Transposon age and non-CG methylation.

Nature Communications
Zhengming Wang, David C Baulcombe

Abstract

Silencing of transposable elements (TEs) is established by small RNA-directed DNA methylation (RdDM). Maintenance of silencing is then based on a combination of RdDM and RNA-independent mechanisms involving DNA methyltransferase MET1 and chromodomain DNA methyltransferases (CMTs). Involvement of RdDM, according to this model should decrease with TE age but here we show a different pattern in tomato and Arabidopsis. In these species the CMTs silence long terminal repeat (LTR) transposons in the distal chromatin that are younger than those affected by RdDM. To account for these findings we propose that, after establishment of primary RdDM as in the original model, there is an RNA-independent maintenance phase involving CMTs followed by secondary RdDM. This progression of epigenetic silencing in the gene-rich distal chromatin is likely to influence the transcriptome either in cis or in trans depending on whether the mechanisms are RNA-dependent or -independent.

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Citations

Jun 25, 2020·Emerging Microbes & Infections·Chasity D AndrewsRachel A Liberatore
Sep 24, 2020·Journal of Biological Rhythms·Benjamin A Unruh, Shihoko Kojima
Dec 31, 2020·Proceedings of the National Academy of Sciences of the United States of America·Katherine DombAssaf Zemach
Mar 23, 2021·Frontiers in Plant Science·Lucia BarraClara Conicella
Apr 17, 2021·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Yulong LiXiaojun Yang
Jun 19, 2020··Hajk-Georg Drost, Hajk-Georg Drost

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Methods Mentioned

BETA
chemical modifications
genotyping
PCR
bisulfite-seq
RNA-seq
ChIP
ChIP-seq

Software Mentioned

bismark
BLASTn
SOL ITAG3
Tophat
segmentSeq
DESeq2
RepeatModeler
LTRpred
Trim Galore !
Bowtie2

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