Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

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-BlancoJorge Andrade, 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, Christa Lanz, Chen Ruei Lee, Dazhe Meng, Todd P P. Michael, Richard Mott, Ni Wayan W. Muliyati, Thomas Nägele, Matthias Nagler, Viktoria Nizhynska, Magnus Nordborg, Polina Novikova, F.  Xavier Picó, Alexander Platzer, Fernando A A. Rabanal, Alex Rodriguez, Beth A A. Rowan, Patrice A A. Salomé, Karl Schmid, Robert J J. Schmitz, Ümit Seren, Felice Gianluca G. Sperone, Mitchell Sudkamp, Hannes Svardal, Matt M M. Tanzer, Donald Todd, Samuel L L. Volchenboum, Congmao Wang, George Wang, Xi Wang, Wolfram Weckwerth, Detlef Weigel, Xuefeng Zhou, Nicholas J. Schork, Detlef Weigel, Magnus Nordborg, Joseph R. Ecker

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)492-505
Number of pages14
JournalCell
Volume166
Issue number2
DOIs
StatePublished - Jul 14 2016

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

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  • Cite this

    Kawakatsu, T., Huang, S. SC., Jupe, F., Sasaki, E., Schmitz, RJ. J., Urich, MA. A., Castanon, R., Nery, JR. R., Barragan, C., He, Y., Chen, H., Dubin, M., Lee, C. R., Wang, C., Bemm, F., Becker, C., O'Neil, R., O'Malley, RC. C., Quarless, DX. X., ... Ecker, J. R. (2016). Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell, 166(2), 492-505. https://doi.org/10.1016/j.cell.2016.06.044