RRM
2011 Rustbelt RNA Meeting
RRM
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Poster abstracts
Abstract:
Pre-mRNA splicing is one of the fundamental post-transcriptional processes in eukaryotic gene expression and regulation. Alternative Splicing (AS) occurs when different splice sites of pre-mRNA are processed to generate distinct transcript isoforms, leading to diverse proteins with functional and/or structural differences from the same genes. Pre-mRNA splicing is guided by the cis-regulatory sequence motifs buried in them; currently in mammals these are well characterized as the consensus splice sites, branch point signal and poly-pyrimidine tract. Focusing on Chlamydomonas reinhardtii, a green alga that shares both animal (e.g., flagella) and plant traits (e.g., chloroplast), we evaluate AS events and their associated cis-regulatory signals. Based on all available Sanger-based ESTs (338,243), JGI 454 cDNAs (6,317,641) and genoscope 454 cDNAs (689,548), we evaluated AS events using GMAP and PASA, and updated AUGUSTUS gene annotation by resultant PASA AS models. Among 17,163 AUGUSTUS protein-coding genes, ~49% are subjected to AS while ~17% of PASA genes shows AS evidence. As observed in other plants analyzed so far, we found the dominant AS mode is intron retention: over 51% of the AS genes retain their introns in their mature mRNAs. In comparison with the constitutively spliced introns, we found that the retained introns tend to have weaker splice sites, with less abundant G triplet (intronic splicing enhancer) and C triplet. Our data also suggests that the majority of AS isoforms are presumably functional and not Non-sense Mediated Decay (NMD) candidates. We also observed that most retained introns are less than 250 nt, which have a potency of being spliced by intron definition splicing mechanism. It suggests that short introns that are spliced by intron definition are more likely to be retained if they possess weak signals.
Keywords: alternative splicing, intron retention, chlamydomonas
