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Series GSE224969 Query DataSets for GSE224969
Status Public on Nov 24, 2023
Title Analysis of alternative exon-dependent interactome remodelling reveals multitasking functions of gene regulatory factors (Chtop 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 35 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 Chtop siRNA knockdown and neural/non-neural isoform rescue on transcript nuclear/cytoplasmic localization in Neuro2a cell lines. For each isoform (with or without exon 5), a total of 18 samples were analyzed including non-targeting control (NTC), Chtop siRNA knockdown, and Chtop siRNA knockdown with Doxycycline-induced rescue (using an siRNA-resistant Chtop cDNA) across total/nuclear/cytoplasmic fractions 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 (35)
GSM7036356 Total_Chtop_mEx5_NTC_BR4: N2a Flp-In rtTA (Chtop_w/oExon5), NT-control, Total frac, Bio rep 1
GSM7036357 Total_Chtop_mEx5_NTC_BR6: N2a Flp-In rtTA (Chtop_w/oExon5), NT-control, Total frac, Bio rep 2
GSM7036358 Total_Chtop_mEx5_KD_BR4: N2a Flp-In rtTA (Chtop_w/oExon5), siChtop, Total frac, Bio rep 1
This SubSeries is part of SuperSeries:
GSE224971 Analysis of alternative exon-dependent interactome remodelling reveals multitasking functions of gene regulatory factors
BioProject PRJNA934536

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE224969_NCFracts_Chtop_COUNTS.txt.gz 685.2 Kb (ftp)(http) TXT
GSE224969_NCFracts_Chtop_DESeq2_normCOUNTS_CytovsTotal_wAnnotations.txt.gz 2.5 Mb (ftp)(http) TXT
GSE224969_NCFracts_Chtop_DESeq2_normCOUNTS_NucvsCyto_wAnnotations.txt.gz 2.5 Mb (ftp)(http) TXT
GSE224969_NCFracts_Chtop_DESeq2_normCOUNTS_NucvsTotal_wAnnotations.txt.gz 2.5 Mb (ftp)(http) TXT 1.9 Mb (ftp)(http) TAB
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