Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

Item Type:	Article
Title:	Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data
Creators Name:	Li, S. and Liberman, L. and Mukherjee, N. and Benfey, P. and Ohler, U.
Abstract:	Pairs of RNA molecules transcribed from partially or entirely complementary loci are called cis-natural antisense transcripts (cis-NATs), and they play key roles in the regulation of gene expression in many organisms. A promising experimental tool for profiling sense and antisense transcription is strand-specific RNA sequencing (ssRNA-seq). To identify cis-NATs using ssRNA-seq, we developed a new computational method based on a model comparison framework that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries. Applying the method to new ssRNA-seq data from whole root and cell-type specific Arabidopsis libraries confirmed most of the known cis-NAT pairs and identified 918 additional cis-NAT pairs. Newly identified cis-NAT pairs are supported by polyadenylation data, alternative splicing patterns and RT-PCR validation. We found 209 cis-NAT pairs that have opposite expression levels in neighboring cell types, implying cell-type specific roles for cis-NATs. By integrating a genome-wide epigenetic profile of Arabidopsis, we identified a unique chromatin signature of cis-NATs, suggesting a connection between cis-NAT transcription and chromatin modification in plants. An analysis of small-RNA sequencing data showed that approximately 4% of cis-NAT pairs produce putative cis-NAT induced siRNAs. Taken together, our data and analyses illustrate the potential for multifaceted regulatory roles of plant cis-NATs.
Keywords:	RNA-seq, Arabidopsis, cis-NAT Genes, Cell Type-Specific Gene Expression
Source:	Genome Research
ISSN:	1088-9051
Publisher:	Cold Spring Harbor Laboratory Press
Volume:	23
Number:	10
Page Range:	1730-1739
Date:	October 2013
Official Publication:	https://doi.org/10.1101/gr.149310.112
PubMed:	View item in PubMed

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