RNA-Seq reveals complexity of the Arabidopsis transcriptome

alternative splicingResearchers at the Medical University of Vienna have conducted a genome-wide study analyzing alternative splicing (AS) in Arabidopsis. AS is a key regulatory mechanism that contributes to transcriptome and proteome diversity.

They performed high-throughput sequencing of a normalized cDNA library which resulted in a high coverage transcriptome map of Arabidopsis.

Major findings:

  • Detected ~150,000 splice junctions derived mostly from typical plant introns, including an 8-fold increase in the number of U12 introns (2,069).
  • ~61% of multi-exonic genes are alternatively spliced under normal growth conditions.
  • The most frequent AS events (~40%) are intron retentions (IR).
  • Many IRs have relatively low read coverage and are less well represented in assembled transcripts.
  • ~51% of Arabidopsis genes produce AS transcripts which do not involve IR.
  • A large set of cryptic introns identified inside annotated coding exons.
  • Extensive AS coupled to nonsense-mediated decay in AFC2, encoding a highly conserved LAMMER kinase which phosphorylates splicing factors, thus establishing a complex loop in AS regulation.

Marquez Y, Brown JW, Simpson CG, Barta A, Kalyna M. (2012) Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res [Epub ahead of print]. [article]