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DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

Eichten, Steven; Stuart, Tim; Srivastava, Akanksha; Lister, Ryan; Borevitz, Justin

Description

DNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole-genome bisulfite sequencing was...[Show more]

dc.contributor.authorEichten, Steven
dc.contributor.authorStuart, Tim
dc.contributor.authorSrivastava, Akanksha
dc.contributor.authorLister, Ryan
dc.contributor.authorBorevitz, Justin
dc.date.accessioned2018-11-29T22:54:40Z
dc.date.available2018-11-29T22:54:40Z
dc.identifier.issn1088-9051
dc.identifier.urihttp://hdl.handle.net/1885/152873
dc.description.abstractDNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole-genome bisulfite sequencing was performed on genetically diverse lines of the model cereal Brachypodium distachyon. Although DNA methylation profiles are broadly similar, thousands of differentially methylated regions are observed between lines. An analysis of novel transposable element indel variation highlighted hundreds of new polymorphisms not seen in the reference sequence. DNA methylation and transposable element variation is correlated with the genome-wide amount of genetic variation present between samples. However, there was minimal evidence that novel transposon insertions or deletions are associated with nearby differential methylation. This study highlights unique relationships between genetic variation and DNA methylation variation within Brachypodium and provides a valuable map of DNA methylation across diverse resequenced accessions of this model cereal species.
dc.format.mimetypeapplication/pdf
dc.publisherCold Spring Harbor Laboratory Press
dc.sourceGenome Research
dc.titleDNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume26
dc.date.issued2016
local.identifier.absfor060702 - Plant Cell and Molecular Biology
local.identifier.ariespublicationa383154xPUB5060
local.type.statusPublished Version
local.contributor.affiliationEichten, Steven, College of Science, ANU
local.contributor.affiliationStuart, Tim, University of Western Australia
local.contributor.affiliationSrivastava, Akanksha, University of Western Australia
local.contributor.affiliationLister, Ryan, University of Western Australia
local.contributor.affiliationBorevitz, Justin, College of Science, ANU
local.bibliographicCitation.issue11
local.identifier.doi10.1101/gr.205468.116
dc.date.updated2018-11-29T08:01:31Z
local.identifier.scopusID2-s2.0-84995688288
local.identifier.thomsonID000386609300006
dcterms.accessRightsOpen Access
CollectionsANU Research Publications

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