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Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

Joanna Y. Ip, Dominic Schmidt, Qun Pan, Arun K. Ramani, Andrew G. Fraser, Duncan T. Odom and Benjamin J. Blencowe

Genome Research, Advance Online 16 December 2010.
doi:10.1101/gr.111070.110

This week’s enlightening summary and analysis by Charles Lin:

There has been a growing appreciation in the last decade that RNA processing and transcription do not occur in isolation. Events thought to be exclusively transcriptional, such as chromatin modifications, elongation rate, and elongation complex factors have been found to interact with almost every aspect of RNA processing—from 5’ cap formation to 3’ end processing and export. Moore and Proudfoot have an excellent 2009 review that describes these interactions in detail.

Of focus this week in RNA journal club is the relationship between alternative splicing (AS) and elongation capacity of the RNA Pol II complex. Ip et al., use multiple techniques to reduce the elongation capacity of RNA Pol II and assay the effect on alternative splicing. They use these perturbations of RNA Pol II to examine two longstanding models coupling elongation/splicing interactions.

The first, the kinetic model, reviewed in Kornblihtt 2006, states that the speed of the RNA Pol II can influence AS through competitive kinetics of 3’ Splice Site choice. The second, the recruitment model, most recently reviewed by Luco et al., 2011 emphasizes the role of chromatin adaptor complexes to couple the splicing apparatus to chromatin modifications and the RNA Pol II.

Ip et al., inhibited RNA Pol II elongation through multiple mechanisms. Inhibition caused a majority of genes to decrease mRNA expression. AS was assayed with a custom array platform that interrogated exon inclusion/exclusion. The authors did not find a compelling trend towards inclusion or exclusion. Instead they focused on the set of genes that experienced exon inclusion. These genes were enriched for splicing factors and in some cases exon inclusion resulted in the addition of a premature termination codon leading to NMD mediated down regulation. This presented an enticing mechanism for coupled coordinated regulation of elongation and splicing machinery. When elongation is down regulated, it causes splicing machinery to be consequently down regulated through NMD.

The authors also find that inclusion of exons is often associated with increased RNA Pol II density flanking the exon. Increased RNA Pol II may be a function of polymerase stalling at the exon or simply a result of a slower elongating complex. It’s unclear whether the RNA Pol II accumulation represents an opportunity for a weaker 3’ Splice Site to be recognized (kinetic model) or additional recruitment of adaptor factors.

Ip et al.’s findings do not discredit one model or the other, and indeed it’s possible for these two models to co-exist. One potential reason for this is that the elongation kinetics of RNA Pol II are intrinsically linked to the ability of the elongating complex to recruit elongation factors/chromatin adaptors. In particular, several of the methods employed by Ip et al. to inhibit elongation kinetics do so by reducing or eliminating serine phosphorylation on the RNA Pol II C-terminal domain repeats. Phosphorylation of these repeats is responsible for both enhanced processivity of the enzyme and also serves as a scaffold for many elongation specific factors.

At the end of the day, the authors propose a set of enticing models built upon their observations. That many of these splicing changes were reproduced through orthologous methods lends weight to the idea that globally, splicing and elongation are coupled processes, and regulation of one may lead to coordinated regulation of the other.