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75 results for “transcriptomics”

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  1. Metadensity: a background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites.

    Bioinformatics advances · 2022 · 2(1): vbac083

    Cross-linking and immunoprecipitation (CLIP) is a technology to map the binding sites of RNA-binding proteins (RBPs). The region where an RBP binds within RNA is often indicative of its molecular function in RNA processing. As an example, the binding sites …

    PMID 36388152 DOI ↗

  2. 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 ↗

  3. 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 ↗

  4. Prions induce an early Arc response and a subsequent reduction in mGluR5 in the hippocampus.

    Neurobiology of disease · 2022 · 172: 105834

    Synapse dysfunction and loss are central features of neurodegenerative diseases, caused in part by the accumulation of protein oligomers. Amyloid-β, tau, prion, and α-synuclein oligomers bind to the cellular prion protein (PrP<sup>C),</sup> resulting in the activation of macromolecular complexes and …

    PMID 35905927 DOI ↗

  5. 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 ↗

  6. 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 ↗

  7. Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq.

    Nature protocols · 2022 · 17(5): 1223-1265

    Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which …

    PMID 35322209 DOI ↗

  8. Crosstalk between CRISPR-Cas9 and the human transcriptome.

    Nature communications · 2022 · 13(1): 1125

    CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 …

    PMID 35236841 DOI ↗

  9. Non-microRNA binding competitively inhibits LIN28 regulation.

    Cell reports · 2021 · 36(6): 109517

    RNA binding protein (RBP) expression is finite. For RBPs that are vastly outnumbered by their potential target sites, a simple competition for binding can set the magnitude of post-transcriptional control. Here, we show that LIN28, best known for its direct …

    PMID 34380031 DOI ↗

  10. 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 ↗

  11. 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 ↗

  12. 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 ↗

  13. Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.

    Molecular cell · 2020 · 80(5): 903-914.e8

    Discovering the interaction mechanism and location of RNA-binding proteins (RBPs) on RNA is critical for understanding gene expression regulation. Here, we apply selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) on in vivo transcripts compared to protein-absent transcripts in four …

    PMID 33242392 DOI ↗

  14. Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program.

    Molecular cell · 2020 · 80(3): 452-469.e9

    Although TP53 is the most commonly mutated gene in human cancers, the p53-dependent transcriptional programs mediating tumor suppression remain incompletely understood. Here, to uncover critical components downstream of p53 in tumor suppression, we perform unbiased RNAi and CRISPR-Cas9-based genetic screens …

    PMID 33157015 DOI ↗

  15. Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing.

    Cell reports · 2020 · 33(5): 108350

    Site-directed RNA editing approaches offer great potential to correct genetic mutations in somatic cells while avoiding permanent off-target genomic edits. Nuclease-dead RNA-targeting CRISPR-Cas systems recruit functional effectors to RNA molecules in a programmable fashion. Here, we demonstrate a Streptococcus pyogenes …

    PMID 33147453 DOI ↗

  16. Transcriptome-wide analysis of PGC-1α-binding RNAs identifies genes linked to glucagon metabolic action.

    Proceedings of the National Academy of Sciences of the United States of America · 2020 · 117(36): 22204-22213

    The peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) is a transcriptional coactivator that controls expression of metabolic/energetic genes, programming cellular responses to nutrient and environmental adaptations such as fasting, cold, or exercise. Unlike other coactivators, PGC-1α contains protein domains involved …

    PMID 32848060 DOI ↗

  17. 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 ↗

  18. Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction.

    Circulation · 2020 · 142(4): 365-379

    Metabolic disorders such as obesity and diabetes mellitus can cause dysfunction of endothelial cells (ECs) and vascular rarefaction in adipose tissues. However, the modulatory role of ECs in adipose tissue function is not fully understood. Other than vascular endothelial growth …

    PMID 32393053 DOI ↗

  19. 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 ↗

  20. 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 ↗

  21. Corrigendum: Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells.

    Frontiers in molecular neuroscience · 2019 · 12: 150

    [This corrects the article DOI: 10.3389/fnmol.2018.00261.].

    PMID 31244603 DOI ↗

  22. 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 ↗

  23. Disruption in A-to-I Editing Levels Affects C. elegans Development More Than a Complete Lack of Editing.

    Cell reports · 2019 · 27(4): 1244-1253.e4

    A-to-I RNA editing, catalyzed by ADAR proteins, is widespread in eukaryotic transcriptomes. Studies showed that, in C. elegans, ADR-2 can actively deaminate dsRNA, whereas ADR-1 cannot. Therefore, we set out to study the effect of each of the ADAR genes …

    PMID 31018137 DOI ↗

  24. Disruption of RNA Metabolism in Neurological Diseases and Emerging Therapeutic Interventions.

    Neuron · 2019 · 102(2): 294-320

    RNA binding proteins are critical to the maintenance of the transcriptome via controlled regulation of RNA processing and transport. Alterations of these proteins impact multiple steps of the RNA life cycle resulting in various molecular phenotypes such as aberrant RNA …

    PMID 30998900 DOI ↗

  25. Overriding FUS autoregulation in mice triggers gain-of-toxic dysfunctions in RNA metabolism and autophagy-lysosome axis.

    eLife · 2019 · 8

    Mutations in coding and non-coding regions of FUS cause amyotrophic lateral sclerosis (ALS). The latter mutations may exert toxicity by increasing FUS accumulation. We show here that broad expression within the nervous system of wild-type or either of two ALS-linked …

    PMID 30747709 DOI ↗

Datasets 5

GSE198212 GSE · GEO

Remodeling of oncogenic transcriptomes by small-molecules targeting the RNA-binding protein NONO

Homo sapiens · GPL24676

GSE154778 GSE · GEO

Single-cell transcriptomics analysis of pancreatic primary tumor and metastatic biopsy tissues

Homo sapiens · GPL20301

GSE279255 GSE · GEO

Tissue-resident memory CD8 T Cell Diversity is Spatiotemporally Imprinted

Mus musculus · GPL24247

GSE279254 GSE · GEO

Tissue-resident memory CD8 T Cell Diversity is Spatiotemporally Imprinted [snRNA-Seq]

Mus musculus · GPL24247

GSE280895 GSE · GEO

Tissue-resident memory CD8 T Cell Diversity is Spatiotemporally Imprinted

Mus musculus · GPL31217

Analyses 3

GSE279255 Spatial transcriptomics Data Processing

GSE279255 · 2 steps · Spatial transcriptomics · geo_data_processing

Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted. (2025)

GSE280895 Spatial transcriptomics Data Processing

GSE280895 · 7 steps · Spatial transcriptomics · geo_data_processing

Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted. (2025)

GSE154778 Processing Pipeline

GSE154778 · 1 step · RNA-Seq · code_examples

A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer. (2023)