Chromatin and epigenetic regulation of pre-mRNA processing

Abstract

New data are revealing a complex landscape of gene regulation shaped by chromatin states that extend into the bodies of transcribed genes and associate with distinct RNA elements such as exons, introns and polyadenylation sites. Exons are characterized by increased levels of nucleosome positioning, DNA methylation and certain histone modifications. As pre-mRNA splicing occurs co-transcriptionally, changes in the transcription elongation rate or epigenetic marks can influence exon splicing. These new discoveries broaden our understanding of the epigenetic code and ascribe a novel role for chromatin in controlling pre-mRNA processing. In this review, we summarize the recently discovered interplay between the modulation of chromatin states and pre-mRNA processing with the particular focus on how these processes communicate with one another to control gene expression.

Figure 1.

Nucleotide composition of exons and nucleosome ‘container sites’. (A) Exons contain elevated GC content relative to introns (19), which favors nucleosome binding (44), while nearby intron sequences are enriched in nucleosome repellant poly-dA:dT stretches (26). This sequence arrangement mirrors the recently identified strong nucleosome-positioning signals termed ‘container sites’ (B), which consist of relatively G/C-rich nucleosome binding core, surrounded by nucleosome repellant A/T-rich sequence that prevents nucleosomes from sliding out of position (24).

Figure 2.

Deposition of H3K36me3 over exons. hnRNP-L directly interacts with RNA elements that place it in close proximity to the exons. Aly/Ref1 is recruited to the pre-mRNA during spliceosome assembly (76). In turn, hnRNP-L and Aly/Ref1 cooperate with RNAPII to bring Kmt3a to the exons where it methylates H3K36.

Figure 3.

Co-transcriptional splicing and kinetic control of alternative splicing by the elongating RNAPII. (A) The genomic region of a hypothetical gene is illustrated containing three exons. Along the gene body, the frequency of RNA-Seq reads from a cell type where total RNA has been harvested is depicted. A characteristic ‘saw-tooth’ pattern is formed by the frequency of RNA-Seq reads across the genomic region. Exonic reads are most prevalent due to the amount of both nascent and partially processed RNAs containing these sequences. Intronic reads are also present albeit at lower levels representing unprocessed RNA species. The diminished frequency of reads toward the 3′ end of introns arises from rapid co-transcriptional splicing that occurs in this region after RNAPII finishes transcribing each intron. (B) The RNAPII elongation rate controls the exon inclusion. Rapid elongation through an alternative exon defined by weak splicing signals does not allow enough time for exon recognition before the competing strong splicing signals of the downstream exon are presented (top). As a result, the alternative exon is skipped. Slowing down RNAPII within and downstream of the alternative exon provides time for the splicing machinery to recognize and splice the weak exon in the mature transcript (bottom).

Figure 4.

Recruitment model for the control of splicing by H3K36me3. The H3K36me3 mark is read by MRG15 (A) or Psip1 (B) protein. In turn, MRG15 and Psip1 recruit Ptbp1 and SR protein family members (Srsf1 and Srsf3), respectively. Ptbp1 represses splicing when bound to the alternative exons or the upstream of them by preventing the conversion of exon definition to an intron definition complex (77). Srsf1 and Srsf3 bind to cis-elements in the exons and promote exon recognition and splicing by recruiting the U1 and U2 snRNPs (6).