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84 results for “mRNA”
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Aberrant host mRNA partitioning in Ebola virus condensates driven by RNA folding perpetuates species-dependent interferon response.
bioRxiv : the preprint server for biology · 2026
RNA viruses form membraneless condensates in host cells to drive replication, but whether these compartments also regulate host RNAs remains unclear. Using MERFISH-based subcellular transcriptomics, we quantified cellular mRNA recruitment into Ebola virus condensates under basal and IFN-stimulated states. We …
PMID 42465340 DOI ↗
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High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay.
Cell reports · 2026 · 45(5): 117348
The CCR4-NOT complex is a central regulator of gene expression, orchestrating mRNA turnover through interactions with RNA-binding proteins (RBPs) and the microRNA (miRNA)-induced silencing complex. However, identifying which RBP- and miRNA-associated RNA elements recruit CCR4-NOT remains challenging, due in part …
PMID 42154591 DOI ↗
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Localized regulation of cell junction mRNAs is required for epithelial cell integrity.
RNA (New York, N.Y.) · 2026 · 32(5): 635-653
Epithelial cells exhibit a highly polarized organization along their apico-basal axis, a feature that is critical to their function and is frequently perturbed in cancer. One less explored process modulating epithelial cell polarity is the subcellular localization of mRNA molecules. …
PMID 41535088 DOI ↗
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RNA-binding protein LARP6 coordinates hepatic stellate cell activation and liver fibrosis.
The Journal of clinical investigation · 2026
Metabolic syndrome and excessive alcohol consumption (MetALD) result in liver injury and fibrosis, which is driven by increased collagen production by activated hepatic stellate cells (HSCs). Our previous studies demonstrated that LARP6, an RNA-binding protein, may facilitate collagen production. However, …
PMID 41746718 DOI ↗
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Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO.
Cell chemical biology · 2026 · 33(2): 256-267.e11
RNA-binding proteins (RBPs) play important roles in mRNA transcription, processing, and translation. Chemical tools are lacking for RBPs, which has hindered efforts to perturb and understand RBP function in cells. We previously described a chloroacetamide compound (R)-SKBG-1 that covalently binds …
PMID 41534524 DOI ↗
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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 ↗
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Dual-targeting snRNA gene therapy rescues STMN2 and UNC13A splicing in TDP-43 proteinopathies.
bioRxiv : the preprint server for biology · 2025
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder caused by the selective deterioration of motor neurons in the central nervous system (CNS). A key driver of this pathogenesis is nuclear loss of ALS-associated protein TDP-43, leading to mis-splicing of TDP-43 …
PMID 41573891 DOI ↗
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The IFIT2-IFIT3 antiviral complex targets short 5' untranslated regions on viral mRNAs for translation inhibition.
Nature microbiology · 2025 · 10(11): 2934-2948
Recognition of foreign RNA is critical for the innate immune response to viruses. Interferon (IFN)-induced proteins with tetratricopeptide repeats (IFIT) 2 and 3 are highly upregulated following viral infection, but mechanistic insight into their antiviral role is lacking. Here we …
PMID 41093992 DOI ↗
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KIF5A binds RNA to orchestrate synaptic mRNA localization and stress granules in ALS.
bioRxiv : the preprint server for biology · 2025
Neuronal health depends on the precise transport and local translation of mRNAs to maintain synaptic function across highly polarized cellular architecture. While kinesin motor proteins are known to mediate mRNA transport, the specificity and direct involvement of individual kinesins as …
PMID 41279899 DOI ↗
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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 ↗
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Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor.
RNA (New York, N.Y.) · 2025 · 31(8): 1195-1205
Translation elongation stalls trigger mRNA decay and degradation of the nascent polypeptide via translation-dependent quality control pathways. One such pathway, non-stop mRNA decay (NSD), targets aberrant mRNAs that lack stop codons, for example, due to premature polyadenylation. Here we identify …
PMID 40441874 DOI ↗
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Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.
RNA (New York, N.Y.) · 2025 · 31(8): 1103-1124
RNA-binding proteins (RBP) play diverse roles in mRNA processing and function. However, from thousands of RBPs encoded in the human genome, a detailed molecular understanding of their interactions with RNA is available only for a small fraction. In most cases, …
PMID 40399037 DOI ↗
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Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO.
bioRxiv : the preprint server for biology · 2025
RNA-binding proteins (RBPs) play important roles in mRNA transcription, processing, and translation. Chemical tools are lacking for RBPs, which has hindered efforts to perturb and understand RBP function in cells. We recently reported a chloroacetamide compound ( <i>R</i> )-SKBG-1 that …
PMID 40661397 DOI ↗
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Short 5' UTRs serve as a marker for viral mRNA translation inhibition by the IFIT2-IFIT3 antiviral complex.
bioRxiv : the preprint server for biology · 2025
Recognition of "non-self" nucleic acids, including cytoplasmic dsDNA, dsRNA, or mRNAs lacking proper 5' cap structures, is critical for the innate immune response to viruses. Here, we demonstrate that short 5' untranslated regions (UTRs), a characteristic of many viral mRNAs, …
PMID 39990370 DOI ↗
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LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis.
bioRxiv : the preprint server for biology · 2025
Metabolic syndrome and excessive alcohol consumption result in liver injury and fibrosis, which is characterized by increased collagen production by activated Hepatic Stellate Cells (HSCs). LARP6, an RNA-binding protein, was shown to facilitate collagen production. However, LARP6 expression and functionality …
PMID 39868246 DOI ↗
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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 ↗
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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 ↗
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Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis.
Nature communications · 2024 · 15(1): 10796
Proteostasis is maintained through regulated protein synthesis and degradation and chaperone-assisted protein folding. However, this is challenging in neuronal projections because of their polarized morphology and constant synaptic proteome remodeling. Using high-resolution fluorescence microscopy, we discover that hippocampal and spinal …
PMID 39737952 DOI ↗
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Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.
Genome research · 2024 · 34(11): 2012-2024
Transcription and translation are intertwined processes in which mRNA isoforms are crucial intermediaries. However, methodological limitations in analyzing translation at the mRNA isoform level have left gaps in our understanding of critical biological processes. To address these gaps, we developed …
PMID 38906680 DOI ↗
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Localized synthesis of molecular chaperones sustains neuronal proteostasis.
bioRxiv : the preprint server for biology · 2024
Neurons are challenged to maintain proteostasis in neuronal projections, particularly with the physiological stress at synapses to support intercellular communication underlying important functions such as memory and movement control. Proteostasis is maintained through regulated protein synthesis and degradation and chaperone-assisted …
PMID 37873158 DOI ↗
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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 ↗
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Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size.
Neuron · 2024 · 112(13): 2157-2176.e12
Mutations in human nonsense-mediated mRNA decay (NMD) factors are enriched in neurodevelopmental disorders. We show that deletion of key NMD factor Upf2 in mouse embryonic neural progenitor cells causes perinatal microcephaly but deletion in immature neurons does not, indicating NMD's …
PMID 38697111 DOI ↗
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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 ↗
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circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA.
bioRxiv : the preprint server for biology · 2024
Circular RNAs (circRNAs) represent a class of widespread endogenous RNAs that regulate gene expression and thereby influence cell biological decisions with implications for the pathogenesis of several diseases. Here, we disclose a novel gene-regulatory role of circHIPK3 by combining analyses …
PMID 37745562 DOI ↗
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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 ↗
Datasets 25+
Zfp697/ZNF697 is an RNA-binding protein that modulates TGF-β1 2 signaling and hepatic inflammation in liver disease
Mus musculus · GPL30172
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay
GPL18573
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [miRNA-Seq]
GPL18573
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [RIP-Seq]
GPL18573
Ythdf m6A readers compensate each other in a context dependent manner [3'UTR RNA-seq]
GPL13112
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [eCLIP]
GPL24676
Single-cell and isoform-specific translational profiling of the mouse brain with long-read sequencing [scRNA-Seq, longread]
GPL34585
Single-cell and isoform-specific translational profiling of the mouse brain [scRNA-seq]
GPL34475
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [CRISPR]
GPL24676
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [eCLIP]
GPL24676
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [RNA-seq]
GPL24676
Single cell and isoform-specific translational profiling of the mouse brain [ribostamp]
GPL24247
Single cell and isoform-specific translational profiling of the mouse brain [Bulk RNA-seq]
GPL24247
Single cell and isoform-specific translational profiling of the mouse brain [Ribo-STAMP]
GPL24247
The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis
6239 · GPL19757
The mRNA decay factor CAR-1 regulates axon regeneration via mitochondrial calcium dynamics
6239 · GPL13657
Integrative Genomic Analysis Reveals Widespread Enhancer Regulation by p53 in Response to DNA Damage
Mus musculus · GPL9115
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
Homo sapiens · GPL20301
Transcriptome-wide Profiling of Multiple RNA Modifications Simultaneously at Single-base Resolution
Homo sapiens · GPL15520
Showing first 25 dataset results.
Analyses 25+
GSE302648 · 3 steps · geo_data_processing
High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)
GSE302649 · 11 steps · eCLIP · geo_data_processing
High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)
GSE302651 · 3 steps · geo_data_processing
High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)
GSE199650 · 11 steps · RIP-Seq · code_examples
Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor. (2025)
GSE278725 · 9 steps · eCLIP · geo_data_processing
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis. (2025)
GSE279064 · 3 steps · eCLIP · geo_data_processing
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis. (2025)
GSE279065 · 9 steps · eCLIP · geo_data_processing
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis. (2025)
GSE284636 · 10 steps · OTHER · code_examples
The IFIT2-IFIT3 antiviral complex targets short 5' untranslated regions on viral mRNAs for translation inhibition. (2025)
GSE193134 · 18 steps · RIP-Seq · code_examples
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function. (2024)
GSE230717 · 9 steps · RIP-Seq · code_examples
Large-scale map of RNA-binding protein interactomes across the mRNA life cycle. (2024)
GSE253825 · 1 step · RNA-Seq · code_examples
Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size. (2024)
GSE122425 · 5 steps · RNA-Seq · code_examples
Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP. (2023)
GSE206674 · 10 steps · eCLIP · geo_data_processing
Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery. (2023)
GSE230349 · 8 steps · OTHER · code_examples
Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery. (2023)
GSE123613 · 9 steps · OTHER · code_examples
Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. (2022)
GSE90963 · 35 steps · RNA-Seq · code_examples
Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. (2022)
GSE157467 · 6 steps · RNA-Seq · code_examples
Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress. (2021)
GSE117290 · 7 steps · OTHER · code_examples
Large-scale tethered function assays identify factors that regulate mRNA stability and translation. (2020)
GSE117291 · 5 steps · RNA-Seq · code_examples
Large-scale tethered function assays identify factors that regulate mRNA stability and translation. (2020)
GSE117293 · 5 steps · RNA-Seq · code_examples
Large-scale tethered function assays identify factors that regulate mRNA stability and translation. (2020)
GSE117294 · 5 steps · GSE · code_examples
Large-scale tethered function assays identify factors that regulate mRNA stability and translation. (2020)
GSE124714 · 14 steps · OTHER · code_examples
The mRNA Decay Factor CAR-1/LSM14 Regulates Axon Regeneration via Mitochondrial Calcium Dynamics. (2020)
GSE98869 · 13 steps · RNA-Seq · code_examples
The <i>C. elegans</i> neural editome reveals an ADAR target mRNA required for proper chemotaxis. (2017)
GSE80664 · 9 steps · RNA-Seq · code_examples
Dysregulation of RBFOX2 Is an Early Event in Cardiac Pathogenesis of Diabetes. (2016)
GSE66696 · 6 steps · GSE · code_examples
Nxf1 natural variant E610G is a semi-dominant suppressor of IAP-induced RNA processing defects. (2015)
Showing first 25 analysis results.