lane 56
PRPF8 eclip and iclip data
This collection focuses on analysing the encode data for the RBP PRPF8 to identify its global binding sites using the distribution map or RNAmap.
Matrin3 regulates AS and forms overlapping regulatory networks with PTB
Matrin3 is an RNA- and DNA-binding nuclear matrix protein found to be associated with neural and muscular degenerative diseases. A number of possible functions of Matrin3 have been suggested, but no widespread role in RNA metabolism has yet been clearly demonstrated. We identified Matrin3 by its interaction with the second RRM domain of the splicing regulator PTB. Using a combination of RNAi knockdown, transcriptome profiling and iCLIP, we find that Matrin3 is a regulator of hundreds of alternative splicing events, principally acting as a splicing repressor with only a small proportion of targeted events being co-regulated by PTB. In contrast to other splicing regulators, Matrin3 binds to an extended region within repressed exons and flanking introns with no sharply defined peaks. The identification of this clear molecular function of Matrin3 should help to clarify the molecular pathology of ALS and other diseases caused by mutations of Matrin3.
Hs HEK293
Mouse Brain P0
hnRNPA2 condensation properties
ELAVL1 and B cell antibody response
Post-transcriptional regulation of mRNA by the RNA binding protein ELAVL1 (HuR) is required in B cells for the germinal centre reaction and for the production of class-switched antibodies in response to T-independent antigens. Transcriptome-wide examination of RNA isoforms, abundance and translation in ELAVL1/HuR-deficient B cells, together with direct measurements of ELAVL1/HuR-RNA interaction, revealed that ELAVL1/HuR-dependent mRNA splicing affects hundreds of transcripts including the dihydrolipoyl succinyltransferase (Dlst), a subunit of the aketoglutaratedehydrogenase (aKGDH) enzyme. In the absence of HuR, defective mitochondrial metabolism results in high levels of reactive oxygen species and B cell death. The study (PMID: 25706746; The RNA-binding protein HuR is essential for the B cell antibody response) shows how post-transcriptional processes control the balance of energy metabolism required for B cell proliferation and differentiation.
lane 54
TDP-43 condensation properties specify its RNA-binding and regulatory repertoire
20191115_CM
m6A miCLIP polyA U2OS
K562_m1G_miCLIP
NanoCompore validation m6A miCLIP
m6A miCLIP produced from MOLM13 cells in either WT or CRISPR-targetted Mettl3 genetic background. This collection also contains an input sample for each condition.
quantseq rat brain STAU2KD vs WT
PTBP1_CLIP_variants_comparison_analysis
A collection focusing upon the analysis of PTBP1 protein for its different CLIP variants such as eCLIP, iCLIP, goldCLIP etc and to try to understand how these methods generate different and/or similar results based on the differences in their wet lab protocols. An attempt to understand the differences between them in terms of sensitivity and specificity.
FICC-Seq profiling of methyl-5-uridine
Methyl-5-uridine (m5U) is one the most abundant non-canonical bases present in cellular RNAs, and is formed via catalytic conversion of uridines. In yeast, m5U is known to be present at position 54 of tRNAs where modification is catalysed by the methyltransferase Trm2. Although the mammalian enzymes that catalyse m5U formation are yet to be identified via experimental evidence, based on sequence homology to Trm2, two candidates currently exist, TRMT2A and TRMT2B. Here we developed a genome-wide single-nucleotide resolution mapping method, Fluorouracil-Induced-Catalytic-Crosslinking-Sequencing (FICC-Seq), in order to map the relevant enzymatic targets in cellular RNA. We demonstrate that TRMT2A is responsible for the majority of m5U present in human RNA, and that it ubiquitously targets U54 of cytosolic tRNAs. By comparison to current methods, we show that FICC-Seq is a particularly robust method for accurate and reliable detection of relevant enzymatic target sites. Our associated demonstration of irreversible human m5U enzyme-RNA crosslinking in vivo following 5-flurouracil exposure is further intriguing, as it suggests a tangible mechanism for a previously suspected RNA-dependent route of 5-fluorouracil-mediated cytotoxicity. Carter, …, Hussain (2019) [FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA](https://www.ncbi.nlm.nih.gov/pubmed/?term=FICC-Seq%3A+a+method+for+enzyme-specified+profiling+of+methyl-5-uridine+in+cellular+RNA)
CD8_miCLIP_FACS
miCLIP and RNA-seq (mock miCLIP) performed on total RNA from FACS-isolated populations of human CD8 T-cells
iMaps genomes and annotations
Genomes, annotations and other commonly used imaps objects
STAU1 KD GRASPS
STAU1 KD polysome profiling
public ptbp1 iclip
MM RNAseq_4 cell lines
MM RNAseq
RNAseq MM cell lines after treatment with BCMA-CARTs