Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions
- Author(s)
- , Taiji Kawakatsu, Shao shan Carol Huang, Florian Jupe, Eriko Sasaki, Robert J J. Schmitz, Mark A A. Urich, Rosa Castanon, Joseph R R. Nery, Cesar Barragan, Yupeng He, Huaming Chen, Manu Dubin, Cheng Ruei Lee, Congmao Wang, Felix Bemm, Claude Becker, Ryan O'Neil, Ronan C C. O'Malley, Danjuma X X. Quarless, Carlos Alonso-Blanco, Jorge Andrade, Claude Becker, Felix Bemm, Joy Bergelson, Karsten Borgwardt, Eunyoung Chae, Todd Dezwaan, Wei Ding, Joseph R R. Ecker, Moisés Expósito-Alonso, Ashley Farlow, Joffrey Fitz, Xiangchao Gan, Dominik G G. Grimm, Angela Hancock, Stefan R R. Henz, Svante Holm, Matthew Horton, Mike Jarsulic, Randall A A. Kerstetter, Arthur Korte, Pamela Korte, Thomas Nägele, Matthias Nagler, Magnus Nordborg, Polina Novikova, Alexander Platzer, Hannes Svardal, Wolfram Weckwerth, Magnus Nordborg
- 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.
- Organisation(s)
- Department of Biochemistry and Cell Biology, Department of Botany and Biodiversity Research, Department of Mathematics, Research Platform Vienna Metabolomics Center
- External organisation(s)
- The Salk Institute for Biological Studies, National Institute of Agrobiological Sciences, Österreichische Akademie der Wissenschaften (ÖAW), University of Georgia, Max-Planck-Institut für Entwicklungsbiologie, Zhejiang Academy of Agricultural Sciences, J Craig Venter Inst Inc, Bioinformat Dept, Unknown External Organisation Unbekannt/undefiniert
- Journal
- Cell
- Volume
- 166
- Pages
- 492-505
- No. of pages
- 14
- ISSN
- 0092-8674
- DOI
- https://doi.org/10.1016/j.cell.2016.06.044
- Publication date
- 07-2016
- Peer reviewed
- Yes
- Austrian Fields of Science 2012
- 106005 Bioinformatics, 106036 Population genetics
- Keywords
- ASJC Scopus subject areas
- General Biochemistry,Genetics and Molecular Biology
- Portal url
- https://ucrisportal.univie.ac.at/en/publications/539d0a6f-9924-4d70-ae01-139743fffe7d