Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Taiji Kawakatsu, Shao-Shan 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 & 57 others Jorge 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)492-506
Number of pages15
JournalCell
Volume166
Issue number2
DOIs
StatePublished - Jul 14 2016

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Arabidopsis
Epigenomics
Genes
Genome
DNA Methylation
Methylation
Phenotype
Transcriptome
Immunity
Transcription
Transcription Factors
Nucleotides
Gene expression
Binding Sites
Gene Expression
Population

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Kawakatsu, T., Huang, S-S., Jupe, F., Sasaki, E., Schmitz, RJ. J., Urich, MA. A., ... Ecker, J. R. (2016). Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell, 166(2), 492-506. https://doi.org/10.1016/j.cell.2016.06.044

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

In: Cell, Vol. 166, No. 2, 14.07.2016, p. 492-506.

Research output: Contribution to journalArticle

Kawakatsu, T, Huang, S-S, Jupe, F, Sasaki, E, Schmitz, RJJ, Urich, MAA, Castanon, R, Nery, JRR, Barragan, C, He, Y, Chen, H, Dubin, M, Lee, CR, Wang, C, Bemm, F, Becker, C, O'Neil, R, O'Malley, RCC, Quarless, DXX, Alonso-Blanco, C, Andrade, J, Bemm, F, Bergelson, J, Borgwardt, K, Chae, E, Dezwaan, T, Ding, W, Ecker, JRR, Expósito-Alonso, M, Farlow, A, Fitz, J, Gan, X, Grimm, DGG, Hancock, A, Henz, SRR, Holm, S, Horton, M, Jarsulic, M, Kerstetter, RAA, Korte, A, Korte, P, Lanz, C, Lee, CR, Meng, D, Michael, TPP, Mott, R, Muliyati, NWW, Nägele, T, Nagler, M, Nizhynska, V, Nordborg, M, Novikova, P, Picó, FX, Platzer, A, Rabanal, FAA, Rodriguez, A, Rowan, BAA, Salomé, PAA, Schmid, K, Schmitz, RJJ, Seren, Ü, Sperone, FGG, Sudkamp, M, Svardal, H, Tanzer, MMM, Todd, D, Volchenboum, SLL, Wang, C, Wang, G, Wang, X, Weckwerth, W, Weigel, D, Zhou, X, Schork, NJ, Weigel, D, Nordborg, M & Ecker, JR 2016, 'Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions', Cell, vol. 166, no. 2, pp. 492-506. https://doi.org/10.1016/j.cell.2016.06.044
Kawakatsu T, Huang S-S, Jupe F, Sasaki E, Schmitz RJJ, Urich MAA et al. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell. 2016 Jul 14;166(2):492-506. https://doi.org/10.1016/j.cell.2016.06.044
Kawakatsu, Taiji ; Huang, Shao-Shan ; Jupe, Florian ; Sasaki, Eriko ; Schmitz, Robert J J. ; Urich, Mark A A. ; Castanon, Rosa ; Nery, Joseph R R. ; Barragan, Cesar ; He, Yupeng ; Chen, Huaming ; Dubin, Manu ; Lee, Cheng Ruei ; Wang, Congmao ; Bemm, Felix ; Becker, Claude ; O'Neil, Ryan ; O'Malley, Ronan C C. ; Quarless, Danjuma X X. ; Alonso-Blanco, Carlos ; Andrade, Jorge ; Bemm, Felix ; Bergelson, Joy ; Borgwardt, Karsten ; Chae, Eunyoung ; Dezwaan, Todd ; Ding, Wei ; Ecker, Joseph R R. ; Expósito-Alonso, Moisés ; Farlow, Ashley ; Fitz, Joffrey ; Gan, Xiangchao ; Grimm, Dominik G G. ; Hancock, Angela ; Henz, Stefan R R. ; Holm, Svante ; Horton, Matthew ; Jarsulic, Mike ; Kerstetter, Randall A A. ; Korte, Arthur ; Korte, Pamela ; Lanz, Christa ; Lee, Chen Ruei ; Meng, Dazhe ; Michael, Todd P P. ; Mott, Richard ; Muliyati, Ni Wayan W. ; Nägele, Thomas ; Nagler, Matthias ; Nizhynska, Viktoria ; Nordborg, Magnus ; Novikova, Polina ; Picó, F.  Xavier ; Platzer, Alexander ; Rabanal, Fernando A A. ; Rodriguez, Alex ; Rowan, Beth A A. ; Salomé, Patrice A A. ; Schmid, Karl ; Schmitz, Robert J J. ; Seren, Ümit ; Sperone, Felice Gianluca G. ; Sudkamp, Mitchell ; Svardal, Hannes ; Tanzer, Matt M M. ; Todd, Donald ; Volchenboum, Samuel L L. ; Wang, Congmao ; Wang, George ; Wang, Xi ; Weckwerth, Wolfram ; Weigel, Detlef ; Zhou, Xuefeng ; Schork, Nicholas J. ; Weigel, Detlef ; Nordborg, Magnus ; Ecker, Joseph R. / Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. In: Cell. 2016 ; Vol. 166, No. 2. pp. 492-506.
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AU - Kawakatsu, Taiji

AU - Huang, Shao-Shan

AU - Jupe, Florian

AU - Sasaki, Eriko

AU - Schmitz, Robert J J.

AU - Urich, Mark A A.

AU - Castanon, Rosa

AU - Nery, Joseph R R.

AU - Barragan, Cesar

AU - He, Yupeng

AU - Chen, Huaming

AU - Dubin, Manu

AU - Lee, Cheng Ruei

AU - Wang, Congmao

AU - Bemm, Felix

AU - Becker, Claude

AU - O'Neil, Ryan

AU - O'Malley, Ronan C C.

AU - Quarless, Danjuma X X.

AU - Alonso-Blanco, Carlos

AU - Andrade, Jorge

AU - Bemm, Felix

AU - Bergelson, Joy

AU - Borgwardt, Karsten

AU - Chae, Eunyoung

AU - Dezwaan, Todd

AU - Ding, Wei

AU - Ecker, Joseph R R.

AU - Expósito-Alonso, Moisés

AU - Farlow, Ashley

AU - Fitz, Joffrey

AU - Gan, Xiangchao

AU - Grimm, Dominik G G.

AU - Hancock, Angela

AU - Henz, Stefan R R.

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AU - Michael, Todd P P.

AU - Mott, Richard

AU - Muliyati, Ni Wayan W.

AU - Nägele, Thomas

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AU - Nizhynska, Viktoria

AU - Nordborg, Magnus

AU - Novikova, Polina

AU - Picó, F.  Xavier

AU - Platzer, Alexander

AU - Rabanal, Fernando A A.

AU - Rodriguez, Alex

AU - Rowan, Beth A A.

AU - Salomé, Patrice A A.

AU - Schmid, Karl

AU - Schmitz, Robert J J.

AU - Seren, Ümit

AU - Sperone, Felice Gianluca G.

AU - Sudkamp, Mitchell

AU - Svardal, Hannes

AU - Tanzer, Matt M M.

AU - Todd, Donald

AU - Volchenboum, Samuel L L.

AU - Wang, Congmao

AU - Wang, George

AU - Wang, Xi

AU - Weckwerth, Wolfram

AU - Weigel, Detlef

AU - Zhou, Xuefeng

AU - Schork, Nicholas J.

AU - Weigel, Detlef

AU - Nordborg, Magnus

AU - Ecker, Joseph R.

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