Systematic Exploration of Dynamic Splicing Networks Reveals Conserved Multistage Regulators of Neurogenesis

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2022 Aug 1

PMID 35914530

Authors

Hong Han

Andrew J Best

Ulrich Braunschweig

Nicholas Mikolajewicz

Jack Daiyang Li

Jonathan Roth

Fuad Chowdhury

Federica Mantica

Syed Nabeel-Shah

Guillermo Parada

Kevin R Brown

Dave OHanlon

Jiarun Wei

Yuxi Yao

Abdelrahman Abou Zid

Lim Caden Comsa

Mark Jen

Jenny Wang

Alessandro Datti

Thomas Gonatopoulos-Pournatzis

Robert J Weatheritt

Jack F Greenblatt

Jeffrey L Wrana

Manuel Irimia

Anne-Claude Gingras

Jason Moffat

Benjamin J Blencowe

Affiliations

Soon will be listed here.

Abstract

Alternative splicing (AS) is a critical regulatory layer; yet, factors controlling functionally coordinated splicing programs during developmental transitions are poorly understood. Here, we employ a screening strategy to identify factors controlling dynamic splicing events important for mammalian neurogenesis. Among previously unknown regulators, Rbm38 acts widely to negatively control neural AS, in part through interactions mediated by the established repressor of splicing, Ptbp1. Puf60, a ubiquitous factor, is surprisingly found to promote neural splicing patterns. This activity requires a conserved, neural-differential exon that remodels Puf60 co-factor interactions. Ablation of this exon rewires distinct AS networks in embryonic stem cells and at different stages of mouse neurogenesis. Single-cell transcriptome analyses further reveal distinct roles for Rbm38 and Puf60 isoforms in establishing neuronal identity. Our results describe important roles for previously unknown regulators of neurogenesis and establish how an alternative exon in a widely expressed splicing factor orchestrates temporal control over cell differentiation.

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References

Zhang X . A pair of new statistical parameters for quality control in RNA interference high-throughput screening assays. Genomics. 2007; 89(4):552-61. DOI: 10.1016/j.ygeno.2006.12.014. View

Ellis J, Barrios-Rodiles M, Colak R, Irimia M, Kim T, Calarco J . Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol Cell. 2012; 46(6):884-92. DOI: 10.1016/j.molcel.2012.05.037. View

Robinson M, McCarthy D, Smyth G . edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009; 26(1):139-40. PMC: 2796818. DOI: 10.1093/bioinformatics/btp616. View

Kolberg L, Kerimov N, Peterson H, Alasoo K . Co-expression analysis reveals interpretable gene modules controlled by -acting genetic variants. Elife. 2020; 9. PMC: 7470823. DOI: 10.7554/eLife.58705. View

Lee J, Villarreal O, Chen X, Zandee S, Young Y, Torok C . QUAKING Regulates Microexon Alternative Splicing of the Rho GTPase Pathway and Controls Microglia Homeostasis. Cell Rep. 2020; 33(13):108560. DOI: 10.1016/j.celrep.2020.108560. View

Trapnell C, Schatz M . Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment. Parallel Comput. 2010; 35(8):429-440. PMC: 2749273. DOI: 10.1016/j.parco.2009.05.002. View

Berriz G, Beaver J, Cenik C, Tasan M, Roth F . Next generation software for functional trend analysis. Bioinformatics. 2009; 25(22):3043-4. PMC: 2800365. DOI: 10.1093/bioinformatics/btp498. View

Hubbard K, Gut I, Lyman M, McNutt P . Longitudinal RNA sequencing of the deep transcriptome during neurogenesis of cortical glutamatergic neurons from murine ESCs. F1000Res. 2013; 2:35. PMC: 3829120. DOI: 10.12688/f1000research.2-35.v1. View

Moore M, Wang Q, Kennedy C, Silver P . An alternative splicing network links cell-cycle control to apoptosis. Cell. 2010; 142(4):625-36. PMC: 2924962. DOI: 10.1016/j.cell.2010.07.019. View

10.

Kralovicova J, Borovska I, Kubickova M, Lukavsky P, Vorechovsky I . Cancer-Associated Substitutions in RNA Recognition Motifs of PUF60 and U2AF65 Reveal Residues Required for Correct Folding and 3' Splice-Site Selection. Cancers (Basel). 2020; 12(7). PMC: 7408900. DOI: 10.3390/cancers12071865. View

11.

Kolberg L, Raudvere U, Kuzmin I, Vilo J, Peterson H . gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler. F1000Res. 2021; 9. PMC: 7859841. DOI: 10.12688/f1000research.24956.2. View

12.

Raj B, Blencowe B . Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles. Neuron. 2015; 87(1):14-27. DOI: 10.1016/j.neuron.2015.05.004. View

13.

El Chehadeh S, Kerstjens-Frederikse W, Thevenon J, Kuentz P, Bruel A, Thauvin-Robinet C . Dominant variants in the splicing factor PUF60 cause a recognizable syndrome with intellectual disability, heart defects and short stature. Eur J Hum Genet. 2016; 25(1):43-51. PMC: 5159768. DOI: 10.1038/ejhg.2016.133. View

14.

Kralovicova J, Sevcikova I, Stejskalova E, Obuca M, Hiller M, Stanek D . PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM. Nucleic Acids Res. 2018; 46(12):6166-6187. PMC: 6093180. DOI: 10.1093/nar/gky389. View

15.

Shu L, Yan W, Chen X . RNPC1, an RNA-binding protein and a target of the p53 family, is required for maintaining the stability of the basal and stress-induced p21 transcript. Genes Dev. 2006; 20(21):2961-72. PMC: 1620019. DOI: 10.1101/gad.1463306. View

16.

Irimia M, Blencowe B . Alternative splicing: decoding an expansive regulatory layer. Curr Opin Cell Biol. 2012; 24(3):323-32. DOI: 10.1016/j.ceb.2012.03.005. View

17.

Baralle F, Giudice J . Alternative splicing as a regulator of development and tissue identity. Nat Rev Mol Cell Biol. 2017; 18(7):437-451. PMC: 6839889. DOI: 10.1038/nrm.2017.27. View

18.

Sterne-Weiler T, Weatheritt R, Best A, Ha K, Blencowe B . Efficient and Accurate Quantitative Profiling of Alternative Splicing Patterns of Any Complexity on a Laptop. Mol Cell. 2018; 72(1):187-200.e6. DOI: 10.1016/j.molcel.2018.08.018. View

19.

Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M . Function of alternative splicing. Gene. 2012; 514(1):1-30. PMC: 5632952. DOI: 10.1016/j.gene.2012.07.083. View

20.

Tejedor J, Papasaikas P, Valcarcel J . Genome-wide identification of Fas/CD95 alternative splicing regulators reveals links with iron homeostasis. Mol Cell. 2014; 57(1):23-38. DOI: 10.1016/j.molcel.2014.10.029. View