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Neuronal activity regulates alternative exon usage

ABSTRACT: Neuronal activity regulates alternative exon usage

PROVIDER: PRJNA622919 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11475300_1.fastq.gz	Fastqsanger.gz
	SRR11475300_2.fastq.gz	Fastqsanger.gz
	SRR11475301_1.fastq.gz	Fastqsanger.gz
	SRR11475301_2.fastq.gz	Fastqsanger.gz
	SRR11475302_1.fastq.gz	Fastqsanger.gz

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KIS counteracts PTBP2 and regulates alternative exon usage in neurons

Project description:Alternative RNA splicing is an essential and dynamic process in neuronal differentiation and synapse maturation, and dysregulation of this process has been associated with neurodegenerative diseases. Recent studies have revealed the importance of RNA-binding proteins in the regulation of neuronal splicing programs. However, the molecular mechanisms involved in the control of these splicing regulators are still unclear. Here we show that KIS, a kinase upregulated in the developmental brain, imposes a genome-wide alteration in exon usage during neuronal differentiation. KIS contains a protein-recognition domain common to spliceosomal components and phosphorylates PTBP2, counteracting the role of this splicing factor in exon exclusion. At the molecular level, phosphorylation of unstructured domains within PTBP2 causes its dissociation from two co-regulators, Matrin3 and hnRNPM, and hinders the RNA-binding capability of the complex. Furthermore, KIS and PTBP2 display strong and opposing functional interactions in synaptic spine emergence and maturation. Taken together, our data uncover a post-translational control of splicing regulators that link transcriptional and alternative exon usage programs in neuronal development.

2024-04-25 | PXD050320 | Pride

KIS counteracts PTBP2 and regulates alternative exon usage in neurons

2024-04-25 | GSE260790 | GEO

KIS counteracts PTBP2 and regulates alternative exon usage in neurons

Project description:KIS counteracts PTBP2 and regulates alternative exon usage in neurons

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Neuronal activity regulates alternative exon usage.

Project description:Neuronal activity-regulated gene transcription underlies plasticity-dependent changes in the molecular composition and structure of neurons. A large number of genes regulated by different neuronal plasticity inducing pathways have been identified, but altered gene expression levels represent only part of the complexity of the activity-regulated transcriptional program. Alternative splicing, the differential inclusion and exclusion of exonic sequence in mRNA, is an additional mechanism that is thought to define the activity-dependent transcriptome. Here, we present a genome wide microarray-based survey to identify exons with increased expression levels at 1, 4 or 8 h following neuronal activity in the murine hippocampus provoked by generalized seizures. We used two different bioinformatics approaches to identify alternative activity-induced exon usage and to predict alternative splicing, ANOSVA (ANalysis Of Splicing VAriation) which we here adjusted to accommodate data from different time points and FIRMA (Finding Isoforms using Robust Multichip Analysis). RNA sequencing, in situ hybridization and reverse transcription PCR validate selected activity-dependent splicing events of previously described and so far undescribed activity-regulated transcripts, including Homer1a, Homer1d, Ania3, Errfi1, Inhba, Dclk1, Rcan1, Cda, Tpm1 and Krt75. Taken together, our survey significantly adds to the comprehensive understanding of the complex activity-dependent neuronal transcriptomic signature. In addition, we provide data sets that will serve as rich resources for future comparative expression analyses.

| S-EPMC7656758 | biostudies-literature

Neuronal activity regulates alternative exon usage

Project description:Kanate was used to induce seizures in mice, and gene expression in the hippocampus was measured

2020-11-18 | GSE148028 | GEO

Inflammation drives alternative first exon usage of critical immune genes including Aim2

Project description:Inflammation drives alternative first exon usage of critical immune genes including Aim2

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Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors

Project description:Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors

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Inflammation drives alternative first exon usage of critical immune genes including Aim2 [nanopore]

Project description:Inflammation drives alternative first exon usage of critical immune genes including Aim2 [nanopore]

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Inflammation drives alternative first exon usage of critical immune genes including Aim2 [RNA-seq]

Project description:Inflammation drives alternative first exon usage of critical immune genes including Aim2 [RNA-seq]

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Neuronal activity-induced late-onset alternative splicing and H3K9me3 modification

Project description:Activity-induced alternative splicing has emerged as an important mechanism for the dynamic modification of neuronal function. To examine whether activity could cause transcriptional programs alteration in alternative splicing and associative H3K9me3 in the specific genomic loci, we performed whole genome RNA-sequencing (RNA-seq) in cultured cortical neurons at 24 hours after membrane depolarization by exposure to high extracellular KCl (50mM, 10min). A transient neuronal activation could induce alternation of splice isoform choice in many genes at 24hrs after stimuli. To detect the correlation of activity-induced H3K9me3 accumulation with the splicing events, we performed ChIP-seq in hippocmapus of mice, which were subjected to enriched environment for 24 hours and kept in homecage for 1 week.

2017-03-16 | GSE93682 | GEO

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