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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 ↗

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 ↗

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^1-11. Among these, alternative splicing has been shown to drive cell-type specificity and, when disrupted, is strongly linked to neurological disorders^12-17. However, genome-wide measurements of mRNA translation with isoform …

PMID 41708856 DOI ↗

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 ↗

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 ↗

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 ↗

Genome-Wide Interrogation of SARS-CoV-2 RNA-Protein Interactions Uncovers Hidden Regulatory Sites.

bioRxiv : the preprint server for biology · 2025

The global impact of the COVID-19 pandemic underscores the critical need for a comprehensive understanding of SARS-CoV-2 replication mechanisms. While the central roles of the RNA dependent RNA polymerase (NSP12), primase protein (NSP8), and nucleocapsid protein (N) in the virus …

PMID 40501555 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 ↗

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 ↗

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 ↗

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 ↗

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 ↗

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 ↗

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 ↗

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.

Nucleic acids research · 2024 · 52(8): 4440-4455

Large-genome bacteriophages (jumbo phages) of the proposed family Chimalliviridae assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and DNA-targeting CRISPR-Cas nucleases. While the nuclear shell provides broad protection against …

PMID 38554115 DOI ↗

Bento: a toolkit for subcellular analysis of spatial transcriptomics data.

Genome biology · 2024 · 25(1): 82

The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell-cell interactions, and spatial expression patterns, they are limited to the multicellular scale. We present Bento, a Python toolkit …

PMID 38566187 DOI ↗

Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics.

Cell · 2023 · 186(26): 5690-5704.e20

The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency …

PMID 38101407 DOI ↗

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.

bioRxiv : the preprint server for biology · 2023

Large-genome bacteriophages (jumbo phages) of the <i>Chimalliviridae</i> family assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and CRISPR/Cas nucleases. While the nuclear shell provides broad protection against host nucleases, …

PMID 37790334 DOI ↗

Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.

Cell genomics · 2023 · 3(6): 100317

Technology for crosslinking and immunoprecipitation (CLIP) followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds of RNA-binding proteins in cells. To increase the power of existing and future CLIP-seq datasets, we introduce Skipper, an end-to-end workflow that converts …

PMID 37388912 DOI ↗

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 ↗

Examination of the Cell Cycle Dependence of Cytosine and Adenine Base Editors.

Frontiers in genome editing · 2022 · 4: 923718

Base editors (BEs) are genome editing agents that install point mutations with high efficiency and specificity. Due to their reliance on uracil and inosine DNA damage intermediates (rather than double-strand DNA breaks, or DSBs), it has been hypothesized that BEs …

PMID 35910415 DOI ↗

VPS13A and VPS13C Influence Lipid Droplet Abundance.

Contact (Thousand Oaks (Ventura County, Calif.)) · 2022 · 5: 25152564221125613

Lipid transfer proteins mediate the exchange of lipids between closely apposed membranes at organelle contact sites and play key roles in lipid metabolism, membrane homeostasis, and cellular signaling. A recently discovered novel family of lipid transfer proteins, which includes the …

PMID 36147729 DOI ↗

Antibody-Oligonucleotide Conjugation Using a SPAAC Copper-Free Method Compatible with 10× Genomics' Single-Cell RNA-Seq.

Methods in molecular biology (Clifton, N.J.) · 2022 · 2463: 67-80

Recent advances in multimodal approaches toward single-cell analyses present valuable data points that can complement standard flow cytometry data. In particular, the overlay of cell-surface proteome data with gene expression analysis presents a necessary advancement, particularly in the field of …

PMID 35344168 DOI ↗

Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.

Nature · 2022 · 609(7925): 101-108

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which …

PMID 35798029 DOI ↗

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.

Nature · 2022 · 605(7909): E3

PMID 35474001 DOI ↗