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29 results for “small RNA”

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  1. 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 ↗

  2. 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 ↗

  3. Phenylpyrazoles as Inhibitors of the m<sup>6</sup>A RNA-Binding Protein YTHDF2.

    JACS Au · 2025 · 5(2): 618-630

    The <i>N</i>6-methyladenosine (m<sup>6</sup>A) modification, which is the most common RNA modification in eukaryotes, is regulated by the "writer" methyltransferases, the "reader" m<sup>6</sup>A binding proteins, and the "eraser" demethylases. m<sup>6</sup>A plays a multifunctional role in physiological and pathological processes, regulating all …

    PMID 40017738 DOI ↗

  4. 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 ↗

  5. 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 ↗

  6. Inhibition of RNA splicing triggers CHMP7 nuclear entry, impacting TDP-43 function and leading to the onset of ALS cellular phenotypes.

    Neuron · 2024 · 112(24): 4033-4047.e8

    Amyotrophic lateral sclerosis (ALS) is linked to the reduction of certain nucleoporins in neurons. Increased nuclear localization of charged multivesicular body protein 7 (CHMP7), a protein involved in nuclear pore surveillance, has been identified as a key factor damaging nuclear …

    PMID 39486415 DOI ↗

  7. 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 ↗

  8. 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 ↗

  9. 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 ↗

  10. 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 ↗

  11. RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine.

    Gut · 2022 · 71(9): 1790-1802

    Tuft cells residing in the intestinal epithelium have diverse functions. In the small intestine, they provide protection against inflammation, combat against helminth and protist infections, and serve as entry portals for enteroviruses. In the colon, they had been implicated in …

    PMID 34853057 DOI ↗

  12. Engineered U1 snRNAs to modulate alternatively spliced exons.

    Methods (San Diego, Calif.) · 2022 · 205: 140-148

    Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, …

    PMID 35764245 DOI ↗

  13. Pre-existing adaptive immunity to the RNA-editing enzyme Cas13d in humans.

    Nature medicine · 2022 · 28(7): 1372-1376

    RNA-guided RNA-targeting nucleases, such as CRISPR-Cas13 proteins, have therapeutic potential for gene editing. Among Cas13d enzymes, Cas13d from the bacteria Ruminococcus flavefaciens (RfxCas13d) is of particular interest owing to its small size and high specificity. However, the existence of pre-existing …

    PMID 35668177 DOI ↗

  14. Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.

    Nature methods · 2021 · 18(5): 507-519

    RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets …

    PMID 33963355 DOI ↗

  15. DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis.

    Life science alliance · 2020 · 3(10)

    Tumorigenesis in different segments of the intestinal tract involves tissue-specific oncogenic drivers. In the colon, complement component 3 (C3) activation is a major contributor to inflammation and malignancies. By contrast, tumorigenesis in the small intestine involves fatty acid-binding protein 1 …

    PMID 32817263 DOI ↗

  16. Early precursors and molecular determinants of tissue-resident memory CD8<sup>+</sup> T lymphocytes revealed by single-cell RNA sequencing.

    Science immunology · 2020 · 5(47)

    During an immune response to microbial infection, CD8<sup>+</sup> T cells give rise to distinct classes of cellular progeny that coordinately mediate clearance of the pathogen and provide long-lasting protection against reinfection, including a subset of noncirculating tissue-resident memory (T<sub>RM</sub>) cells …

    PMID 32414833 DOI ↗

  17. Small-Molecule Modulation of TDP-43 Recruitment to Stress Granules Prevents Persistent TDP-43 Accumulation in ALS/FTD.

    Neuron · 2019 · 103(5): 802-819.e11

    Stress granules (SGs) form during cellular stress and are implicated in neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). To yield insights into the role of SGs in pathophysiology, we performed a high-content screen to identify small …

    PMID 31272829 DOI ↗

  18. A protein-RNA interaction atlas of the ribosome biogenesis factor AATF.

    Scientific reports · 2019 · 9(1): 11071

    AATF is a central regulator of the cellular outcome upon p53 activation, a finding that has primarily been attributed to its function as a transcription factor. Recent data showed that AATF is essential for ribosome biogenesis and plays a role …

    PMID 31363146 DOI ↗

  19. An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys.

    RNA (New York, N.Y.) · 2018 · 24(9): 1255-1265

    During terminal erythropoiesis, the splicing machinery in differentiating erythroblasts executes a robust intron retention (IR) program that impacts expression of hundreds of genes. We studied IR mechanisms in the <i>SF3B1</i> splicing factor gene, which expresses ∼50% of its transcripts in …

    PMID 29959282 DOI ↗

  20. Sequence, Structure, and Context Preferences of Human RNA Binding Proteins.

    Molecular cell · 2018 · 70(5): 854-867.e9

    RNA binding proteins (RBPs) orchestrate the production, processing, and function of mRNAs. Here, we present the affinity landscapes of 78 human RBPs using an unbiased assay that determines the sequence, structure, and context preferences of these proteins in vitro by …

    PMID 29883606 DOI ↗

  21. Self-Transfecting Micellar RNA: Modulating Nanoparticle Cell Interactions via High Density Display of Small Molecule Ligands on Micelle Coronas.

    Bioconjugate chemistry · 2018 · 29(1): 126-135

    The intracellular delivery of synthetic nucleic acids represents a major challenge in biotechnology and in biomedicine. Methods to deliver short, double-stranded RNA to living cells are of particular interest because of the potential to engage the RNA interference machinery and …

    PMID 29286237 DOI ↗

  22. Nol12 is a multifunctional RNA binding protein at the nexus of RNA and DNA metabolism.

    Nucleic acids research · 2017 · 45(21): 12509-12528

    To counteract the breakdown of genome integrity, eukaryotic cells have developed a network of surveillance pathways to prevent and resolve DNA damage. Recent data has recognized the importance of RNA binding proteins (RBPs) in DNA damage repair (DDR) pathways. Here, …

    PMID 29069457 DOI ↗

  23. NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing.

    Nature structural & molecular biology · 2017 · 24(10): 816-824

    MicroRNA (miRNA) biogenesis is known to be modulated by a variety of RNA-binding proteins (RBPs), but in most cases, individual RBPs appear to influence the processing of a small subset of target miRNAs. Here, we report that the RNA-binding NONO-PSF …

    PMID 28846091 DOI ↗

  24. Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells.

    Nature · 2016 · 532(7600): 508-511

    Umbilical cord blood-derived haematopoietic stem cells (HSCs) are essential for many life-saving regenerative therapies. However, despite their advantages for transplantation, their clinical use is restricted because HSCs in cord blood are found only in small numbers. Small molecules that enhance …

    PMID 27121842 DOI ↗

  25. A Small RNA-Catalytic Argonaute Pathway Tunes Germline Transcript Levels to Ensure Embryonic Divisions.

    Cell · 2016 · 165(2): 396-409

    Multiple division cycles without growth are a characteristic feature of early embryogenesis. The female germline loads proteins and RNAs into oocytes to support these divisions, which lack many quality control mechanisms operating in somatic cells undergoing growth. Here, we describe …

    PMID 27020753 DOI ↗

Datasets 10

GSE33584 GSE · GEO

High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection

Homo sapiens · GPL10999

GSE109423 GSE · GEO

A transcriptome-wide divergence in protein translation scales with LIN28B expression

Mus musculus · GPL20301

GSE86227 GSE · GEO

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_small_rnaseq]

Mus musculus · GPL15520

GSE75128 GSE · GEO

A Small RNA-Catalytic Argonaute Pathway Tunes Germline Transcript Levels to Ensure Embryonic Divisions

6239 · GPL18245

GSE136911 GSE · GEO

small RNA Seq of Subcutaneous adipose tissue from endothelial-AGO1-knockout (EC-AGO1-KO) mice and wild-type (WT) littermates fed 16 week of high fat high sucrose diet

Mus musculus · GPL17021

GSE13483 GSE · GEO

Divergent transcription from active promoters

Homo sapiens · GPL7564

GSE47626 GSE · GEO

Differential LINE-1 retrotransposition in induced pluripotent stem cells between humans and great apes

9598 · GPL11154

GSE102497 GSE · GEO

Systematic discovery of RNA binding proteins that control microRNA processing

Homo sapiens · GPL20301

GSE136907 GSE · GEO

Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

Homo sapiens · GPL11154

GSE90650 GSE · GEO

The LncRNA NEAT1 Nests RNA Binding Proteins and the Microprocessor to Globally Enhance Pri-miRNA Processing

Homo sapiens · GPL20301

Analyses 3

GSE136911 Processing Pipeline

GSE136911 · 2 steps · miRNA-Seq · code_examples

Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction. (2020)

GSE75128 Processing Pipeline

GSE75128 · 7 steps · RNA-Seq · code_examples

A Small RNA-Catalytic Argonaute Pathway Tunes Germline Transcript Levels to Ensure Embryonic Divisions. (2016)

GSE33584 Processing Pipeline

GSE33584 · 2 steps · RNA-Seq · code_examples

High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection. (2012)