Literature DB >> 23313553

Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.

Hume Stroud1, Maxim V C Greenberg, Suhua Feng, Yana V Bernatavichute, Steven E Jacobsen.   

Abstract

Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome largely remain unknown. Here we have surveyed the methylomes of a comprehensive list of 86 Arabidopsis gene silencing mutants by generating single-nucleotide resolution maps of DNA methylation. We find that DNA methylation is site specifically regulated by different factors. Furthermore, we have identified additional regulators of DNA methylation. These data and analyses will serve as a comprehensive community resource for further understanding the control of DNA methylation patterning.
Copyright © 2013 Elsevier Inc. All rights reserved.

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Year:  2013        PMID: 23313553      PMCID: PMC3597350          DOI: 10.1016/j.cell.2012.10.054

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  56 in total

1.  Conservation and divergence of methylation patterning in plants and animals.

Authors:  Suhua Feng; Shawn J Cokus; Xiaoyu Zhang; Pao-Yang Chen; Magnolia Bostick; Mary G Goll; Jonathan Hetzel; Jayati Jain; Steven H Strauss; Marnie E Halpern; Chinweike Ukomadu; Kirsten C Sadler; Sriharsa Pradhan; Matteo Pellegrini; Steven E Jacobsen
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-15       Impact factor: 11.205

Review 2.  Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing.

Authors:  Jeremy R Haag; Craig S Pikaard
Journal:  Nat Rev Mol Cell Biol       Date:  2011-07-22       Impact factor: 94.444

3.  Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.

Authors:  Gary C Hon; R David Hawkins; Otavia L Caballero; Christine Lo; Ryan Lister; Mattia Pelizzola; Armand Valsesia; Zhen Ye; Samantha Kuan; Lee E Edsall; Anamaria Aranha Camargo; Brian J Stevenson; Joseph R Ecker; Vineet Bafna; Robert L Strausberg; Andrew J Simpson; Bing Ren
Journal:  Genome Res       Date:  2011-12-07       Impact factor: 9.043

4.  Arabidopsis Histone Lysine Methyltransferases.

Authors:  Frédéric Pontvianne; Todd Blevins; Craig S Pikaard
Journal:  Adv Bot Res       Date:  2010-01-01       Impact factor: 2.175

5.  Functional genomic analysis of CAF-1 mutants in Arabidopsis thaliana.

Authors:  Nicole Schönrock; Vivien Exner; Aline Probst; Wilhelm Gruissem; Lars Hennig
Journal:  J Biol Chem       Date:  2006-02-01       Impact factor: 5.157

6.  Determining DNA methylation profiles using sequencing.

Authors:  Suhua Feng; Liudmilla Rubbi; Steven E Jacobsen; Matteo Pellegrini
Journal:  Methods Mol Biol       Date:  2011

7.  Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana.

Authors:  Lin Xu; Zhong Zhao; Aiwu Dong; Ludivine Soubigou-Taconnat; Jean-Pierre Renou; Andre Steinmetz; Wen-Hui Shen
Journal:  Mol Cell Biol       Date:  2007-12-10       Impact factor: 4.272

8.  Maintenance of genomic methylation requires a SWI2/SNF2-like protein.

Authors:  J A Jeddeloh; T L Stokes; E J Richards
Journal:  Nat Genet       Date:  1999-05       Impact factor: 38.330

9.  ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing.

Authors:  Yannick Jacob; Suhua Feng; Chantal A LeBlanc; Yana V Bernatavichute; Hume Stroud; Shawn Cokus; Lianna M Johnson; Matteo Pellegrini; Steven E Jacobsen; Scott D Michaels
Journal:  Nat Struct Mol Biol       Date:  2009-06-07       Impact factor: 15.369

10.  Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana.

Authors:  Yana V Bernatavichute; Xiaoyu Zhang; Shawn Cokus; Matteo Pellegrini; Steven E Jacobsen
Journal:  PLoS One       Date:  2008-09-08       Impact factor: 3.240

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  374 in total

1.  HISTONE DEACETYLASE6 Acts in Concert with Histone Methyltransferases SUVH4, SUVH5, and SUVH6 to Regulate Transposon Silencing.

Authors:  Chun-Wei Yu; Ready Tai; Shen-Chi Wang; Ping Yang; Ming Luo; Songguang Yang; Kai Cheng; Wen-Chun Wang; Yi-Sheng Cheng; Keqiang Wu
Journal:  Plant Cell       Date:  2017-08-04       Impact factor: 11.277

Review 2.  DNA methylation pathways and their crosstalk with histone methylation.

Authors:  Jiamu Du; Lianna M Johnson; Steven E Jacobsen; Dinshaw J Patel
Journal:  Nat Rev Mol Cell Biol       Date:  2015-09       Impact factor: 94.444

3.  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

4.  A Dicer-Independent Route for Biogenesis of siRNAs that Direct DNA Methylation in Arabidopsis.

Authors:  Ruiqiang Ye; Zulong Chen; Bi Lian; M Jordan Rowley; Ning Xia; Jijie Chai; Yan Li; Xin-Jian He; Andrzej T Wierzbicki; Yijun Qi
Journal:  Mol Cell       Date:  2015-12-17       Impact factor: 17.970

5.  Dicer-independent RNA-directed DNA methylation in Arabidopsis.

Authors:  Dong-Lei Yang; Guiping Zhang; Kai Tang; Jingwen Li; Lan Yang; Huan Huang; Heng Zhang; Jian-Kang Zhu
Journal:  Cell Res       Date:  2015-12-08       Impact factor: 25.617

6.  Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression.

Authors:  Jie Zhang; Yuan Liu; En-Hua Xia; Qiu-Yang Yao; Xiang-Dong Liu; Li-Zhi Gao
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-30       Impact factor: 11.205

7.  Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses.

Authors:  Pankaj Barah; Mahantesha Naika B N; Naresh Doni Jayavelu; Ramanathan Sowdhamini; Khader Shameer; Atle M Bones
Journal:  Nucleic Acids Res       Date:  2015-12-17       Impact factor: 16.971

8.  Establishing epigenetic variation during genome reprogramming.

Authors:  Filipe Borges; Robert A Martienssen
Journal:  RNA Biol       Date:  2013-04       Impact factor: 4.652

9.  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

10.  New discoveries generate new questions about RNA-directed DNA methylation in Arabidopsis.

Authors:  Huiming Zhang; Jian-Kang Zhu
Journal:  Natl Sci Rev       Date:  2017-03-28       Impact factor: 17.275

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