Literature DB >> 20081358

Accurate sodium bisulfite sequencing in plants.

Ian R Henderson1, Simon R Chan, Xiaofeng Cao, Lianna Johnson, Steven E Jacobsen.   

Abstract

DNA cytosine methylation is a conserved epigenetic modification frequently correlating with transcriptional silencing in a wide variety of eukaryotic organisms. Sodium bisulfite treatment of DNA converts unmethylated cytosine to uracil, while 5-methylated cytosine is protected. We describe techniques that ensure reliable sequencing data following sodium bisulfite conversion and to avoid common pitfalls such as amplification of unconverted DNA and inclusion of sibling clones.

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Year:  2010        PMID： 20081358      PMCID： PMC2829377          DOI： 10.4161/epi.5.1.10560

Source DB:  PubMed          Journal:  Epigenetics        ISSN： 1559-2294            Impact factor:   4.528


  9 in total

1.  Hairpin-bisulfite PCR: assessing epigenetic methylation patterns on complementary strands of individual DNA molecules.

Authors:  Charles D Laird; Nicole D Pleasant; Aaron D Clark; Jessica L Sneeden; K M Anwarul Hassan; Nathan C Manley; Jay C Vary; Todd Morgan; R Scott Hansen; Reinhard Stöger
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-12       Impact factor: 11.205

2.  A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.

Authors:  M Frommer; L E McDonald; D S Millar; C M Collis; F Watt; G W Grigg; P L Molloy; C L Paul
Journal:  Proc Natl Acad Sci U S A       Date:  1992-03-01       Impact factor: 11.205

3.  Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.

Authors:  Xiaoyu Zhang; Junshi Yazaki; Ambika Sundaresan; Shawn Cokus; Simon W-L Chan; Huaming Chen; Ian R Henderson; Paul Shinn; Matteo Pellegrini; Steve E Jacobsen; Joseph R Ecker
Journal:  Cell       Date:  2006-08-31       Impact factor: 41.582

Review 4.  Epigenetic inheritance in plants.

Authors:  Ian R Henderson; Steven E Jacobsen
Journal:  Nature       Date:  2007-05-24       Impact factor: 49.962

5.  Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases.

Authors:  M McClelland; M Nelson; E Raschke
Journal:  Nucleic Acids Res       Date:  1994-09       Impact factor: 16.971

6.  Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.

Authors:  Daniel Zilberman; Mary Gehring; Robert K Tran; Tracy Ballinger; Steven Henikoff
Journal:  Nat Genet       Date:  2006-11-26       Impact factor: 38.330

7.  Highly integrated single-base resolution maps of the epigenome in Arabidopsis.

Authors:  Ryan Lister; Ronan C O'Malley; Julian Tonti-Filippini; Brian D Gregory; Charles C Berry; A Harvey Millar; Joseph R Ecker
Journal:  Cell       Date:  2008-05-02       Impact factor: 41.582

8.  High sensitivity mapping of methylated cytosines.

Authors:  S J Clark; J Harrison; C L Paul; M Frommer
Journal:  Nucleic Acids Res       Date:  1994-08-11       Impact factor: 16.971

9.  Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.

Authors:  Shawn J Cokus; Suhua Feng; Xiaoyu Zhang; Zugen Chen; Barry Merriman; Christian D Haudenschild; Sriharsa Pradhan; Stanley F Nelson; Matteo Pellegrini; Steven E Jacobsen
Journal:  Nature       Date:  2008-02-17       Impact factor: 49.962
  9 in total
  26 in total

1.  Level of tissue differentiation influences the activation of a heat-inducible flower-specific system for genetic containment in poplar (Populus tremula L.).

Authors:  Hans Hoenicka; Denise Lehnhardt; Suneetha Nunna; Richard Reinhardt; Albert Jeltsch; Valentina Briones; Matthias Fladung
Journal:  Plant Cell Rep       Date:  2015-10-31       Impact factor: 4.570

2.  DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis.

Authors:  Nataliya E Yelina; Christophe Lambing; Thomas J Hardcastle; Xiaohui Zhao; Bruno Santos; Ian R Henderson
Journal:  Genes Dev       Date:  2015-10-15       Impact factor: 11.361

3.  Reconstructing de novo silencing of an active plant retrotransposon.

Authors:  Arturo Marí-Ordóñez; Antonin Marchais; Mathilde Etcheverry; Antoine Martin; Vincent Colot; Olivier Voinnet
Journal:  Nat Genet       Date:  2013-07-14       Impact factor: 38.330

4.  Accurate CpG and non-CpG cytosine methylation analysis by high-throughput locus-specific pyrosequencing in plants.

Authors:  Alexandre How-Kit; Antoine Daunay; Nicolas Mazaleyrat; Florence Busato; Christian Daviaud; Emeline Teyssier; Jean-François Deleuze; Philippe Gallusci; Jörg Tost
Journal:  Plant Mol Biol       Date:  2015-06-14       Impact factor: 4.076

5.  Retroelements and DNA Methylation Could Contribute to Diversity of 5S rDNA in Agave L.

Authors:  Y J Tamayo-Ordóñez; J A Narváez-Zapata; M C Tamayo-Ordóñez; L F Sánchez-Teyer
Journal:  J Mol Evol       Date:  2018-07-10       Impact factor: 2.395

6.  Expression analysis and promoter methylation under osmotic and salinity stress of TaGAPC1 in wheat (Triticum aestivum L).

Authors:  Ying Fei; Yuanxia Xue; Peixiu Du; Shushen Yang; Xiping Deng
Journal:  Protoplasma       Date:  2016-08-03       Impact factor: 3.356

7.  Determination of DNA methylation of imprinted genes in Arabidopsis endosperm.

Authors:  Matthew Rea; Ming Chen; Shan Luan; Drutdaman Bhangu; Max Braud; Wenyan Xiao
Journal:  J Vis Exp       Date:  2011-01-28       Impact factor: 1.355

Review 8.  High-throughput approaches for plant epigenomic studies.

Authors:  Robert J Schmitz; Xiaoyu Zhang
Journal:  Curr Opin Plant Biol       Date:  2011-04-04       Impact factor: 7.834

9.  Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs.

Authors:  Padubidri V Shivaprasad; Ruth M Dunn; Bruno Acm Santos; Andrew Bassett; David C Baulcombe
Journal:  EMBO J       Date:  2011-12-16       Impact factor: 11.598

10.  DNA Methylation Influences the Expression of DICER-LIKE4 Isoforms, Which Encode Proteins of Alternative Localization and Function.

Authors:  Nathan Pumplin; Alexis Sarazin; Pauline E Jullien; Nicolas G Bologna; Stefan Oberlin; Olivier Voinnet
Journal:  Plant Cell       Date:  2016-11-14       Impact factor: 11.277
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