Genome-wide view of natural antisense transcripts in Arabidopsis thaliana

被引：36

作者：

Yuan, Chunhui ^{[1
]}

Wang, Jingjing ^{[1
,2
]}

Harrison, Andrew P. ^{[3
]}

Meng, Xianwen ^{[1
]}

Chen, Dijun ^{[1
,4
]}

Chen, Ming ^{[1
,2
]}

机构：

[1] Zhejiang Univ, Coll Life Sci, Dept Bioinformat, Hangzhou 310058, Zhejiang, Peoples R China

[2] Zhejiang Univ, James D Watson Inst Genome Sci, Hangzhou 310058, Zhejiang, Peoples R China

[3] Univ Essex, Dept Math Sci, Colchester CO4 3SQ, Essex, England

[4] Leibniz Inst Plant Genet & Crop Plant Res Gatersl, Dept Mol Genet, Gatersleben, Germany

来源：

DNA RESEARCH | 2015年 / 22卷 / 03期

关键词：

genome-wide; natural antisense transcript; NAT-siRNA; epigenetic modification; regulation; EPIGENETIC REGULATION; CYTOSINE METHYLATION; ENDOGENOUS SIRNAS; DNA METHYLATION; NONCODING RNAS; EXPRESSION; GENE; CHROMATIN; PLANTS; DIFFERENTIATION;

D O I：

10.1093/dnares/dsv008

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：233 / 243

页数：11

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