Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA174879 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR567525.fastq.gz | Fastqsanger.gz | |||
| SRR567526.fastq.gz | Fastqsanger.gz | |||
| SRR567527.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:The exon junction complex (EJC) is a central effector of mRNAs fate, linking nuclear processing to mRNA transport, translation and surveillance. Little is known about its transcriptome-wide targets. We used high-throughput sequencing after crosslinking and immunoprecipitation (HITS-CLIP) in human cells to identify the binding sites of the DEAD-box helicase eIF4AIII, an EJC core component. CLIP reads form peaks mainly located in spliced mRNAs. Most expressed exons harbour peaks equally distributed between the canonical EJC region ∼24 nucleotides upstream of exonic junctions and other non-canonical regions. Unexpectedly, both are preferentially associated to unstructured and purine-rich sequences containing the motif GAAGA, a potential binding site of EJC-associated factors. Therefore, EJC positions vary spatially and quantitatively between exons. This transcriptome-wide mapping of human eIF4AIII reveals unanticipated aspects of the EJC and broadens its potential impact on post-transcriptional regulation. To identify direct RNA binding sites of the EJC core component eIF4AIII, two biological CLIP-seq replicates were performed in HeLa cells. Additionally, mRNA-seq of the HeLa transcriptome was performed to normalize for the mRNA expression levels.
2012-10-21 | E-GEOD-40778 | biostudies-arrayexpress
Project description:The exon junction complex (EJC) is a central effector of mRNAs fate, linking nuclear processing to mRNA transport, translation and surveillance. Little is known about its transcriptome-wide targets. We used high-throughput sequencing after crosslinking and immunoprecipitation (HITS-CLIP) in human cells to identify the binding sites of the DEAD-box helicase eIF4AIII, an EJC core component. CLIP reads form peaks mainly located in spliced mRNAs. Most expressed exons harbour peaks equally distributed between the canonical EJC region ∼24 nucleotides upstream of exonic junctions and other non-canonical regions. Unexpectedly, both are preferentially associated to unstructured and purine-rich sequences containing the motif GAAGA, a potential binding site of EJC-associated factors. Therefore, EJC positions vary spatially and quantitatively between exons. This transcriptome-wide mapping of human eIF4AIII reveals unanticipated aspects of the EJC and broadens its potential impact on post-transcriptional regulation.
2012-10-21 | GSE40778 | GEO
Project description:Transcriptome-wide modulation of splicing by the exon junction complex
| PRJNA266584 | ENA
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:We have identified Mbnl2 mediated splicing events and mRNA expression regulation by comparing WT and Mbnl2 ΔE2/ΔE2 mouse hippocampii using Affymetrix Mouse Exon Junction Array and mRNA sequencing. The splicing microarray data has already been submitted under GSE37908 which also includes a re-analysis of RNA-seq data. The TableS1.xls contains Splicing microarray analysis data of Mbnl2+/+ vs. MBNL2 ΔE2/ΔE2 knockout hippocampus. The TableS2.xls files contain RNA-Seq, Gene Ontology, HITS-CLIP and CIMS summary of Mbnl2+/+ vs. MBNL2 ΔE2/ΔE2 knockout hippocampus. The file contents are descibed in the 'TableS1_S2_readme.pdf' and data processing details are included in the 'data_processing_readme.pdf' file. The Mbnl2_TableS2.xls contains data from exon junction microarrays for splicing analysis between WT and Mbnl2 delta2 mice. It also contains RNA-seq based splicing analysis between WT and Mbnl2 delta2 mice. Mbnl2_TableS2 further contains common targets between the two analyses, Gene Ontology and finally the HITS-CLIP data. CLIP tag summary describes read numbers for the three biological replicates. CLIP sig peaks contains significant HITS-CLIP unique reads/peaks after processing the data (BED files). Finally, CIMS analysis describes the Mbnl2 binding motif.
2012-08-16 | GSE38497 | GEO
Project description:The exon junction complex is deposited at 24nt upstream of exon-exon junctions, but not at every junction. The core complex is comprosed of 4 proteins, eIF4A3, Magoh, Y14 and MLN51. Here we performed immunoprecipitation of Y14 with subsequent iCLIP of eIF4A3 in HeLa cells to identify the crosslink sites of the exon junction complex, in particular eIF4A3.
2016-11-24 | E-MTAB-3618 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE37037: Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length: A-seq GSE37398: Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length: CLIP Refer to individual Series
2012-05-14 | E-GEOD-37401 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE34992: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splice array) GSE34993: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq) GSE34995: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (RNA-Seq) Refer to individual Series
2012-02-20 | E-GEOD-34996 | biostudies-arrayexpress
Project description:The U2AF heterodimer has been well studied for its role in defining functional 3M-bM-^@M-^Y splice sites in pre-mRNA splicing, but many fundamental questions still remain unaddressed regarding the function of U2AF in mammalian genomes. Through genome-wide analysis of U2AF-RNA interactions, we report that U2AF has the capacity to directly define ~88% of functional 3M-bM-^@M-^Y splice sites in the human genome, but numerous U2AF binding events also occur in intronic locations. Mechanistic dissection reveals that upstream intronic binding events interfere with the immediate downstream 3M-bM-^@M-^Y splice site associated with either the alternative exon to cause exon skipping or with the competing constitutive exon to induce exon inclusion. We further demonstrate partial functional impairment with mutations in U2AF35, but not U2AF65, in regulated splicing. These findings reveal the genomic function and regulatory mechanism of U2AF in both normal and disease states. Examination of U2AF heterodimer regulated splicing in Hela cells with CLIP-seq (U2AF65), paired-end RNA-seq (si-NC and si-U2AF65) and RASL-seq (respective three biological replicates of WT, si-NC, si-U2AF65, si-U2AF35, si-NC + pcDNA3.0, si-U2AF65 + pcDNA3.0, and si-U2AF65 + Flag-U2AF35)
2014-10-08 | E-GEOD-61603 | biostudies-arrayexpress