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Series GSE71916 Query DataSets for GSE71916
Status Public on Dec 10, 2015
Title Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown and rescue with cytoplasmic or nuclear Rbfox1 isoform [RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes induced by knockdown, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that in nascent RNA Rbfox1 bound predominantly to introns, while cytoplasmic Rbox1 bound to 3' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and overlapped significantly with miRNA binding sites. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease. In this data set, we included the data from RNA-seq experiments.
 
Overall design We performed RNA-seq to profile gene expression and splicing changes. The expression levels of Rbfox1 and Rbfox3 in cultured mouse hippocampal neurons were reduced by siRNAs. The reduction of Rbfox1 and 3 was rescued by expression of cytoplasmic or nuclear Rbfox1 splice isoform. The gene expression and splicing profiles were compared between different treatments. Eight samples were analyzed.
 
Contributor(s) Lee J, Lin C, Martin KC, Black DL
Citation(s) 26687839
Submission date Aug 10, 2015
Last update date May 15, 2019
Contact name Chia-ho Lin
E-mail(s) CHIAHOLI@g.UCLA.EDU
Organization name UCLA
Lab BLACK LAB
Street address 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH
City LOS ANGELES
State/province CA
ZIP/Postal code 90095
Country USA
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (8)
GSM1847354 siNT_EGFP_Rep1
GSM1847355 siNT_EGFP_Rep2
GSM1847356 siRbfox1&3_EGFP_Rep1
This SubSeries is part of SuperSeries:
GSE71917 Cytoplasmic Rbfox1 regulates the neuronal expression of synaptic and autism-related genes
Relations
BioProject PRJNA292447
SRA SRP062242

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Supplementary file Size Download File type/resource
GSE71916_Expression_Cufflinks_siRbfox1_3+EGFP_compared_to_siNT+EGFP.txt.gz 829.3 Kb (ftp)(http) TXT
GSE71916_Expression_Cufflinks_siRbfox1_3+Flag-Rbfox1_C_compared_to_siRbfox1_3+EGFP.txt.gz 820.5 Kb (ftp)(http) TXT
GSE71916_Expression_Cufflinks_siRbfox1_3+Flag-Rbfox1_N_compared_to_siRbfox1_3+EGFP.txt.gz 807.0 Kb (ftp)(http) TXT
GSE71916_Splicing_SpliceTrap_CassetteExon_siRbfox1_3+EGFP_compared_to_siNT+EGFP.txt.gz 29.2 Kb (ftp)(http) TXT
GSE71916_Splicing_SpliceTrap_CassetteExon_siRbfox1_3+Flag-Rbfox1_C_compared_to_siRbfox1_3+EGFP.txt.gz 20.9 Kb (ftp)(http) TXT
GSE71916_Splicing_SpliceTrap_CassetteExon_siRbfox1_3+Flag-Rbfox1_N_compared_to_siRbfox1_3+EGFP.txt.gz 42.3 Kb (ftp)(http) TXT
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