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206 results for “protein”
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Zfp697/ZNF697 is an RNA-binding protein that modulates TGF-β1 signaling and hepatic inflammation in liver disease.
Molecular metabolism · 2026 : 102457
Liver diseases driven by metabolic dysfunction, inflammation, and fibrosis such as metabolic dysfunction-associated steatotic liver disease (MASLD), including metabolic dysfunction-associated steatohepatitis (MASH), and acute liver injury represent a growing global health burden. The zinc finger protein Zfp697 (ZNF697 in humans) …
PMID 42875003 DOI ↗
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RNA dysregulation as a determinant of aging and neurodegenerative vulnerability.
Trends in cell biology · 2026
In the nervous system, aging causes deterioration of cellular and molecular processes that are associated with declines in cognition, sensory perception, and motor coordination. Aging is also the strongest risk factor for neurodegenerative disease, yet the mechanisms by which aging …
PMID 42711219 DOI ↗
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The YTHDF proteins modulate Alzheimer's disease-associated brain gene signatures.
Molecular neurodegeneration · 2026 · 21(1)
Gene signatures of Alzheimer's disease (AD) brains reflect the output of a complex interplay of genetic, epigenetic, epi-transcriptomic, and post-transcriptional regulations. To nominate candidate factors modulating these signatures, we developed a machine learning model to integrate cellular and molecular features …
PMID 42811341 DOI ↗
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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 ↗
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ESCAPE: assigning site-specific activity to covalent ligands in cells by prime editing.
bioRxiv : the preprint server for biology · 2026
Chemical proteomics has identified covalent ligands targeting cysteine residues across many hundreds of human proteins. The functional effects of these liganding events, however, remain challenging to assign at scale. Here we describe ESCAPE (Endogenous Site-specific Competition Assays using Prime Editors), …
PMID 42619774 DOI ↗
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Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection.
Molecular cell · 2026
Alternative polyadenylation (APA) generates transcript isoforms with distinct 3' ends, yet the repertoire of its protein regulators remains poorly defined. Using a large-scale tethered function screen, we profiled 879 human RNA-binding proteins (RBPs) and identified 63 high-confidence activators of poly(A) …
PMID 42361791 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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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 ↗
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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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Flipper: An advanced framework for identifying differential RNA binding behavior with eCLIP data.
bioRxiv : the preprint server for biology · 2026
Crosslinking and immunoprecipitation (CLIP) methods remain the gold standard for characterizing RNA binding protein (RBP) behavior. As a result, many researchers rely on CLIP to assess how treatments targeting RBPs alter binding patterns and regulatory activity. However, current tools for …
PMID 41959526 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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MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy.
Neurobiology of disease · 2026 · 221: 107305
Myotonic dystrophy type 1 (DM1) arises from toxic CUG-expanded DMPK transcripts that sequester Muscleblind-like (MBNL) proteins, yet how this molecular lesion perturbs brain development in congenital DM1 (CDM) remains unknown. Here, we identify an unanticipated developmental role for MBNL2 in …
PMID 41644016 DOI ↗
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Identification of RBP binding sites using RNA deaminases.
Methods in enzymology · 2025 · 713: 287-297
RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing. Identification of their binding sites has important implications for their physiological and disease-related functions. Crosslinking and immunoprecipitation, followed by sequencing (CLIP-seq) and its derivatives, are the most commonly …
PMID 40250958 DOI ↗
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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 ↗
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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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Imaging Cellular Metabolic Rewiring with SuMMIT-SRS.
bioRxiv : the preprint server for biology · 2025
Cells dynamically rewire their metabolic pathways in response to physiological and pathological cues. Such plasticity is particularly critical in neurons, stem cells, cancer cells, and immune cells, where biosynthetic demands can shift rapidly. However, current metabolic imaging techniques using isotope …
PMID 41279865 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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RNA triggers chronic stress during neuronal aging.
bioRxiv : the preprint server for biology · 2025
Neurodegenerative diseases are linked with dysregulation of the integrated stress response (ISR), which coordinates cellular homeostasis during and after stress events. Cellular stress can arise from several sources, but there is significant disagreement about which stress might contribute to aging …
PMID 40799579 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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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 ↗
Datasets 25+
Zfp697/ZNF697 is an RNA-binding protein that modulates TGF-β1 2 signaling and hepatic inflammation in liver disease
Mus musculus · GPL30172
Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (eCLIP).
Homo sapiens · GPL24676
Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (RNA-Seq).
Homo sapiens · Illumina
Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [RIP-Seq]
Homo sapiens · Illumina
Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [eclip]
Homo sapiens · Illumina
Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [cutnrun]
Homo sapiens · Illumina
Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [rna-seq]
Homo sapiens · Illumina
RBP Footprint Grand Challenge: An evaluation of novel computational approaches to RNA-binding protein target prediction from structural data
Homo sapiens · GPL20301
RNA secondary structome of different cell lines
Homo sapiens, Mus musculus · GPL20795, GPL21273
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
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [PAS-seq]
Homo sapiens · Illumina
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [RNA-Seq]
Homo sapiens · Illumina
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [eCLIP]
Homo sapiens · Illumina
Multi-Modal Comparison of human Hepatic Stellate Cells identifies novel therapeutic targets for Metabolic Dysfunction-Associated Steatotic Liver Disease
Homo sapiens · GPL24676, GPL37309
Ythdf m6A readers compensate each other in a context dependent manner [eCLIP]
GPL17021
Ythdf m6A readers compensate each other in a context dependent manner [Ribo-seq]
GPL21626
Ythdf m6A readers compensate each other in a context dependent manner [3'UTR RNA-seq]
GPL13112
Ythdf m6A readers compensate each other in a context dependent manner [RNA-seq]
GPL21626
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [scRNA-Seq]
GPL24676
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE)
GPL20301, GPL24676, GPL34284
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset2]
GPL20301, GPL24676, GPL34284
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset1]
GPL20301, GPL24676
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
Showing first 25 dataset results.
Analyses 25+
GSE244832 · 9 steps · scRNA-seq · geo_data_processing
RNA-binding protein LARP6 coordinates hepatic stellate cell activation and liver fibrosis. (2026)
GSE290248 · 1 step · geo_data_processing
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection. (2026)
GSE290281 · 1 step · eCLIP · geo_data_processing
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection. (2026)
GSE290282 · 3 steps · RNA-seq · geo_data_processing
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection. (2026)
GSE299099 · 3 steps · RNA-Seq · code_examples
Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO. (2026)
GSE315347 · 4 steps · eCLIP · geo_data_processing
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces. (2026)
GSE315406 · 4 steps · eCLIP · geo_data_processing
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces. (2026)
GSE315407 · 4 steps · eCLIP · geo_data_processing
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces. (2026)
GSE145805 · 7 steps · SHAPE-seq · geo_data_processing
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
GSE227455 · 7 steps · eCLIP · geo_data_processing
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
GSE262542 · 4 steps · RNA-Seq · code_examples
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
GSE276985 · 2 steps · RIP-Seq · code_examples
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress. (2025)
GSE276986 · 1 step · RNA-Seq · code_examples
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress. (2025)
GSE277082 · 2 steps · RNA-Seq · code_examples
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress. (2025)
GSE106493 · 4 steps · RIP-Seq · code_examples
Transcriptome regulation by PARP13 in basal and antiviral states in human cells. (2024)
GSE114820 · 4 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE143437 · 7 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE145480 · 11 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE147127 · 5 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE193134 · 18 steps · RIP-Seq · code_examples
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function. (2024)
GSE210263 · 10 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE230097 · 6 steps · RNA-Seq · code_examples
ePRINT: exonuclease assisted mapping of protein-RNA interactions. (2024)
GSE230717 · 9 steps · RIP-Seq · code_examples
Large-scale map of RNA-binding protein interactomes across the mRNA life cycle. (2024)
GSE232513 · 3 steps · RNA-Seq · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE232514 · 5 steps · RNA-Seq · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
Showing first 25 analysis results.