Search publications

18 results for “Splicing enhancer”

Clear

  1. Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces.

    Cell systems · 2026 : 101588

    RNA-binding proteins (RBPs) orchestrate post-transcriptional processes, including splicing, cleavage and polyadenylation, and translation. Our updated RBP resource integrates data from 92 additional RBPs (286 in total) profiled by enhanced CLIP (eCLIP), enabling comprehensive characterization of RNA elements within human K562 …

    PMID 42025161 DOI ↗

  2. Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs.

    Nature chemical biology · 2025

    Endogenous uridine-rich small nuclear RNAs (U snRNAs) form RNA-protein complexes to process eukaryotic pre-mRNA into mRNA. Previous studies have demonstrated programmable U snRNA guide-targeted exon inclusion and exclusion. Here we investigated whether snRNAs can also enhance RNA base editing over …

    PMID 40968292 DOI ↗

  3. Phenylpyrazoles as Inhibitors of the m<sup>6</sup>A RNA-Binding Protein YTHDF2.

    JACS Au · 2025 · 5(2): 618-630

    The <i>N</i>6-methyladenosine (m<sup>6</sup>A) modification, which is the most common RNA modification in eukaryotes, is regulated by the "writer" methyltransferases, the "reader" m<sup>6</sup>A binding proteins, and the "eraser" demethylases. m<sup>6</sup>A plays a multifunctional role in physiological and pathological processes, regulating all …

    PMID 40017738 DOI ↗

  4. Inhibition of RNA splicing triggers CHMP7 nuclear entry, impacting TDP-43 function and leading to the onset of ALS cellular phenotypes.

    Neuron · 2024 · 112(24): 4033-4047.e8

    Amyotrophic lateral sclerosis (ALS) is linked to the reduction of certain nucleoporins in neurons. Increased nuclear localization of charged multivesicular body protein 7 (CHMP7), a protein involved in nuclear pore surveillance, has been identified as a key factor damaging nuclear …

    PMID 39486415 DOI ↗

  5. Large-scale map of RNA-binding protein interactomes across the mRNA life cycle.

    Molecular cell · 2024 · 84(19): 3790-3809.e8

    mRNAs interact with RNA-binding proteins (RBPs) throughout their processing and maturation. While efforts have assigned RBPs to RNA substrates, less exploration has leveraged protein-protein interactions (PPIs) to study proteins in mRNA life-cycle stages. We generated an RNA-aware, RBP-centric PPI map …

    PMID 39303721 DOI ↗

  6. Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion.

    Nature biotechnology · 2024 · 42(9): 1429-1441

    RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we developed tethered function luciferase-based splicing reporters that provide rapid, scalable and robust readouts of exon inclusion …

    PMID 38168984 DOI ↗

  7. Small nuclear RNAs enhance protein-free RNA-programmable base conversion on mammalian coding transcripts.

    bioRxiv : the preprint server for biology · 2024

    Endogenous U small nuclear RNAs (U snRNAs) form RNA-protein complexes responsible for eukaryotic processing of pre-mRNA into mature mRNA. Previous studies have demonstrated the utility of guide-programmable U snRNAs in targeted exon inclusion and exclusion. We investigated whether snRNAs can …

    PMID 38915553 DOI ↗

  8. Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms.

    Cancer discovery · 2022 · 12(3): 836-855

    Mutations in splicing factors (SF) are the predominant class of mutations in myelodysplastic syndrome (MDS), but convergent downstream disease drivers remain elusive. To identify common direct targets of missplicing by mutant U2AF1 and SRSF2, we performed RNA sequencing and enhanced …

    PMID 34620690 DOI ↗

  9. Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.

    Genome biology · 2020 · 21(1): 90

    A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis …

    PMID 32252787 DOI ↗

  10. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription.

    Cell · 2019 · 178(1): 107-121.e18

    Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA-binding proteins (RBPs). Although multiple RBPs have been implicated in transcription control, it has remained unclear how extensively RBPs directly act on …

    PMID 31251911 DOI ↗

  11. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.

    Nature communications · 2019 · 10(1): 1338

    Allele-specific protein-RNA binding is an essential aspect that may reveal functional genetic variants (GVs) mediating post-transcriptional regulation. Recently, genome-wide detection of in vivo binding of RNA-binding proteins is greatly facilitated by the enhanced crosslinking and immunoprecipitation (eCLIP) method. We developed …

    PMID 30902979 DOI ↗

  12. ALS-causative mutations in FUS/TLS confer gain and loss of function by altered association with SMN and U1-snRNP.

    Nature communications · 2015 · 6: 6171

    The RNA-binding protein FUS/TLS, mutation in which is causative of the fatal motor neuron disease amyotrophic lateral sclerosis (ALS), is demonstrated to directly bind to the U1-snRNP and SMN complexes. ALS-causative mutations in FUS/TLS are shown to abnormally enhance their …

    PMID 25625564 DOI ↗

  13. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges.

    Nature structural & molecular biology · 2013 · 20(12): 1434-42

    Alternative splicing (AS) enables programmed diversity of gene expression across tissues and development. We show here that binding in distal intronic regions (>500 nucleotides (nt) from any exon) by Rbfox splicing factors important in development is extensive and is an …

    PMID 24213538 DOI ↗

  14. Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.

    Molecular cell · 2013 · 50(2): 223-35

    SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. …

    PMID 23562324 DOI ↗

  15. ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43.

    Proceedings of the National Academy of Sciences of the United States of America · 2013 · 110(8): E736-45

    Transactivating response region DNA binding protein (TDP-43) is the major protein component of ubiquitinated inclusions found in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) with ubiquitinated inclusions. Two ALS-causing mutants (TDP-43(Q331K) and TDP-43(M337V)), but not wild-type human TDP-43, …

    PMID 23382207 DOI ↗

  16. Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43.

    Nature neuroscience · 2011 · 14(4): 459-68

    We used cross-linking and immunoprecipitation coupled with high-throughput sequencing to identify binding sites in 6,304 genes as the brain RNA targets for TDP-43, an RNA binding protein that, when mutated, causes amyotrophic lateral sclerosis. Massively parallel sequencing and splicing-sensitive junction …

    PMID 21358643 DOI ↗

  17. Inference of splicing regulatory activities by sequence neighborhood analysis.

    PLoS genetics · 2006 · 2(11): e191

    Sequence-specific recognition of nucleic-acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood Inference (NI) that predicts sequences with activity in regulating a biochemical process based on the local density of known …

    PMID 17121466 DOI ↗

  18. RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons.

    Nucleic acids research · 2004 · 32(Web Server issue): W187-90

    A typical gene contains two levels of information: a sequence that encodes a particular protein and a host of other signals that are necessary for the correct expression of the transcript. While much attention has been focused on the effects …

    PMID 15215377 DOI ↗

Datasets 1

GSE44591 GSE · GEO

Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

Mus musculus · GPL9250

Analyses 0

No analyses match this query.