Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Gene Yeo
PROVIDER: E-GEOD-77634 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2016-04-07 | E-GEOD-78509 | biostudies-arrayexpress
Project description:Human pluripotent stem cells (hPSCs) require precise control of post-transcriptional RNA networks to maintain proliferation and survival. Using a recently developed enhanced UV crosslinking and immunoprecipitation (eCLIP) approach, we identify RNA targets of the IMP/IGF2BP family of RNA-binding proteins in hPSCs. At the broad region- and binding site-level IMP1 and IMP2 show reproducible binding to a large and overlapping set of 3'UTR-enriched targets. RNA Bind-N-Seq applied to recombinant full-length IMP1 and IMP2 reveals CA-rich motifs that are enriched in eCLIP-defined binding sites. We observe that IMP1 loss in hPSCs recapitulates IMP1 phenotypes, including a reduction in cell adhesion and an increase in cell death. For cell adhesion, in hPSCs we find IMP1 maintains levels of integrin mRNA, specifically regulating RNA stability of ITGB5. Additionally, we show IMP1 can be linked to hPSC survival via direct target BCL2. Thus, transcriptome-wide binding profiles identify hPSC targets modulating well-characterized IMP1 roles. eCLIP-seq was performed in biological replicate for IGF2BP1/IMP1 and IGF2BP2/IMP2, as well as one replicate each for IGF2BP3/IMP3, RBFOX2, and an IgG control. Each sample has a size-matched input control for analysis
2016-04-07 | E-GEOD-78507 | biostudies-arrayexpress
Project description:iCLIP-seq experiment to asses the binding of mitochondrially targeted MRB8170 and MRB4160 involved in RNA editing on a genomic scale. Furthermore, to investigate what subsets of maxicircles transcripts (pan-edited, minimally-edited and never-edited) are bound to both the above proteins in vivo.
2016-08-14 | E-MTAB-4934 | biostudies-arrayexpress
Project description:The vertebrate and neural-specific SR-related protein nSR100/SRRM4 regulates an extensive program of alternative splicing with critical roles in nervous system development. However, the mechanism by which nSR100 controls its target exons is poorly understood. We demonstrate that nSR100-dependent neural exons are associated with a unique configuration of intronic cis-elements that promote rapid switch-like regulation during neurogenesis. A key feature of this configuration is the insertion of specialized intronic enhancers between polypyrimidine tracts and acceptor sites that bind nSR100 to potently activate exon inclusion in neural cells, while weakening 3' splice site recognition and contributing to exon skipping in non-neural cells. nSR100 further operates by forming multiple interactions with early spliceosome components bound proximal to 3' splice sites. These multifaceted interactions achieve dominance over neural exon silencing mediated by the splicing regulator PTBP1. The results thus illuminate a widespread mechanism by which a critical neural exon network is activated during neurogenesis. RNA-Seq was used to obtain mRNA profiles of various N2A and 293T cell lines from human and mouse, respectively, to investigate the roles of nSR100, Ptbp1 and U2af65 in alternative splicing regulation. PAR-iCLIP and iCLIP experiments followed by high throughput sequencing were conducted to obtain RNA binding profiles of nSR100, PTBP1 and U2af65.
2014-09-11 | E-GEOD-57278 | biostudies-arrayexpress
Project description:iCLIP experiment to assess the binding of the highly abundant nuclear RNA-binding protein hnRNP C and core splicing factor U2AF65 on a genomic scale. To investigate how both proteins compete for binding at a subset of sites, U2AF65 iCLIP experiments were performed from both HNRNPC knockdown and control HeLa cells.
2013-01-31 | E-MTAB-1371 | biostudies-arrayexpress
Project description:RNA Binding Protein immunoprecipitation study for multiple target proteins in HepG2 cell line as part of the ENCODE consortium. Analyzed data tracks available for view on UCSC Genome browser. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Three sample replicates per sample type. Total input RNA and Negative target RIP (antibody for bacteriophage coat protein) are provided as controls. Individual samples reflect biological replicates defined as separate RIP runs (as opposed to technical replicate defined as multiple arrays run with same RIP sample as starting material)
2011-09-18 | E-GEOD-31720 | biostudies-arrayexpress
Project description:RNA Binding Protein immunoprecipitation study for multiple target proteins in GM12878 cell line as part of the ENCODE consortium. Analyzed data tracks available for view on UCSC Genome browser. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Three sample replicates per sample type. Total input RNA and Negative target RIP (antibody for bacteriophage coat protein) are provided as controls. Individual samples reflect biological replicates defined as separate RIP runs (as opposed to technical replicate defined as multiple arrays run with same RIP sample as starting material)
2011-09-18 | E-GEOD-31716 | biostudies-arrayexpress
Project description:RNA Binding Protein immunoprecipitation study for multiple target proteins in K562 cell line as part of the ENCODE consortium. Analyzed data tracks available for view on UCSC Genome browser. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Three sample replicates per sample type. Total input RNA and Negative target RIP (antibody for bacteriophage coat protein) are provided as controls. Individual samples reflect biological replicates defined as separate RIP runs (as opposed to technical replicate defined as multiple arrays run with same RIP sample as starting material)
2011-09-18 | E-GEOD-31717 | biostudies-arrayexpress
Project description:RNA Binding Protein immunoprecipitation study for multiple target proteins in HeLaS3 cell line as part of the ENCODE consortium. Analyzed data tracks available for view on UCSC Genome browser. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Three sample replicates per sample type. Total input RNA and Negative target RIP (antibody for bacteriophage coat protein) are provided as controls. Individual samples reflect biological replicates defined as separate RIP runs (as opposed to technical replicate defined as multiple arrays run with same RIP sample as starting material)
2011-09-18 | E-GEOD-31719 | biostudies-arrayexpress
Project description:Individual nucleotide resolution cross-linking immunoprecipitation (iCLIP) detects protein-RNA binding sites at a single nucleotide resolution. We aimed to identify the transcripts directly bound to DDX3X and DDX54 in human breast cancer MCF7 cells and to characterize the site of interaction at a single nucleotide resolution.
2018-11-21 | E-MTAB-6230 | biostudies-arrayexpress