Project description:Stau2 iCLIP of mouse brain was performed to identify RNA binding sites of Stau2 protein in mouse brain cells. The experiment was performed in triplicate, and each of the replicates was split into two separate halves at the cDNA stage, which together led to 6 separate datasets. The iCLIP protocol includes the following steps; Embryonic day 18 whole mouse brain was dissociated and irradiated with UV-C light, and the cells were then lysed using a buffer containing detergents. The RNAs were partially digested, and Stau2 and the cross-linked RNA fragments were immunoprecipitated using anti-Stau2 antibody. A DNA adaptor was then ligated to the RNA fragments and the cross-linked RNAs were further purified by SDS-PAGE and nitrocellulose membrane transfer. The RNAs were extracted from the membrane by proteinase K treatment, and converted into a high-throughput DNA sequencing compatible library by reverse transcription and PCR. For further details, see the methods of the associated manuscript. Note that the sequence reads start with (3 nucleotides of unique molecular identifiers) + (4 nucleotides of experimental barcode) + (2 nucleotides of unique molecular identifiers) followed by the sequence of the cross-linked RNA fragments.
Project description:Using an improved hiCLIP protocol (Lee & Chakrabarti et al.), we mapped the binding sites of STAU2 in rat cortex and their secondary structure context.
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.
Project description:Endogenous SRSF3 and SRSF4 RNA binding sites were identified genome-wide by iCLIP in P19 BAC trangenic cell lines using GFP-epitope tag.
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).
Project description:We report here the sequencing and analysis of RNA isolated through RNA immunoprecipitation (RIP) of embryonic mouse cortical tissue. STAU2 antibodies were used to perform these RIPs at four different ages, and the RNA was compared against matching input samples. This allowed characterization of putative STAU2 binding sites in different RNA classes over the course of development, important as STAU2 is a known double-stranded RNA binding protein with a role in asymmetric division of neural progenitor cells.
Project description:Staufen2 (Stau2) is an RNA-binding protein that is involved in dendritic spine morphogenesis and function. Several studies have recently investigated the role of Stau2 in the regulation of its neuronal target mRNAs, with particular focus on the hippocampus. Here, we provide evidence for Stau2 expression and function in cerebellar Purkinje cells. We show that Stau2 downregulation (Stau2GT) lead to an increase of the glutamate receptor ionotropic delta subunit 2 (GluD2) in Purkinje cells when animals performed physical activity by voluntary wheel running. Furthermore, Stau2GT mice showed lower performance in motor coordination assays but enhanced motor learning abilities, concomitantly with an increase in dendritic GluD2 expression. Together, our results suggest a novel role of Stau2 in Purkinje cell synaptogenesis in the mouse cerebellum