Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data
- 1 Institute for Genome Sciences & Policy, Duke University;
- 2 Department of Biology, Duke University;
- 3 Duke Center for Systems Biology, Duke University
- ↵* Corresponding author; email: uwe.ohler{at}duke.edu
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.
- Received September 18, 2012.
- Accepted May 14, 2013.
- © 2013, Published by Cold Spring Harbor Laboratory Press
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