Genome-wide view of natural antisense transcripts in Arabidopsis thaliana

DNA Res. 2015 Jun;22(3):233-43. doi: 10.1093/dnares/dsv008. Epub 2015 Apr 28.

Abstract

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.

Keywords: NAT-siRNA; epigenetic modification; genome-wide; natural antisense transcript; regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • DNA Methylation
  • Gene Regulatory Networks
  • Genome, Plant*
  • Histones / metabolism
  • Protein Processing, Post-Translational
  • RNA, Antisense / genetics*
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / metabolism

Substances

  • Histones
  • RNA, Antisense
  • RNA, Small Interfering