Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA314955 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3222136.fastq.gz | Fastqsanger.gz | |||
| SRR3222137.fastq.gz | Fastqsanger.gz | |||
| SRR3222138.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:Ptbp2 controls an alternative splicing network required for cell communication during spermatogenesis
| PRJNA314953 | ENA
Project description:Ptbp2 controls an alternative splicing network required for cell communication during spermatogenesis [RNA-Seq]
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Project description:Two polypyrimidine tract RNA-binding proteins (PTBs), one near-ubiquitously expressed (Ptbp1) and another highly tissue-restricted (Ptbp2), regulate RNA in interrelated but incompletely understood ways. Ptbp1, a splicing regulator, is replaced in the brain and differentiated neuronal cell lines by Ptbp2. To define the roles of Ptbp2 in the nervous system, we generated two independent Ptbp2-null strains, unexpectedly revealing that Ptbp2 is expressed in neuronal progenitors and is essential for postnatal survival. A HITS-CLIP (high-throughput sequencing crosslinking immunoprecipitation)-generated map of reproducible Ptbp2–RNA interactions in the developing mouse neocortex, combined with results from splicing-sensitive microarrays, demonstrated that the major action of Ptbp2 is to inhibit adult-specific alternative exons by binding pyrimidine-rich sequences upstream of and/or within them. These regulated exons are present in mRNAs encoding proteins associated with control of cell fate, proliferation, and the actin cytoskeleton, suggesting a role for Ptbp2 in neurogenesis. Indeed, neuronal progenitors in the Ptbp2-null brain exhibited an aberrant polarity and were associated with regions of premature neurogenesis and reduced progenitor pools. Thus, Ptbp2 inhibition of a discrete set of adult neuronal exons underlies early brain development prior to neuronal differentiation and is essential for postnatal survival. Eight Ptbp2 HITS-CLIP libraries generated from mouse embryonic brain (four libraries from each of two biologic replicates).
2013-05-31 | E-GEOD-47564 | biostudies-arrayexpress
Project description:To determine direct targets of PTBP2-dependent alternative splicing, we performed CLIP-seq analysis of PTBP2 binding in both human cortical tissue and human neurons derived from induced-pluripotent stem cells (iPSC-neurons), and we combine this with splicing analysis following PTBP2 depletion in iPSC-neurons.
2023-04-13 | GSE206650 | GEO
Project description:Alternative splicing (AS) plays key roles in the specialization of cell functions in different tissues and stages of development. In spermatogenic cells, the complexity of AS isoforms exceeds that of most whole tissues, but the regulation, dynamics, and functions of AS in spermatogenesis have remained poorly defined. We previously demonstrated that the RNA binding protein Ptbp2 is essential for cell survival during spermatogenesis; however, the underlying mechanisms were not explored. Here, we demonstrate that Ptbp2 is a critical AS regulator in spermatogenic cells, and controls a functionally-related network of genes involved in germ cell adhesion and protein trafficking to and from the plasma membrane. In parallel, we identify distinct AS programs in different stages of spermatogenesis, and demonstrate an important role for Ptbp2 in stage-specific AS regulation. Collectively, the data provide new insights into the temporal dynamics and importance of AS in mammalian germ cell development, and demonstrate a central role for Ptbp2 in its regulation.
2017-06-20 | GSE79104 | GEO
Project description:Alternative splicing (AS) plays key roles in the specialization of cell functions in different tissues and stages of development. In spermatogenic cells, the complexity of AS isoforms exceeds that of most whole tissues, but the regulation, dynamics, and functions of AS in spermatogenesis have remained poorly defined. We previously demonstrated that the RNA binding protein Ptbp2 is essential for cell survival during spermatogenesis, however the underlying mechanisms were not explored. To investigate this, we generated paired-end RNA-Seq data from wild type (WT) and Ptbp2 conditional knockout (cKO) testes at postnatal day 25 (p25) using Illumina ScriptSeq™ v2 RNA-Seq library preparation kits and sequenced at the CWRU Sequencing Core. Our resulting analyses demonstrate that Ptbp2 is a critical AS regulator in spermatogenic cells, where it controls a functionally-related network of genes involved in germ cell adhesion and protein trafficking to and from the plasma membrane. In parallel, we identified distinct AS programs in different stages of spermatogenesis, and defined a role for Ptbp2 in stage-specific AS regulation. Collectively, the data provide new insights into the importance of AS in mammalian germ cell development and demonstrate a central role for Ptbp2 in its regulation.
2017-06-20 | GSE79105 | GEO
Project description:Two polypyrimidine tract RNA-binding proteins (PTBs), one near-ubiquitously expressed (Ptbp1) and another highly tissue-restricted (Ptbp2), regulate RNA in interrelated but incompletely understood ways. Ptbp1, a splicing regulator, is replaced in the brain and differentiated neuronal cell lines by Ptbp2. To define the roles of Ptbp2 in the nervous system, we generated two independent Ptbp2-null strains, unexpectedly revealing that Ptbp2 is expressed in neuronal progenitors and is essential for postnatal survival. A HITS-CLIP (high-throughput sequencing crosslinking immunoprecipitation)-generated map of reproducible Ptbp2–RNA interactions in the developing mouse neocortex, combined with results from splicing-sensitive microarrays, demonstrated that the major action of Ptbp2 is to inhibit adult-specific alternative exons by binding pyrimidine-rich sequences upstream of and/or within them. These regulated exons are present in mRNAs encoding proteins associated with control of cell fate, proliferation, and the actin cytoskeleton, suggesting a role for Ptbp2 in neurogenesis. Indeed, neuronal progenitors in the Ptbp2-null brain exhibited an aberrant polarity and were associated with regions of premature neurogenesis and reduced progenitor pools. Thus, Ptbp2 inhibition of a discrete set of adult neuronal exons underlies early brain development prior to neuronal differentiation and is essential for postnatal survival.
2013-05-31 | GSE47564 | GEO
Project description:To assess the requirement of Nova2 for alternative processing of RNA in mouse brain. Protein-RNA interactions play critical roles in all aspects of gene expression. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). HITS-CLIP analysis of the neuron-specific splicing factor Nova2 revealed extremely reproducible RNA binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo. HITS-CLIP revealed a large number of Nova-RNA interactions in 3â UTRs, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo. Keywords: Comparative analysis Refer to individual Series. This SuperSeries is composed of the following subset Series: GSE17374: Wild type vs. Nova2 KO mouse: Exon array data GSE17376: Wild type vs. Nova2 KO mouse: Exon junction array data
2010-06-20 | E-GEOD-12965 | biostudies-arrayexpress
Project description:To assess the requirement of Nova2 for alternative processing of RNA in mouse brain. Protein-RNA interactions play critical roles in all aspects of gene expression. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). HITS-CLIP analysis of the neuron-specific splicing factor Nova2 revealed extremely reproducible RNA binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo. HITS-CLIP revealed a large number of Nova-RNA interactions in 3’ UTRs, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo.
2009-11-04 | GSE17374 | GEO
Project description:To assess the requirement of Nova2 for alternative processing of RNA in mouse brain. Protein-RNA interactions play critical roles in all aspects of gene expression. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). HITS-CLIP analysis of the neuron-specific splicing factor Nova2 revealed extremely reproducible RNA binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo. HITS-CLIP revealed a large number of Nova-RNA interactions in 3’ UTRs, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo.
2009-11-04 | GSE17376 | GEO