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Transcriptome-wide mapping of RNA binding sites of the RNA-binding protein Unkempt using iCLIP-seq

ABSTRACT: Transcriptome-wide mapping of RNA binding sites of the RNA-binding protein Unkempt using iCLIP-seq

PROVIDER: PRJEB5286 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR419253.fastq.gz	Fastqsanger.gz
	ERR419254.fastq.gz	Fastqsanger.gz
	ERR419255.fastq.gz	Fastqsanger.gz
	ERR419256.fastq.gz	Fastqsanger.gz
	ERR419257.fastq.gz	Fastqsanger.gz

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Transcriptome-wide mapping of RNA binding sites of the RNA-binding protein Unkempt using iCLIP-seq

Project description:iCLIP experiments tomap the RNA binding sites of the RNA-binding protein Unkempt across the transcriptome in SH-SY5Y cells, HeLa cells with ectopic Unk expression and mouse E15 embryonic brain samples. Expression of Unk is normally largely restricted to the nervous system. We therefore mapped the binding sites in human SH-SY5Y and mouse E15 brain to detect its physiological binding sites (in SH-SY5Y, we also performed the RNAseq experiment upon Unk knockdown). HeLa cells on the other hand normally don't express Unk, but convert to neuron-like shape when the protein is ectopically expressed. So, here we hoped to identify those binding events (and hence target transcripts) that are critical for this morphological transformation.

2015-03-09 | E-MTAB-2279 | biostudies-arrayexpress

Regulation by the RNA-binding protein Unkempt at its effector interface [iCLIP]

Project description:Regulation by the RNA-binding protein Unkempt at its effector interface [iCLIP]

| PRJNA1004240 | ENA

Regulation by the RNA-binding protein Unkempt at its effector interface [iCLIP]

Project description:How RNA-binding proteins (RBPs) convey regulatory instructions to the core effectors of RNA processing is unclear. Here we document the existence and functions of a multivalent RBP–effector interface. We show that the effector interface of a conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of ‘dual-purpose’ peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by Unkempt. Systems analyses reveal that multivalent RBP–effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP–effector interface.

2024-03-17 | GSE240562 | GEO

iCLIP transcriptome-wide mapping of UNR (CSDE1) binding sites

Project description:Analysis of UNR (CSDE1) binding to RNA targets by iCLIP transcriptome-wide mapping.

2016-11-07 | E-MTAB-3818 | biostudies-arrayexpress

Transcriptional profiling upon knockdown of the RNA-binding protein Unkempt

Project description:RNAseq to assess changes in transcript abundance upon knockdown of the RNA-binding protein Unkempt in human SH-SY5Y cell lines.

2015-01-15 | E-MTAB-2277 | biostudies-arrayexpress

Regulation by the RNA-binding protein Unkempt at its effector interface

2024-04-11 | PXD050601 | Pride

Ribosome profiling upon overexpression of the RNA-binding protein Unkempt

Project description:Ribosome profiling to assess changes in ribosome occpancy upon overexpression of the RNA-binding protein Unkempt (most likely acts as a translational regulator) in human HeLa cell lines.

2015-03-09 | E-MTAB-2278 | biostudies-arrayexpress

Mapping hnRNP H binding sites on the RON wildtype minigene via iCLIP.

Project description:We developed a high-throughput mutagenesis screen to comprehensively identify the cis-regulatory elements that control a target splicing event from the MST1R gene that codes for the RON receptor tyrosine kinase. Skipping of alternative exon 11 results in a constitutively active isoform that promotes epithelial to mesenchymal transition and thereby contributes to the invasive phenotype of tumors. We identified the RNA binding protein hnRNP H as an important regulator of RON exon 11 splicing. To map hnRNP H binding sites on the RON minigene, we performed hnRNP H iCLIP with RON wildtype minigene transfected HEK293T cells. iCLIP was performed according to a previously published protocol (PMID: 26463384). The iCLIP libraries were made from two replicates of HEK293T cells at 24 h after RON minigene transfection. The cells were irradiated with 150 mJ/cm2 UV light at 254 nm. For the immunoprecipitation step, we used 7.5 µg of a polyclonal rabbit anti-HNRNPH antibody from Abcam (AB10374). RNase digestion was performed by adding 10 µl of 1/100 diluted RNase I (Ambion) to each sample. We performed the sequencing on an Illumina HiSeq2000 (75-nt single-end reads).

2018-06-27 | E-MTAB-6220 | biostudies-arrayexpress

iCLIP transcriptome-wide mapping of UNR (CSDE1) binding sites

Project description:iCLIP transcriptome-wide mapping of UNR (CSDE1) binding sites

| PRJEB10303 | ENA

Regulation by the RNA-binding protein Unkempt at its effector interface [RNA]

2024-03-17 | GSE240565 | GEO