Data from: Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice
Choi, Jae Young, New York University
Purugganan, Michael D., New York University Abu Dhabi
Published Nov 14, 2017 on Dryad.
Cite this dataset
Choi, Jae Young; Purugganan, Michael D. (2017). Data from: Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice [Dataset]. Dryad. https://doi.org/10.5061/dryad.1q778
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.
indica reference japonica query genome alignment result in BED format
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.
japonica reference indica query genome alignment result in BED format
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.