Systematic analysis of alternative exon-dependent interactome remodeling reveals multitasking functions of gene regulatory factors

Jonathan F Roth; Ulrich Braunschweig; Mingkun Wu; Jack Daiyang Li; Zhen-Yuan Lin; Brett Larsen; Robert J Weatheritt; Anne-Claude Gingras; Benjamin J Blencowe

doi:10.1016/j.molcel.2023.10.034

Systematic analysis of alternative exon-dependent interactome remodeling reveals multitasking functions of gene regulatory factors

Mol Cell. 2023 Dec 7;83(23):4222-4238.e10. doi: 10.1016/j.molcel.2023.10.034.

Authors

Jonathan F Roth¹, Ulrich Braunschweig², Mingkun Wu², Jack Daiyang Li³, Zhen-Yuan Lin⁴, Brett Larsen⁴, Robert J Weatheritt⁵, Anne-Claude Gingras⁶, Benjamin J Blencowe⁷

Affiliations

¹ Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
² Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
³ Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
⁴ Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada.
⁵ Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
⁶ Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: gingras@lunenfeld.ca.
⁷ Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: b.blencowe@utoronto.ca.

PMID: 38065061
DOI: 10.1016/j.molcel.2023.10.034

Abstract

Alternative splicing significantly expands biological complexity, particularly in the vertebrate nervous system. Increasing evidence indicates that developmental and tissue-dependent alternative exons often control protein-protein interactions; yet, only a minor fraction of these events have been characterized. Using affinity purification-mass spectrometry (AP-MS), we show that approximately 60% of analyzed neural-differential exons in proteins previously implicated in transcriptional regulation result in the gain or loss of interaction partners, which in some cases form unexpected links with coupled processes. Notably, a neural exon in Chtop regulates its interaction with the Prmt1 methyltransferase and DExD-Box helicases Ddx39b/a, affecting its methylation and activity in promoting RNA export. Additionally, a neural exon in Sap30bp affects interactions with RNA processing factors, modulating a critical function of Sap30bp in promoting the splicing of <100 nt "mini-introns" that control nuclear RNA levels. AP-MS is thus a powerful approach for elucidating the multifaceted functions of proteins imparted by context-dependent alternative exons.

Keywords: affinity purification-mass spectrometry; alternative splicing; intron retention; mRNA export; neurogenesis; protein-protein interactions; transcriptional regulation.

MeSH terms

Alternative Splicing*
Exons / genetics
Introns
RNA
RNA Splicing*

Substances

RNA