Regulated splicing of large exons is linked to phase‐separation of vertebrate transcription factors. (4th October 2021)

• Record Type: Journal Article
• Authors: Kawachi, Toshihiko; Masuda, Akio; Yamashita, Yoshihiro; Takeda, Jun‐ichi; Ohkawara, Bisei; Ito, Mikako; Ohno, Kinji
• Is Part Of: EMBO journal. Volume 40:Number 22(2021)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2021-10-04
• Subjects: evolution -- intrinsically disordered region -- large exon -- splicing -- transcription factors; Molecular biology -- Periodicals; 572.805
• DOI: 10.15252/embj.2020107485
• Languages: English
• ISSNs: 0261-4189

Abstract

Abstract: Although large exons cannot be readily recognized by the spliceosome, many are evolutionarily conserved and constitutively spliced for inclusion in the processed transcript. Furthermore, whether large exons may be enriched in a certain subset of proteins, or mediate specific functions, has remained unclear. Here, we identify a set of nearly 3, 000 SRSF3‐dependent large constitutive exons (S3‐LCEs) in human and mouse cells. These exons are enriched for cytidine‐rich sequence motifs, which bind and recruit the splicing factors hnRNP K and SRSF3. We find that hnRNP K suppresses S3‐LCE splicing, an effect that is mitigated by SRSF3 to thus achieve constitutive splicing of S3‐LCEs. S3‐LCEs are enriched in genes for components of transcription machineries, including mediator and BAF complexes, and frequently contain intrinsically disordered regions (IDRs). In a subset of analyzed S3‐LCE‐containing transcription factors, SRSF3 depletion leads to deletion of the IDRs due to S3‐LCE exon skipping, thereby disrupting phase‐separated assemblies of these factors. Cytidine enrichment in large exons introduces proline/serine codon bias in intrinsically disordered regions and appears to have been evolutionarily acquired in vertebrates. We propose that layered splicing regulation by hnRNP K and SRSF3 ensures proper phase‐separation of these S3‐LCE‐containing transcription factors in vertebrates. Synopsis: Although their recognition poses a challenge to spliceosomes, large exons are often conserved and spliced. Here, this is linked to their nucleotide composition, which drives splicing factor recruitment and endows encoded proteins with specific properties. Analysis of ˜ 3, 000 SRSF3‐dependent large exons reveals enrichment for cytidine nucleotides Cytidine enrichment favors recruitment of splicing factors SRSF3 and hnRNP K Inclusion of cytidine‐rich large exons encoding serine/proline‐rich intrinsically disordered regions (IDRs) is found in vertebrate transcription factors Loss of IDR inclusion upon SRSF3 depletion‐induced exon‐skipping disrupts transcription factor phase separation. Abstract : Cytidine bias in large exons ensures their recognition by splicing factors SRSF3 and hnRNP K, as well as expression of Pro/Ser‐rich intrinsically disordered regions.