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Series GSE250098 Query DataSets for GSE250098
Status Public on Dec 16, 2023
Title The dilated cardiomyopathy-associated RNA Binding Motif Protein 20 regulates long pre-mRNAs in neurons [seCLIP-Seq]
Organism Mus musculus
Experiment type Other
Summary Precise coordination of molecular programs and neuronal growth govern the formation, maintenance, and adaptation of neuronal circuits. RNA metabolism has emerged as a key regulatory node of neural development and nervous system pathologies. To uncover novel cell-type-specific RNA regulators, we systematically investigated expression of RNA recognition motif-containing proteins in the mouse neocortex. Surprisingly, we found RBM20, an alternative splicing regulator associated with dilated cardiomyopathy, to be expressed in cortical parvalbumin interneurons and mitral cells of the olfactory bulb. Genome-wide mapping of RBM20 target mRNAs revealed that neuronal RBM20 binds distal intronic regions. Loss of neuronal RBM20 has only modest impact on alternative splice isoforms but results in a significant reduction in an array of mature mRNAs in the neuronal cytoplasm. This phenotype is particularly pronounced for genes with long introns that encode synaptic proteins. We hypothesize that RBM20 ensures fidelity of pre-mRNA splicing by suppressing non-productive splicing events in long neuronal genes. This work highlights a common requirement of two excitable cell types, cardiomyocytes and neurons, for RBM20-dependent transcriptome regulation.
 
Overall design eCLIP-seq, RBM20 WT heart and olfactory bulb, size matched input used as a contorl. All samples libraries were single-end. However OBrep3 and its SMI were sequenced paired-end and only R1 fastq file was used for further analysis.
 
Contributor(s) Di Bartolomei G, Ortiz R, Schreiner D, Falkner S, Creemers EE, Scheiffele P
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Submission date Dec 13, 2023
Last update date Dec 16, 2023
Contact name peter scheiffele
E-mail(s) peter.scheiffele@unibas.ch
Organization name Biozentrum, university of Basel
Street address spitalstrasse 41
City basel
ZIP/Postal code 4056
Country Switzerland
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (10)
GSM7973956 olfactory bulb, WT, eCLIP, rep1
GSM7973957 olfactory bulb, WT, eCLIP, rep2
GSM7973958 olfactory bulb, WT, eCLIP, rep3
This SubSeries is part of SuperSeries:
GSE250100 The dilated cardiomyopathy-associated RNA Binding Motif Protein 20 regulates long pre-mRNAs in neurons
Relations
BioProject PRJNA1052024

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

Supplementary file Size Download File type/resource
GSE250098_Appendix_Table_S1.xlsx 20.6 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA

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