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

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

PROVIDER: PRJEB10303 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR981548.fastq.gz	Fastqsanger.gz
	ERR981549.fastq.gz	Fastqsanger.gz
	ERR981550.fastq.gz	Fastqsanger.gz
	ERR981551.fastq.gz	Fastqsanger.gz

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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

Unbiased identification of CSDE1-regulated targets during oncogene-induced senescence [RNA-Seq]

Project description:We show that the RNA-binding protein CSDE1/UNR promotes oncogene-induced senescence (OIS) in primary mouse keratynocytes challenged by over-expression of H-RASv12. Depletion of CSDE1 leads to senescence bypass, cell immortalization and tumor formation. Combining individual nucleotide cross-linking and immunoprecipitation (iCLIP), RNA-seq and polysome profiling followed by functional studies, we identify targets regulated by CSDE1 and uncover the downstream molecular mechanisms.

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Unbiased identification of CSDE1-regulated targets during oncogene-induced senescence [polysome profiling]

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Unbiased identification of CSDE1-regulated targets during oncogene-induced senescence [RNA-Seq-sh]

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Ribosome profiling of UNR (CSDE1) KD

Project description:Investigation of the effects of UNR (CSDE1) knock-down on translation in Melanoma Cells using Ribosome Profiling

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polyA+ and total RNA sequencing profiling of UNR (CSDE1) knock down

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

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

| PRJEB23565 | ENA

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).

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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

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