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69 results for “RNA splicing”

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  1. ARID5A RNA-binding coordinates microglial defense and ferroptosis in iPSC-derived models.

    Nature communications · 2026 · 17(1)

    RNA-binding proteins (RBPs) are key regulators of gene expression that shape cellular function in health and disease. However, the roles of RBPs in immune cells within the central nervous system (CNS) remain poorly understood. Here, we identify ARID5A as an …

    PMID 42717200 DOI ↗

  2. 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 ↗

  3. Single-cell and isoform-specific translational profiling of the mouse brain.

    Nature · 2026

    The brain displays the richest repertoire of post-transcriptional mechanisms regulating mRNA translation<sup>1-11</sup>. Among these, alternative splicing has been shown to drive cell-type specificity and, when disrupted, is strongly linked to neurological disorders<sup>12-17</sup>. However, genome-wide measurements of mRNA translation with isoform …

    PMID 41708856 DOI ↗

  4. Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression.

    Cancer research · 2025

    RNA-binding proteins (RBPs) are important regulators of post-transcriptional gene expression. Understanding which and how RBPs promote cancer progression is crucial for cancers that lack effective targeted therapies, such as triple negative breast cancer (TNBC). Here, we employed both in vitro …

    PMID 41411621 DOI ↗

  5. Dosage-sensitive <i>RBFOX2</i> autoregulation promotes cardiomyocyte differentiation by maturing the transcriptome.

    bioRxiv : the preprint server for biology · 2025

    Haploinsufficiency of the RNA splicing regulator, <i>RBFOX2</i> , is linked to congenital heart disease (CHD), yet its pathogenic mechanisms remain unclear. Here, we demonstrate that RBFOX2 is essential for progressing cardiomyocyte (CM) differentiation by shifting exon usage profiles to more …

    PMID 41280054 DOI ↗

  6. 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 ↗

  7. Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress.

    Nature neuroscience · 2025 · 28(6): 1174-1184

    Aging is one of the most prominent risk factors for neurodegeneration, yet the molecular mechanisms underlying the deterioration of old neurons are mostly unknown. To efficiently study neurodegeneration in the context of aging, we transdifferentiated primary human fibroblasts from aged …

    PMID 40456907 DOI ↗

  8. Integrative CRISPR Screens and RNA-Omics Discover an Essential Role for PUF60-3' Splice Site Interactions in Cancer Progression.

    bioRxiv : the preprint server for biology · 2025

    RNA-binding proteins (RBPs) are important regulators of post-transcriptional gene expression. Understanding which and how RBPs promote cancer progression is crucial for cancers that lack effective targeted therapies such as triple negative breast cancer (TNBC). Here, we employ both <i>in vitro</i> …

    PMID 40655003 DOI ↗

  9. 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 ↗

  10. Strategies for programmable manipulation of alternative splicing.

    Current opinion in genetics & development · 2024 · 89: 102272

    Alternative splicing (AS) plays a pivotal role in protein diversity and mRNA maturation. Programmable control of targeted AS events is of longstanding interest in RNA biology, promising correction of dysregulated splicing in disease and discovery of AS events. This review …

    PMID 39471777 DOI ↗

  11. Steering research on mRNA splicing in cancer towards clinical translation.

    Nature reviews. Cancer · 2024 · 24(12): 887-905

    Splicing factors are affected by recurrent somatic mutations and copy number variations in several types of haematologic and solid malignancies, which is often seen as prima facie evidence that splicing aberrations can drive cancer initiation and progression. However, numerous spliceosome …

    PMID 39384951 DOI ↗

  12. 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 ↗

  13. 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 ↗

  14. Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation.

    Molecular cell · 2024 · 84(19): 3826-3842.e8

    RNA interactome studies have revealed that hundreds of zinc-finger proteins (ZFPs) are candidate RNA-binding proteins (RBPs), yet their RNA substrates and functional significance remain largely uncharacterized. Here, we present a systematic multi-omics analysis of the DNA- and RNA-binding targets and …

    PMID 39303722 DOI ↗

  15. 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 ↗

  16. Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data.

    Cell genomics · 2024 · 4(7): 100603

    The uncovering of protein-RNA interactions enables a deeper understanding of RNA processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP) technologies such as antibody-barcoded eCLIP (ABC) dramatically increase the throughput of mapping RNA binding protein (RBP) binding sites. However, multiplex CLIP datasets …

    PMID 38955188 DOI ↗

  17. 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 ↗

  18. ePRINT: exonuclease assisted mapping of protein-RNA interactions.

    Genome biology · 2024 · 25(1): 140

    RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purifying single proteins at a time. Our new …

    PMID 38807229 DOI ↗

  19. Remodeling oncogenic transcriptomes by small molecules targeting NONO.

    Nature chemical biology · 2023 · 19(7): 825-836

    Much of the human proteome is involved in mRNA homeostasis, but most RNA-binding proteins lack chemical probes. Here we identify electrophilic small molecules that rapidly and stereoselectively decrease the expression of transcripts encoding the androgen receptor and its splice variants …

    PMID 36864190 DOI ↗

  20. In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target.

    Blood cancer discovery · 2023 · 4(3): 180-207

    Acute myeloid leukemia (AML) is fueled by leukemic stem cells (LSC) whose determinants are challenging to discern from hematopoietic stem cells (HSC) or uncover by approaches focused on general cell properties. We have identified a set of RNA-binding proteins (RBP) …

    PMID 36763002 DOI ↗

  21. Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death.

    Nature communications · 2023 · 14(1): 551

    Regulation of RNA processing contributes profoundly to tissue development and physiology. Here, we report that serine-arginine-rich splicing factor 1 (SRSF1) is essential for hepatocyte function and survival. Although SRSF1 is mainly known for its many roles in mRNA metabolism, it …

    PMID 36759613 DOI ↗

  22. Metadensity: a background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites.

    Bioinformatics advances · 2022 · 2(1): vbac083

    Cross-linking and immunoprecipitation (CLIP) is a technology to map the binding sites of RNA-binding proteins (RBPs). The region where an RBP binds within RNA is often indicative of its molecular function in RNA processing. As an example, the binding sites …

    PMID 36388152 DOI ↗

  23. Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis.

    Acta neuropathologica · 2022 · 144(3): 413-435

    Amyotrophic lateral sclerosis (ALS) is a fatal disease characterized by aberrant alternative splicing (AS). Nuclear loss and cytoplasmic accumulation of the splicing factor TDP-43 in motor neurons (MN) are hallmarks of ALS at late stages of the disease. However, it …

    PMID 35778567 DOI ↗

  24. Engineered U1 snRNAs to modulate alternatively spliced exons.

    Methods (San Diego, Calif.) · 2022 · 205: 140-148

    Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, …

    PMID 35764245 DOI ↗

  25. Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms.

    Nucleic acids research · 2022 · 50(8): 4685-4702

    The poly(A)-tail appended to the 3'-end of most eukaryotic transcripts plays a key role in their stability, nuclear transport, and translation. These roles are largely mediated by Poly(A) Binding Proteins (PABPs) that coat poly(A)-tails and interact with various proteins involved …

    PMID 35438785 DOI ↗

Datasets 21

GSE254209 GSE · GEO

Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (eCLIP).

Homo sapiens · GPL24676

GSE254210 GSE · GEO

Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS

Homo sapiens · GPL24676

GSE254208 GSE · GEO

Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (RNA-Seq).

Homo sapiens · Illumina

GSE114922 GSE · GEO

RNA sequencing of bone marrow CD34+ hematopoietic stem and progenitor cells from patients with myelodysplastic syndrome and healthy controls

Homo sapiens · GPL20301

GSE63816 GSE · GEO

Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome

Homo sapiens · GPL11154

GSE56504 GSE · GEO

Loss of nuclear TDP-43 in ALS causes altered expression of splicing machinery and widespread dysregulation of RNA splicing in motor neurons

Mus musculus · GPL5188

GSE127944 GSE · GEO

In vivo CRISPR screening unveils RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a potential therapeutic target [eCLIPseq]

Mus musculus · GPL21103

GSE127743 GSE · GEO

In vivo CRISPR screening unveils RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a potential therapeutic target [RNA-seq]

Mus musculus · GPL18480

GSE34992 GSE · GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splicing arrays)

Homo sapiens · GPL15106

GSE277160 GSE · GEO

Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [RNA-seq]

Homo sapiens · GPL24676

GSE64078 GSE · GEO

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

Homo sapiens · GPL11154

GSE277047 GSE · GEO

Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [RBNS]

synthetic construct · GPL34014

GSE34993 GSE · GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq)

Homo sapiens · GPL9052

GSE268963 GSE · GEO

Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [SLAM-Seq]

Homo sapiens · GPL24676

GSE34995 GSE · GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (RNA-Seq)

Homo sapiens · GPL9115

GSE249245 GSE · GEO

Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [Cut&Run]

Homo sapiens · GPL24676

GSE157917 GSE · GEO

Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS

Homo sapiens · GPL16791

GSE249246 GSE · GEO

Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [eCLIP]

Homo sapiens · GPL24676

GSE224548 GSE · GEO

A two-step in vivo CRISPR screen unveils pervasive RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a therapeutic target

Homo sapiens · GPL18460

GSE146916 GSE · GEO

A role for alternative splicing in circadian control of insulin secretion and glucose homeostasis

Mus musculus · GPL19057

GSE277161 GSE · GEO

Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [Ribo-STAMP cell lines]

Homo sapiens · GPL24676

Analyses 2

GSE25421 Processing Pipeline

GSE25421 · 1 step · GSE · code_examples

Inhibition of RNA splicing triggers CHMP7 nuclear entry, impacting TDP-43 function and leading to the onset of ALS cellular phenotypes. (2024)

GSE56504 Processing Pipeline

GSE56504 · 2 steps · GSE · code_examples

Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)