Core splicing architecture and early spliceosomal recognition determine microexon sensitivity to SRRM3/4

Abstract

Data de publicació electrònica: 07-08-2025

Microexons are essential for the proper operation of neurons and pancreatic endocrine cells, in which their inclusion depends on the splicing factors SRRM3 and SRRM4 (SRRM3/4). However, in pancreatic cells, lower expression of these regulators limits inclusion to only the most sensitive subset among all neuronal microexons. Although various cis-acting elements can contribute to microexon regulation, how they determine this differential dose response and the corresponding high or low sensitivity to SRRM3/4 remains unknown. Here we use massively parallel splicing assays probing 28,535 variants to show that sensitivity to SRRM4 is conserved across vertebrates. Our data support a regulatory model whereby high or low microexon sensitivity is largely determined by the interplay between core splicing architecture and length constraints. This conclusion is further supported by distinct spliceosome activities in the absence of SRRM3/4 and by a mathematical model that assumes that the two types of microexons differ only in their efficiency to recruit early spliceosomal components.

The research was funded by the European Research Council under the European Union’s Horizon 2020 research and innovation program (ERC-CoG, grant agreement 101002275 to M.I.) and Spanish Ministry of Science and Innovation (PID2020-115040GB-I00/AEI/10.13039/501100011033 to M.I.). R.M.-C. acknowledges support from RYC2021-033860-I funded by MCIN/AEI/10.13039/501100011033 and by European Union NextGeneration EU/PRTR. CRG acknowledges support of the Spanish Ministry of Science and Innovation through the Centro de Excelencia Severo Ochoa (CEX2020-001049-S, MCIN/AEI/10.13039/501100011033) and the Generalitat de Catalunya through the CERCA program.