Widespread natural variation of DNA methylation within angiosperms

Chad E. Niederhuth, Adam J. Bewick, Lexiang Ji, Magdy S. Alabady, Kyung Do Kim, Qing Li, Nicholas A. Rohr, Aditi Rambani, John M. Burke, Joshua A. Udall, Chiedozie Egesi, Jeremy Schmutz, Jane Grimwood, Scott A. Jackson, Nathan M. Springer, Robert J. Schmitz

Research output: Contribution to journalArticle

108 Citations (Scopus)

Abstract

Background: DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. Results: By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. Conclusions: These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.

Original languageEnglish (US)
Article number194
JournalGenome biology
Volume17
Issue number1
DOIs
StatePublished - Sep 27 2016

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Angiosperms
methylation
DNA methylation
DNA Methylation
angiosperm
Angiospermae
Methylation
DNA
transposons
Brassicaceae
bisulfites
Heterochromatin
heterochromatin
Poaceae
Genes
genes
life history
Genome
gene
genomics

Cite this

Niederhuth, C. E., Bewick, A. J., Ji, L., Alabady, M. S., Kim, K. D., Li, Q., ... Schmitz, R. J. (2016). Widespread natural variation of DNA methylation within angiosperms. Genome biology, 17(1), [194]. https://doi.org/10.1186/s13059-016-1059-0

Widespread natural variation of DNA methylation within angiosperms. / Niederhuth, Chad E.; Bewick, Adam J.; Ji, Lexiang; Alabady, Magdy S.; Kim, Kyung Do; Li, Qing; Rohr, Nicholas A.; Rambani, Aditi; Burke, John M.; Udall, Joshua A.; Egesi, Chiedozie; Schmutz, Jeremy; Grimwood, Jane; Jackson, Scott A.; Springer, Nathan M.; Schmitz, Robert J.

In: Genome biology, Vol. 17, No. 1, 194, 27.09.2016.

Research output: Contribution to journalArticle

Niederhuth, CE, Bewick, AJ, Ji, L, Alabady, MS, Kim, KD, Li, Q, Rohr, NA, Rambani, A, Burke, JM, Udall, JA, Egesi, C, Schmutz, J, Grimwood, J, Jackson, SA, Springer, NM & Schmitz, RJ 2016, 'Widespread natural variation of DNA methylation within angiosperms', Genome biology, vol. 17, no. 1, 194. https://doi.org/10.1186/s13059-016-1059-0
Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q et al. Widespread natural variation of DNA methylation within angiosperms. Genome biology. 2016 Sep 27;17(1). 194. https://doi.org/10.1186/s13059-016-1059-0
Niederhuth, Chad E. ; Bewick, Adam J. ; Ji, Lexiang ; Alabady, Magdy S. ; Kim, Kyung Do ; Li, Qing ; Rohr, Nicholas A. ; Rambani, Aditi ; Burke, John M. ; Udall, Joshua A. ; Egesi, Chiedozie ; Schmutz, Jeremy ; Grimwood, Jane ; Jackson, Scott A. ; Springer, Nathan M. ; Schmitz, Robert J. / Widespread natural variation of DNA methylation within angiosperms. In: Genome biology. 2016 ; Vol. 17, No. 1.
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