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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 ↗

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 ↗

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 ↗

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 ↗

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 ↗

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 ↗

System-level measurement, modeling, and manipulation of RNA.

RNA (New York, N.Y.) · 2026 · 32(4): 409-411

PMID 41839511 DOI ↗

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 ↗

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 ↗

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 ↗

A splice-switching antisense oligonucleotide approach for pediatric genetic epilepsies.

bioRxiv : the preprint server for biology · 2025

Variants in ion channel genes are common causes of pediatric epilepsy, often leading to intractable seizures, developmental delay and other comorbidities, which increases risk of death. Pathogenic variants in the <i>SCN8A</i> gene, which encodes a voltage-gated sodium channel critical for …

PMID 41278710 DOI ↗

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 ↗

Investigational eIF2B activator DNL343 modulates the integrated stress response in preclinical models of TDP-43 pathology and individuals with ALS in a randomized clinical trial.

Nature communications · 2025 · 16(1): 7690

Neuronal TDP-43 aggregates are a hallmark ALS pathology. The integrated stress response (ISR) occurs downstream of TDP-43 pathology and may promote neurodegeneration. Here we demonstrate that a CNS penetrant small molecule eIF2B activator inhibits the ISR in cellular models of …

PMID 40825784 DOI ↗

Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders.

Cell systems · 2025 · 16(4): 101204

The molecular composition of the excitatory synapse is incompletely defined due to its dynamic nature across developmental stages and neuronal populations. To address this gap, we apply proteomic mass spectrometry to characterize the synapse in multiple biological models, including the …

PMID 40054464 DOI ↗

Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted.

Nature · 2025 · 639(8054): 483-492

Tissue-resident memory CD8 T (T_RM) cells provide protection from infection at barrier sites. In the small intestine, T_RM cells are found in at least two distinct subpopulations: one with higher expression of effector molecules and another with greater memory potential¹. …

PMID 39843748 DOI ↗

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 ↗

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 ↗

Protocol to process crosslinking and immunoprecipitation data into annotated binding sites.

STAR protocols · 2024 · 5(2): 103040

Here, we present a protocol for using Skipper, a pipeline designed to process crosslinking and immunoprecipitation (CLIP) data into annotated binding sites. We describe steps for partitioning annotated transcript regions and fitting data to a beta-binomial model to call windows …

PMID 38669139 DOI ↗

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 ↗

Functional Diversity of Memory CD8 T Cells is Spatiotemporally Imprinted.

bioRxiv : the preprint server for biology · 2024

Tissue-resident memory CD8 T cells (T_RM) kill infected cells and recruit additional immune cells to limit pathogen invasion at barrier sites. Small intestinal (SI) T_RM cells consist of distinct subpopulations with higher expression of effector molecules or greater memory potential. …

PMID 38585842 DOI ↗

HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence.

Molecular cell · 2023 · 83(14): 2595-2611.e11

RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression and, when dysfunctional, underlie human diseases. Proteome-wide discovery efforts predict thousands of RBP candidates, many of which lack canonical RNA-binding domains (RBDs). Here, we present a hybrid ensemble RBP classifier …

PMID 37421941 DOI ↗

An RNA-targeting CRISPR-Cas13d system alleviates disease-related phenotypes in Huntington's disease models.

Nature neuroscience · 2023 · 26(1): 27-38

Huntington's disease (HD) is a fatal, dominantly inherited neurodegenerative disorder caused by CAG trinucleotide expansion in exon 1 of the huntingtin (HTT) gene. Since the reduction of pathogenic mutant HTT messenger RNA is therapeutic, we developed a mutant allele-sensitive CAG^EX …

PMID 36510111 DOI ↗

The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients.

Cellular and molecular gastroenterology and hepatology · 2022 · 14(1): 35-53

Hyperbaric oxygen therapy (HBOT) is a promising treatment for moderate-to-severe ulcerative colitis. However, our current understanding of the host and microbial response to HBOT remains unclear. This study examined the molecular mechanisms underpinning HBOT using a multi-omic strategy. Pre- and …

PMID 35378331 DOI ↗

Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma.

Nature communications · 2022 · 13(1): 7506

Pediatric medulloblastoma (MB) is the most common solid malignant brain neoplasm, with Group 3 (G3) MB representing the most aggressive subgroup. MYC amplification is an independent poor prognostic factor in G3 MB, however, therapeutic targeting of the MYC pathway remains …

PMID 36473869 DOI ↗

MECP2-related pathways are dysregulated in a cortical organoid model of myotonic dystrophy.

Science translational medicine · 2022 · 14(651): eabn2375

Myotonic dystrophy type 1 (DM1) is a multisystem, autosomal-dominant inherited disorder caused by CTG microsatellite repeat expansions (MREs) in the 3' untranslated region of the dystrophia myotonica-protein kinase (<i>DMPK</i>) gene. Despite its prominence as the most common adult-onset muscular dystrophy, …

PMID 35767654 DOI ↗