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

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 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. The researchers 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, they 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 ∼4% of cis-NAT pairs produce putative cis-NAT-induced siRNAs. Taken together, these data and analyses illustrate the potential for multifaceted regulatory roles of plant cis-NATs.

rna-seq

Availability – The method is implemented in an R package and can be downloaded from: http://www.genome.duke.edu/labs/ohler/research/NASTIseq/

Li S, Liberman LM, Mukherjee N, Benfey PN, Ohler U. (2013) Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Res 23(10), 1730-9. [abstract]