More than a splicing code: integrating the role of RNA, chromatin and non-coding RNA in alternative splicing regulation

Abstract

Large portions of the genome undergo alternative pre-mRNA splicing in often intricate patterns. Alternative splicing regulation requires extensive control mechanisms since errors can have deleterious consequences and may lead to developmental defects and disease. Recent work has identified a complex network of regulatory RNA elements which guide splicing decisions. In addition, the discovery that transcription and splicing are intimately coupled has opened up new directions into alternative splicing regulation. Work at the interface of chromatin and RNA biology has revealed unexpected molecular links between histone modifications, the transcription machinery, and non-coding RNAs (ncRNAs) in the determination of alternative splicing patterns.

Figure 1

The role of chromatin in alternative splicing. (a) RNAP II elongation rate affects recruitment of the splicing machinery. Fast elongation favors inclusion of a downstream exon with strong splice sites. (b) A change in chromatin conformation, such as localized heterochromatinization (blue ovals and higher density of nucleosomes), slows down RNAP II which favors recruitment of splicing factors (yellow oval) to the weaker exon (blue rectangle), inducing exon inclusion. (c) Histone modifications (small red circles) can directly recruit splicing factors via a chromatin-adaptor system (red ovals) which consists of a chromatin-binding protein that reads the histone marks and modulates recruitment of the splicing factor to the pre-mRNA (red rectangle).

Figure 2

A ‘histone code’ in alternative splicing. Histone modifications may transmit their information in several modes. (a) Histone marks may act linearly with increasing levels of a single histone mark recruiting increasing levels of a chromatin-adaptor protein complex leading to increased usage of a given site. Competing levels of different histone marks modulate the recruitment of competing chromatin-adaptor complexes determining the final splicing outcome. (b) Histone modifications may act in combination by favoring (left) or inhibiting (right) the recruitment of a single chromatin-splicing complex. (c) Multiple histone marks may recruit in combination multiple chromatin-adaptor complexes that will favor or inhibit exon inclusion. CBP: chromatin-binding protein; SF: splicing factor.

Figure 3

Mechanisms of alternative splicing regulation by ncRNAs. (a) MicroRNAs (red hairpin) regulate the protein levels of key developmental splicing factors (SF, blue rectangle). (b) siRNA-mediated heterochromatinization (red ovals) of a weak exon favors its inclusion. (c) The long intergenic ncRNA MALAT-1 (red line) maintains a pool of inactive SR proteins (dark green spheres) stored in splicing factor compartments (speckle). Splicing factors are released from speckles when needed. (d) The binding of a psnoRNA (red line) by sequence complementarity to an RNA silencer in the exon interferes with the recruitment of a splicing factor (blue rectangle) and subsequent exon inclusion.