaolan Zhou
Journal:  Front Biol (Beijing)       Date:  2016-07-18

9.  CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso.

Authors:  Evgenia N Nikolova; Robyn L Stanfield; H Jane Dyson; Peter E Wright
Journal:  Biochemistry       Date:  2018-03-26       Impact factor: 3.162

Review 10.  DNA methylation of cancer genome.

Authors:  Hoi-Hung Cheung; Tin-Lap Lee; Owen M Rennert; Wai-Yee Chan
Journal:  Birth Defects Res C Embryo Today       Date:  2009-12
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