Ribosome profiling of Rbfox1 fl/fl-Cre and control cortical culture
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1047149 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27005086.fastq.gz | Fastqsanger.gz | |||
| SRR27005087.fastq.gz | Fastqsanger.gz | |||
| SRR27005088.fastq.gz | Fastqsanger.gz | |||
| SRR27005089.fastq.gz | Fastqsanger.gz |
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Project description:The goal of this experiment is to analyze differences in translation of mRNA transcripts in absence vs presence of Rbfox1 using ribosome profiling of Rbfox1-cKO and control mature primary neuronal cultures
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Project description: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 microarray experiments. We performed microarray analysis to profile gene expression and splicing changes in mouse hippocampal cultures (14 DIV) with Rbfox1 and Rbfox3 double knockdown by siRNAs. Before the treatment of siRNAs, the hippocampal cultures were treated with AraC to eliminate glial cells and co-cultured with cortical cultures to support the growth of neurons. Six samples were analyzed.
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| PRJNA491199 | ENA