SOX2_bs
SOX2Δbs
Patrick Toolan-Kerr
3' QuantSeq of mESC lines that are either wildtype (WT), catalytic mutant (CM) or knockout (KO) for METTL3. Cells were either grown in 2iLIF, to maintain them in a naive pluripotent state, or for 2 days in N2B27, which induces spontaneous differentiation to a primed state, in which MEK signalling is active. Additionally conditions in which the WT cells were treated with a PARP inhibitor (Velaparib) or the KO cells were treated with a PARG inhibitor (PD00007273) for 24 hours were also added.
test-collection
A test collection
Sam Collection 2
Second test collection
ELAVL1-4 iCLIP rat brain
iLIN28AGFP_naive6_24_primed24
timecourse upon LIN28AGFP overexpression
TRA2Beta in Mouse testis
Alternative splicing amplifies the information content of the genome, creating multiple mRNA isoforms from single genes. The evolutionarily conserved splicing activator Tra2β (Sfrs10) is essential for mouse embryogenesis and implicated in spermatogenesis. Here we find that Tra2β is up-regulated as the mitotic stem cell containing population of male germ cells differentiate into meiotic and post-meiotic cells. Using CLIP coupled to deep sequencing, we found that Tra2β binds a high frequency of exons and identified specific G/A rich motifs as frequent targets. Significantly, for the first time we have analysed the splicing effect of Sfrs10 depletion in vivo by generating a conditional neuronal-specific Sfrs10 knock-out mouse (Sfrs10(fl/fl); Nestin-Cre(tg/+)). This mouse has defects in brain development and allowed correlation of genuine physiologically Tra2β regulated exons. These belonged to a novel class which were longer than average size and importantly needed multiple cooperative Tra2β binding sites for efficient splicing activation, thus explaining the observed splicing defects in the knockout mice. Regulated exons included a cassette exon which produces a meiotic isoform of the Nasp histone chaperone that helps monitor DNA double-strand breaks. We also found a previously uncharacterised poison exon identifying a new pathway of feedback control between vertebrate Tra2 proteins. Both Nasp-T and the Tra2a poison exon are evolutionarily conserved, suggesting they might control fundamental developmental processes. Tra2β protein isoforms lacking the RRM were able to activate specific target exons indicating an additional functional role as a splicing co-activator. Significantly the N-terminal RS1 domain conserved between flies and humans was essential for the splicing activator function of Tra2β. Versions of Tra2β lacking this N-terminal RS1 domain potently repressed the same target exons activated by full-length Tra2β protein.
4SU-iCLIP of MATR3 and hnRNPC
making regional segmentation for GRCh37
can be deleted
Community PTB CLIP public eCLIP
PARclip of MSI2
The RNA-binding protein Musashi 2 (MSI2) has emerged as an important regulator in cancer initiation, progression, and drug resistance. Translocations and deregulation of the MSI2 gene are diagnostic of certain cancers, including chronic myeloid leukemia (CML) with translocation t(7;17), acute myeloid leukemia (AML) with translocation t(10;17), and some cases of B-precursor acute lymphoblastic leukemia (pB-ALL). To better understand the function of MSI2 in leukemia, the mRNA targets that are bound and regulated by MSI2 and their MSI2-binding motifs need to be identified. To this end, using photoactivatable ribonucleoside cross-linking and immunoprecipitation (PARCLIP) and the multiple EM for motif elicitation (MEME) analysis tool, here we identified MSI2’s mRNA targets and the consensus RNA-recognition element (RRE) motif recognized by MSI2 (UUAG). Of note, MSI2 knockdown altered the expression of several genes with roles in eukaryotic initiation factor 2 (eIF2), hepatocyte growth factor (HGF), and epidermal growth factor (EGF) signaling pathways. We also show that MSI2 regulates classic interleukin-6 (IL-6) signaling by promoting the degradation of the mRNA of IL-6 signal transducer (IL6ST or GP130), which, in turn, affected the phosphorylation statuses of signal transducer and activator of transcription 3 (STAT3) and the mitogen-activated protein kinase ERK. In summary, we have identified multiple MSI2-regulated mRNAs and provided evidence that MSI2 controls IL6ST activity that control oncogenic signaling networks. Our findings may help inform strategies for unraveling the role of MSI2 in leukemia to pave the way for the development of targeted therapies.
Sm_CLIP_LU99
This experiment compares spliceosome positioning in LU99 cells plus and minus PRMT5 inhibition, by using iCLIP with antibodies against SmB. Control samples were treated with DMSO for either 24hr or 48hrs and test samples were treated with 500nM GSK-595 or 100nM LLY-283 PRMT5 inhibitors for 24hr or 48 hours. A non-crosslinked sample were also prepared using cells treated with DMSO for 48 hours. RNase treatments = 0.8 units/ml.
Test Jure 2020-07-15
public STAU2 eCLIP K562
Public dataset: SRP216536 An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia
STAU1 rat brain hiCLIP
SlamSeq-Tcells
SNRPA iCLIP
FUS iCLIP Mouse brain
DEPRECATED genomes and annotations
A meta collection that holds deprecated Genome and Annotation files
m6A_human_CD8_Tcells
This data contains the m6A miCLIP data for the project with primary human CD8+ T lymphocytes.
iCLIP ELAVL1 fractionation fibroblast
This experiment aims to identify ELAVL1-RNA binding sites in TGFb and cigarette smoke extract-stimulated human fibroblast cell line MRC-5. This is a collaboration with Llywelyn Griffith.
Lane61 ASF CLIP FL JAZ
These are i/hiCLIP experiments from FL (STAU1/2) JAZ (RBM20,DAZL,ZNF638) and Pierre Klein (IGF2BP1, SYNCRIP)
CPEB1 mESC
Tutorial Collection
This is a model tutorial collection to demonstrate how to analyse iCLIP data using the iMaps platform.