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dc.contributor.author Choi, Jae Young
dc.contributor.author Purugganan, Michael D.
dc.date.accessioned 2017-11-14T17:34:42Z
dc.date.available 2017-11-14T17:34:42Z
dc.date.issued 2017-11-06
dc.identifier doi:10.5061/dryad.1q778
dc.identifier.citation Choi JY, Purugganan MD (2017) Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice. Molecular Biology and Evolution, online in advance of print.
dc.identifier.uri http://hdl.handle.net/10255/dryad.162551
dc.description Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between TE and proximal host gene silencing by studying the epigenomic regulation of repressing long terminal repeat (LTR) retrotransposons (RTs) in Oryza sativa. Results showed significant evidence of methylation spreading originating from the LTR-RT sequences, and the extent of spreading was dependent on 5 factors: 1) LTR-RT family, 2) time since the LTR-RT insertion, 3) recombination rate of the LTR-RT region, 4) level of LTR-RT sequence methylation, and 5) chromosomal location. Methylation spreading had negative effects by reducing host gene expression, but only on host genes with LTR-RT inserted in its introns. Our results also suggested high levels of LTR-RT methylation might have a role in suppressing TE-mediated deleterious ectopic recombination. In the end, despite the methylation spreading, no strong epigenetic trade-off was detected and majority of LTR-RT may have only minor epigenetic effects on nearby host genes.
dc.relation.haspart doi:10.5061/dryad.1q778/1
dc.relation.haspart doi:10.5061/dryad.1q778/2
dc.relation.haspart doi:10.5061/dryad.1q778/3
dc.relation.haspart doi:10.5061/dryad.1q778/4
dc.relation.haspart doi:10.5061/dryad.1q778/5
dc.relation.haspart doi:10.5061/dryad.1q778/6
dc.relation.haspart doi:10.5061/dryad.1q778/7
dc.relation.haspart doi:10.5061/dryad.1q778/8
dc.relation.haspart doi:10.5061/dryad.1q778/9
dc.relation.haspart doi:10.5061/dryad.1q778/10
dc.relation.isreferencedby doi:10.1093/molbev/msx284
dc.subject retrotransposon
dc.subject epigenomics
dc.subject transposable element
dc.title Data from: Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice
dc.type Article
dwc.ScientificName Oryza sativa
dc.contributor.correspondingAuthor Choi, Jae Young
prism.publicationName Molecular Biology and Evolution
dryad.fundingEntity IOS-1546218@National Science Foundation (United States)

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Title indica reference japonica query genome alignment result in BED format
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Description BED format genome alignment results where indica 93-11 was used as reference and japonica nipponbare genome was used as query genome. Indica chromosome was named as SAI.chromosome_number and japonica chromosome named as SAJ.chromosome_number.
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Title japonica reference indica query genome alignment result in BED format
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Description BED format genome alignment results where japonica nipponbare was used as reference and indica 93-11 was used as query genome. Indica chromosome was named as SAI.chromosome_number and japonica chromosome named as SAJ.chromosome_number.
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Title japonica genome LTR-RT and nearby host gene and the host genes' expression values
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Title indica genome LTR-RT and nearby host gene and the host genes' expression values
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Title japonica genome LTR-RT methylation levels
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Title indica genome LTR-RT methylation levels
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Title japonica genome LTR-RT up and downstream region methylation levels
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Title indica genome LTR-RT up and downstream region methylation levels
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Title Methylation level for LTR-RT and its up or downstream region in japonica genome and its orthologous region in indica
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Title Methylation level for LTR-RT and its up or downstream region in indica genome and its orthologous region in japonica
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