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Series GSE224970 Query DataSets for GSE224970
Status Public on Nov 24, 2023
Title Analysis of alternative exon-dependent interactome remodelling reveals multitasking functions of gene regulatory factors (Sap30bp RNA-Seq)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Alternative splicing is fundamental for the expansion of biological complexity, particularly in the vertebrate nervous system. Increasing evidence indicates that developmental stage and tissue-dependent alternative exons often control protein-protein interactions, yet only a minor fraction of these events has been characterized at the protein level. 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. Focusing on Chtop and Sap30bp, the neural exons in these proteins unexpectedly remodel interactions with partners associated with mRNA processing and trafficking. Sap30bp additionally controls RNA localization by regulating the splicing of <100 nt ‘mini-introns’ that contribute to the nuclear retention of transcripts. These activities of Chtop and Sap30bp are linked to programs of transcriptomic regulation associated with development of the nervous system. AP-MS is thus a powerful approach for elucidating multifaceted functions of proteins imparted by context-dependent alternative exons.
 
Overall design This dataset consists of 12 RNA-seq files associated with the manuscript "Analysis of alternative exon-dependent interactome remodelling reveals multitasking functions of gene regulatory factors" characterizing the effect of Sap30bp siRNA knockdown and neural/non-neural isoform rescue on gene expression and splicing in Neuro2a cell lines. For each isoform (with or without exon 3), a total of 6 samples were analyzed including non-targeting control (NTC), Sap30bp siRNA knockdown, and siRNA knockdown with Doxycycline-induced rescue with an siRNA-resistant Sap30bp cDNA performed in two biological replicates.
 
Contributor(s) Roth JF, Braunschweig U, Lin Z, Larsen B, Weatheritt RJ, Gingras A, Blencowe BJ
Citation(s) 38065061
Submission date Feb 09, 2023
Last update date Feb 23, 2024
Contact name Ulrich Braunschweig
Organization name University of Toronto
Department Donnelly Centre
Lab Benjamin J. Blencowe
Street address 160 College Street
City Toronto
State/province Ontario
ZIP/Postal code M5S 3E1
Country Canada
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (12)
GSM7036391 Sap_mEx3_NTC_BR1: N2a Flp-In rtTA (Sap30bp_withoutEx3), NT-control, Biological rep 1
GSM7036392 Sap_mEx3_NTC_BR2: N2a Flp-In rtTA (Sap30bp_withoutEx3), NT-control, Biological rep 2
GSM7036393 Sap_mEx3_KD_BR1: N2a Flp-In rtTA (Sap30bp_withoutEx3), siSap30bp, Biological rep 1
This SubSeries is part of SuperSeries:
GSE224971 Analysis of alternative exon-dependent interactome remodelling reveals multitasking functions of gene regulatory factors
Relations
BioProject PRJNA934535

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE224970_AS.DiffEvents_Sap30bp_dPSI.15.tab.gz 129.1 Kb (ftp)(http) TAB
GSE224970_DE_Sap30bp.tab.gz 2.2 Mb (ftp)(http) TAB
GSE224970_vast.tools_INCLUSION_LEVELS_Altsplicing_Sap30bp_Mmu12-mm9.tab.gz 12.8 Mb (ftp)(http) TAB
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Raw data are available in SRA
Processed data are available on Series record

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