Genome-wide view of natural antisense transcripts in Arabidopsis thaliana

Natural antisense transcripts (NATs) are endogenous transcripts that can form double-stranded RNA structures. Many protein-coding genes (PCs) and non-protein-coding genes (NPCs) tend to form cis-NATs and trans-NATs, respectively. In this work, we identified 4,080 cis-NATs and 2,491 trans-NATs genome...

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Bibliographic Details
Published in:DNA research 2015-06, Vol.22 (3), p.233-243
Main Authors: Yuan, Chunhui, Wang, Jingjing, Harrison, Andrew P, Meng, Xianwen, Chen, Dijun, Chen, Ming
Format: Article
Language:English
Subjects:
Arabidopsis
Arabidopsis - genetics
Arabidopsis thaliana
DNA Methylation
Gene Regulatory Networks
Genome, Plant
Histones - metabolism
Protein Processing, Post-Translational
RNA, Antisense - genetics
RNA, Small Interfering - genetics
RNA, Small Interfering - metabolism
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Summary:Natural antisense transcripts (NATs) are endogenous transcripts that can form double-stranded RNA structures. Many protein-coding genes (PCs) and non-protein-coding genes (NPCs) tend to form cis-NATs and trans-NATs, respectively. In this work, we identified 4,080 cis-NATs and 2,491 trans-NATs genome-widely in Arabidopsis. Of these, 5,385 NAT-siRNAs were detected from the small RNA sequencing data. NAT-siRNAs are typically 21nt, and are processed by Dicer-like 1 (DCL1)/DCL2 and RDR6 and function in epigenetically activated situations, or 24nt, suggesting these are processed by DCL3 and RDR2 and function in environment stress. NAT-siRNAs are significantly derived from PC/PC pairs of trans-NATs and NPC/NPC pairs of cis-NATs. Furthermore, NAT pair genes typically have similar pattern of epigenetic status. Cis-NATs tend to be marked by euchromatic modifications, whereas trans-NATs tend to be marked by heterochromatic modifications.
ISSN:1340-2838
1756-1663
DOI:10.1093/dnares/dsv008