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74 results for “RNA biology”

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  1. 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 ↗

  2. 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 ↗

  3. 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 ↗

  4. RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression.

    Molecular cell · 2023 · 83(19): 3421-3437.e11

    The nuclear receptor co-repressor (NCoR) complex mediates transcriptional repression dependent on histone deacetylation by histone deacetylase 3 (HDAC3) as a component of the complex. Unexpectedly, we found that signaling by the receptor activator of nuclear factor κB (RANK) converts the …

    PMID 37751740 DOI ↗

  5. Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.

    bioRxiv : the preprint server for biology · 2023

    RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize …

    PMID 37808757 DOI ↗

  6. 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 ↗

  7. 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 ↗

  8. Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and regeneration.

    bioRxiv : the preprint server for biology · 2023

    Muscular atrophy is a mortality risk factor that happens with disuse, chronic disease, and aging. Recovery from atrophy requires changes in several cell types including muscle fibers, and satellite and immune cells. Here we show that Zfp697/ZNF697 is a damage-induced …

    PMID 37398033 DOI ↗

  9. Large-scale map of RNA binding protein interactomes across the mRNA life-cycle.

    bioRxiv : the preprint server for biology · 2023

    Messenger RNAs (mRNAs) interact with RNA-binding proteins (RBPs) in diverse ribonucleoprotein complexes (RNPs) during distinct life-cycle stages for their processing and maturation. While substantial attention has focused on understanding RNA regulation by assigning proteins, particularly RBPs, to specific RNA substrates, …

    PMID 37333282 DOI ↗

  10. Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection.

    PLoS biology · 2023 · 21(1): e3001983

    During a microbial infection, responding CD8+ T cells give rise to effector cells that provide acute host defense and memory cells that provide sustained protection. An alternative outcome is exhaustion, a state of T cell dysfunction that occurs in the …

    PMID 36716323 DOI ↗

  11. 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 ↗

  12. APEX Proximity Labeling of Stress Granule Proteins.

    Methods in molecular biology (Clifton, N.J.) · 2022 · 2428: 381-399

    Ascorbate peroxidase (APEX)-catalyzed proximity labeling has been recently established as a robust approach to uncover localized protein environments and transient protein-protein interactions occurring across mammalian cells. This molecular tool enables improved identification of individual proteins localized to and involved in …

    PMID 35171492 DOI ↗

  13. Aging RNA granule dynamics in neurodegeneration.

    Frontiers in molecular biosciences · 2022 · 9: 991641

    Disordered RNA-binding proteins and repetitive RNA sequences are the main genetic causes of several neurodegenerative diseases, including amyotrophic lateral sclerosis and Huntington's disease. Importantly, these components also seed the formation of cytoplasmic liquid-like granules, like stress granules and P bodies. …

    PMID 36188213 DOI ↗

  14. Illuminating RNA biology through imaging.

    Nature cell biology · 2022 · 24(6): 815-824

    RNA processing plays a central role in accurately transmitting genetic information into functional RNA and protein regulators. To fully appreciate the RNA life-cycle, tools to observe RNA with high spatial and temporal resolution are critical. Here we review recent advances …

    PMID 35697782 DOI ↗

  15. The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression.

    The Journal of experimental medicine · 2022 · 219(6)

    During an immune response to microbial infection, CD8+ T cells give rise to short-lived effector cells and memory cells that provide sustained protection. Although the transcriptional programs regulating CD8+ T cell differentiation have been extensively characterized, the role of long …

    PMID 35593887 DOI ↗

  16. Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.

    bioRxiv : the preprint server for biology · 2022

    The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral …

    PMID 35233578 DOI ↗

  17. Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence.

    bioRxiv : the preprint server for biology · 2021

    Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with COVID-19 and inform appropriate infection mitigation responses. Research groups have reported detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on surfaces days or weeks …

    PMID 34312621 DOI ↗

  18. Repeat RNA expansion disorders of the nervous system: post-transcriptional mechanisms and therapeutic strategies.

    Critical reviews in biochemistry and molecular biology · 2021 · 56(1): 31-53

    Dozens of incurable neurological disorders result from expansion of short repeat sequences in both coding and non-coding regions of the transcriptome. Short repeat expansions underlie microsatellite repeat expansion (MRE) disorders including myotonic dystrophy (DM1, CUG<sub>50-3,500</sub> in <i>DMPK</i>; DM2, CCTG<sub>75-11,000</sub> in …

    PMID 33172304 DOI ↗

  19. Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.

    Genome medicine · 2020 · 12(1): 112

    Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions …

    PMID 33287884 DOI ↗

  20. Large-scale tethered function assays identify factors that regulate mRNA stability and translation.

    Nature structural & molecular biology · 2020 · 27(10): 989-1000

    The molecular functions of the majority of RNA-binding proteins (RBPs) remain unclear, highlighting a major bottleneck to a full understanding of gene expression regulation. Here, we develop a plasmid resource of 690 human RBPs that we subject to luciferase-based 3'-untranslated-region …

    PMID 32807991 DOI ↗

  21. A large-scale binding and functional map of human RNA-binding proteins.

    Nature · 2020 · 583(7818): 711-719

    Many proteins regulate the expression of genes by binding to specific regions encoded in the genome<sup>1</sup>. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part …

    PMID 32728246 DOI ↗

  22. Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors.

    Nature methods · 2020 · 17(6): 636-642

    Genetic screens using pooled CRISPR-based approaches are scalable and inexpensive, but restricted to standard readouts, including survival, proliferation and sortable markers. However, many biologically relevant cell states involve cellular and subcellular changes that are only accessible by microscopic visualization, and …

    PMID 32393832 DOI ↗

  23. Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.

    Genome biology · 2020 · 21(1): 90

    A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis …

    PMID 32252787 DOI ↗

  24. RNA-targeting CRISPR systems from metagenomic discovery to transcriptomic engineering.

    Nature cell biology · 2020 · 22(2): 143-150

    Deployment of RNA-guided DNA endonuclease CRISPR-Cas technology has led to radical advances in biology. As the functional diversity of CRISPR-Cas and parallel systems is further explored, RNA manipulation is emerging as a powerful mode of CRISPR-based engineering. In this Perspective, …

    PMID 32015437 DOI ↗

  25. Regulation of RNA editing by RNA-binding proteins in human cells.

    Communications biology · 2019 · 2: 19

    Adenosine-to-inosine (A-to-I) editing, mediated by the ADAR enzymes, diversifies the transcriptome by altering RNA sequences. Recent studies reported global changes in RNA editing in disease and development. Such widespread editing variations necessitate an improved understanding of the regulatory mechanisms of …

    PMID 30652130 DOI ↗

Datasets 3

GSE276986 GSE · GEO

Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [RNA-seq]

Homo sapiens · GPL24676

GSE276985 GSE · GEO

Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [eCLIP-seq]

Mus musculus · GPL24676

GSE277082 GSE · GEO

Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [RNASeq, RiboSeq]

Homo sapiens · GPL24676

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