Patterns of population epigenomic diversity

被引：423

作者：

Schmitz, Robert J. ^{[1
,2
]}

Schultz, Matthew D. ^{[2
,3
]}

Urich, Mark A. ^{[1
,2
]}

Nery, Joseph R. ^{[2
]}

Pelizzola, Mattia ^{[2
]}

Libiger, Ondrej ^{[4
,5
]}

Alix, Andrew ^{[1
]}

McCosh, Richard B. ^{[1
]}

Chen, Huaming ^{[2
]}

Schork, Nicholas J. ^{[4
,5
]}

Ecker, Joseph R. ^{[1
,2
,6
]}

机构：

[1] Salk Inst Biol Studies, Plant Biol Lab, La Jolla, CA 92037 USA

[2] Salk Inst Biol Studies, Genom Anal Lab, La Jolla, CA 92037 USA

[3] Univ Calif San Diego, Bioinformat Program, La Jolla, CA 92093 USA

[4] Scripps Res Inst, Scripps Translat Sci Inst, La Jolla, CA 92037 USA

[5] Scripps Res Inst, Dept Mol & Expt Med, La Jolla, CA 92037 USA

[6] Salk Inst Biol Studies, Howard Hughes Med Inst, La Jolla, CA 92037 USA

来源：

NATURE | 2013年 / 495卷 / 7440期

基金：

美国国家科学基金会;

关键词：

GENOME-WIDE ASSOCIATION; DNA METHYLATION; ARABIDOPSIS-THALIANA; EPIGENETIC MUTATION; NATURAL VARIATION; GENE; ELEMENTS; MODEL; DEMETHYLATION; PLANTS;

D O I：

10.1038/nature11968

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to such diversity, its interaction with genetic variation requires further investigation. Here we report population-wide DNA sequencing of genomes, transcriptomes and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are not linked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified thousands of methylation quantitative trait loci, which revealed the population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically activated in pollen and seeds, which facilitates proper development of these structures.

引用

页码：193 / 198

页数：6

共 37 条

[1] Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis [J].

Ahmed, Ikhlak ;

Sarazin, Alexis ;

Bowler, Chris ;

Colot, Vincent ;

Quesneville, Hadi .

NUCLEIC ACIDS RESEARCH, 2011, 39 (16) :6919-6931

[2] Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines [J].

Atwell, Susanna ;

Huang, Yu S. ;

Vilhjalmsson, Bjarni J. ;

Willems, Glenda ;

Horton, Matthew ;

Li, Yan ;

Meng, Dazhe ;

Platt, Alexander ;

Tarone, Aaron M. ;

Hu, Tina T. ;

Jiang, Rong ;

Muliyati, N. Wayan ;

Zhang, Xu ;

Amer, Muhammad Ali ;

Baxter, Ivan ;

Brachi, Benjamin ;

Chory, Joanne ;

Dean, Caroline ;

Debieu, Marilyne ;

de Meaux, Juliette ;

Ecker, Joseph R. ;

Faure, Nathalie ;

Kniskern, Joel M. ;

Jones, Jonathan D. G. ;

Michael, Todd ;

Nemri, Adnane ;

Roux, Fabrice ;

Salt, David E. ;

Tang, Chunlao ;

Todesco, Marco ;

Traw, M. Brian ;

Weigel, Detlef ;

Marjoram, Paul ;

Borevitz, Justin O. ;

Bergelson, Joy ;

Nordborg, Magnus .

NATURE, 2010, 465 (7298) :627-631

[3] Spontaneous epigenetic variation in the Arabidopsis thaliana methylome [J].

Becker, Claude ;

Hagmann, Joerg ;

Mueller, Jonas ;

Koenig, Daniel ;

Stegle, Oliver ;

Borgwardt, Karsten ;

Weigel, Detlef .

NATURE, 2011, 480 (7376) :245-U127

[4] EPIGENETIC CONTROL OF AN ENDOGENOUS GENE FAMILY IS REVEALED BY A NOVEL BLUE FLUORESCENT MUTANT OF ARABIDOPSIS [J].

BENDER, J ;

FINK, GR .

CELL, 1995, 83 (05) :725-734

[5] Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA [J].

Calarco, Joseph P. ;

Borges, Filipe ;

Donoghue, Mark T. A. ;

Van Ex, Frederic ;

Jullien, Pauline E. ;

Lopes, Telma ;

Gardner, Rui ;

Berger, Frederic ;

Feijo, Jose A. ;

Becker, Joerg D. ;

Martienssen, Robert A. .

CELL, 2012, 151 (01) :194-205

[6] Whole-genome sequencing of multiple Arabidopsis thaliana populations [J].

Cao, Jun ;

Schneeberger, Korbinian ;

Ossowski, Stephan ;

Guenther, Torsten ;

Bender, Sebastian ;

Fitz, Joffrey ;

Koenig, Daniel ;

Lanz, Christa ;

Stegle, Oliver ;

Lippert, Christoph ;

Wang, Xi ;

Ott, Felix ;

Mueller, Jonas ;

Alonso-Blanco, Carlos ;

Borgwardt, Karsten ;

Schmid, Karl J. ;

Weigel, Detlef .

NATURE GENETICS, 2011, 43 (10) :956-U60

[7] Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana [J].

Clark, Richard M. ;

Schweikert, Gabriele ;

Toomajian, Christopher ;

Ossowski, Stephan ;

Zeller, Georg ;

Shinn, Paul ;

Warthmann, Norman ;

Hu, Tina T. ;

Fu, Glenn ;

Hinds, David A. ;

Chen, Huaming ;

Frazer, Kelly A. ;

Huson, Daniel H. ;

Schoelkopf, Bernhard ;

Nordborg, Magnus ;

Raetsch, Gunnar ;

Ecker, Joseph R. ;

Weigel, Detlef .

SCIENCE, 2007, 317 (5836) :338-342

[8] An epigenetic mutation responsible for natural variation in floral symmetry [J].

Cubas, P ;

Vincent, C ;

Coen, E .

NATURE, 1999, 401 (6749) :157-161

[9] Widespread dynamic DNA methylation in response to biotic stress [J].

Dowen, Robert H. ;

Pelizzola, Mattia ;

Schmitz, Robert J. ;

Lister, Ryan ;

Dowen, Jill M. ;

Nery, Joseph R. ;

Dixon, Jack E. ;

Ecker, Joseph R. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (32) :E2183-E2191

[10] Conservation and divergence of methylation patterning in plants and animals [J].

Feng, Suhua ;

Cokus, Shawn J. ;

Zhang, Xiaoyu ;

Chen, Pao-Yang ;

Bostick, Magnolia ;

Goll, Mary G. ;

Hetzel, Jonathan ;

Jain, Jayati ;

Strauss, Steven H. ;

Halpern, Marnie E. ;

Ukomadu, Chinweike ;

Sadler, Kirsten C. ;

Pradhan, Sriharsa ;

Pellegrini, Matteo ;

Jacobsen, Steven E. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (19) :8689-8694

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