Splicing regulation: from a parts list of regulatory elements to an integrated splicing code

Abstract

Alternative splicing of pre-mRNAs is a major contributor to both proteomic diversity and control of gene expression levels. Splicing is tightly regulated in different tissues and developmental stages, and its disruption can lead to a wide range of human diseases. An important long-term goal in the splicing field is to determine a set of rules or "code" for splicing that will enable prediction of the splicing pattern of any primary transcript from its sequence. Outside of the core splice site motifs, the bulk of the information required for splicing is thought to be contained in exonic and intronic cis-regulatory elements that function by recruitment of sequence-specific RNA-binding protein factors that either activate or repress the use of adjacent splice sites. Here, we summarize the current state of knowledge of splicing cis-regulatory elements and their context-dependent effects on splicing, emphasizing recent global/genome-wide studies and open questions.

FIGURE 1.

(A) Major forms of alternative splicing. In many cases, these common forms can be combined to generate more complicated alternative splicing events. (B) A schematic of regulated splicing. (Open boxes) Exons, (jagged lines) introns, (brackets) splice sites (ss). The consensus motifs of ss are shown in pictogram, and the branch point adenosine is indicated. (Dashed lines) Two alternative splicing pathways, with the middle exon either included or excluded. Splicing is regulated by cis-elements (ESE, ESS, ISS, and ISE) and trans-acting splicing factors (SR proteins, hnRNP, and unknown factors).

FIGURE 2.

Schematic of two types of context dependence for SREs. (A) Location-dependent activity of SREs, in which activity varies with pre-mRNA position. For example, G runs can function as both ESSs and ISEs (upper panel), and some SR protein binding sites can function as both ESEs and ISSs (lower panel). (Yellow) Alternative exons; (blue) constitutive exons. (B) Gene-dependent activity of SREs, in which activity observed in one gene is lost when the SRE is moved to another. Different genes are shown in different colors.

FIGURE 3.

Schematic diagram of a general splicing simulator, ExonScan. (Green boxes) Splicing enhancers, (red boxes) silencers. For simplicity, only ESSs and ESEs are indicated. Step 1, Identify the exon candidate as a pair of splice site (shown as brackets) that is 50–250 bp apart. Step 2, Score the splice sites and splicing enhancers and silencers, and sum up for the score of each exon candidate. Step 3, Determine the threshold and make the final prediction.