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-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.
Department of Bioinformatics, College of Life Sciences, Zhejiang University, Zijingang Campus, Yu Hang Tang Road 866#, Hangzhou 310058, China.
Chunhui
C
Yuan
Department of Bioinformatics, College of Life Sciences, Zhejiang University, Zijingang Campus, Yu Hang Tang Road 866#, Hangzhou 310058, China James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China.
Jingjing
J
Wang
Department of Mathematical Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK.
Andrew P
AP
Harrison
Department of Bioinformatics, College of Life Sciences, Zhejiang University, Zijingang Campus, Yu Hang Tang Road 866#, Hangzhou 310058, China.
Xianwen
X
Meng
Department of Bioinformatics, College of Life Sciences, Zhejiang University, Zijingang Campus, Yu Hang Tang Road 866#, Hangzhou 310058, China Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Gatersleben, Germany.
Dijun
D
Chen
Department of Bioinformatics, College of Life Sciences, Zhejiang University, Zijingang Campus, Yu Hang Tang Road 866#, Hangzhou 310058, China James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China mchen@zju.edu.cn.
Ming
M
Chen
D017360:Arabidopsis / Q000235:genetics*; D019175:DNA Methylation; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D006657:Histones / Q000378:metabolism; D011499:Protein Processing, Post-Translational; D016372:RNA, Antisense / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism
D006657:Histones; D016372:RNA, Antisense; D034741:RNA, Small Interfering
NAT-siRNA; epigenetic modification; genome-wide; natural antisense transcript; regulation