Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Autoren

Taiji Kawakatsu
Shao-shan Carol Huang
Florian Jupe
Eriko Sasaki
Robert J Schmitz
Mark A Urich
Rosa Castanon
Joseph R Nery
Cesar Barragan
Yupeng He
Huaming Chen
Manu Dubin
Cheng-Ruei Lee
Congmao Wang
Felix Bemm
Claude Becker
Ryan O’Neil
Ronan C O’Malley
Danjuma X Quarless
Nicholas J Schork
Detlef Weigel
Magnus Nordborg
Joseph R Ecker
Carlos Alonso-Blanco
Jorge Andrade
Claude Becker
Felix Bemm
Joy Bergelson
Karsten Borgwardt
Eunyoung Chae
Todd Dezwaan
Wei Ding
Joseph R Ecker
Moisés Expósito-Alonso
Ashley Farlow
Joffrey Fitz
Xiangchao Gan
Dominik G Grimm
Angela Hancock
Stefan R Henz
Svante Holm
Matthew Horton
Mike Jarsulic
Randall A Kerstetter
Arthur Korte
Pamela Korte
Christa Lanz
Chen-Ruei Lee
Dazhe Meng
Todd P Michael
Richard Mott
Ni Wayan Muliyati
Thomas Nägele
Matthias Nagler
Viktoria Nizhynska
Magnus Nordborg
Polina Novikova
F Xavier Picó
Alexander Platzer
Fernando A Rabanal
Alex Rodriguez
Beth A Rowan
Patrice A Salomé
Karl Schmid
Robert J Schmitz
Ümit Seren
Felice Gianluca Sperone
Mitchell Sudkamp
Hannes Svardal
Matt M Tanzer
Donald Todd
Samuel L Volchenboum
Congmao Wang
George Wang
Xi Wang
Wolfram Weckwerth
Detlef Weigel
Xuefeng Zhou

DOI

10.1016/j.cell.2016.06.044

ISSN

0092-8674

Ausgabe der Veröffentlichung

2

Zeitschrift

Cell

Sprache

en

Paginierung

492 - 505

Datum der Veröffentlichung

2016

Status

Published

Herausgeber

Elsevier BV

Herausgeber URL

http://dx.doi.org/10.1016/j.cell.2016.06.044

Datum der Datenerfassung

2018

Titel

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Ausgabe der Zeitschrift

166

Datenquelle: Crossref

Abstract

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Addresses

Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.

Autoren

Taiji Kawakatsu
Shao-Shan Carol Huang
Florian Jupe
Eriko Sasaki
Robert J Schmitz
Mark A Urich
Rosa Castanon
Joseph R Nery
Cesar Barragan
Yupeng He
Huaming Chen
Manu Dubin
Cheng-Ruei Lee
Congmao Wang
Felix Bemm
Claude Becker
Ryan O'Neil
Ronan C O'Malley
Danjuma X Quarless
1001 Genomes Consortium
Nicholas J Schork
Detlef Weigel
Magnus Nordborg
Joseph R Ecker

DOI

10.1016/j.cell.2016.06.044

eISSN

1097-4172

Externe Identifier

PubMed Identifier: 27419873
PubMed Central ID: PMC5172462

Funding acknowledgements

Austrian Science Fund FWF: W 1225
Howard Hughes Medical Institute:
NIGMS NIH HHS: R00 GM100000

Open access

false

ISSN

0092-8674

Ausgabe der Veröffentlichung

2

Zeitschrift

Cell

Schlüsselwörter

1001 Genomes Consortium
Arabidopsis
DNA Methylation
Epigenesis, Genetic
Gene Expression Regulation, Plant
Genome, Plant
Epigenomics
Transcriptome

Sprache

eng

Medium

Print

Paginierung

492 - 505

Datum der Veröffentlichung

2016

Status

Published

Datum der Datenerfassung

2016

Titel

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

Sub types

research-article
Research Support, U.S. Gov't, Non-P.H.S.
Journal Article
Research Support, N.I.H., Extramural

Ausgabe der Zeitschrift

166

Files

http://www.cell.com/article/S0092867416308522/pdf https://europepmc.org/articles/PMC5172462?pdf=render

Datenquelle: Europe PubMed Central

Abstract

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Date of acceptance

2016

Autoren

Taiji Kawakatsu
Shao-Shan Carol Huang
Florian Jupe
Eriko Sasaki
Robert J Schmitz
Mark A Urich
Rosa Castanon
Joseph R Nery
Cesar Barragan
Yupeng He
Huaming Chen
Manu Dubin
Cheng-Ruei Lee
Congmao Wang
Felix Bemm
Claude Becker
Ryan O'Neil
Ronan C O'Malley
Danjuma X Quarless
1001 Genomes Consortium
Nicholas J Schork
Detlef Weigel
Magnus Nordborg
Joseph R Ecker

Autoren-URL

https://www.ncbi.nlm.nih.gov/pubmed/27419873

DOI

10.1016/j.cell.2016.06.044

eISSN

1097-4172

Externe Identifier

NIH Manuscript Submission ID: NIHMS836043
PubMed Central ID: PMC5172462

Funding acknowledgements

Howard Hughes Medical Institute:
NIGMS NIH HHS: R00 GM100000
Austrian Science Fund FWF: W 1225

Ausgabe der Veröffentlichung

2

Zeitschrift

Cell

Schlüsselwörter

Arabidopsis
DNA Methylation
Epigenesis, Genetic
Epigenomics
Gene Expression Regulation, Plant
Genome, Plant
Transcriptome

Sprache

eng

Country

United States

Paginierung

492 - 505

PII

S0092-8674(16)30852-2

Datum der Veröffentlichung

2016

Status

Published

Datum, an dem der Datensatz öffentlich gemacht wurde

2017

Titel

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

Sub types

Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

Ausgabe der Zeitschrift

166

Datenquelle: PubMed

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Files

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