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75 results for “transcriptome”

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  1. 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 ↗

  2. 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 ↗

  3. High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay.

    Cell reports · 2026 · 45(5): 117348

    The CCR4-NOT complex is a central regulator of gene expression, orchestrating mRNA turnover through interactions with RNA-binding proteins (RBPs) and the microRNA (miRNA)-induced silencing complex. However, identifying which RBP- and miRNA-associated RNA elements recruit CCR4-NOT remains challenging, due in part …

    PMID 42154591 DOI ↗

  4. Dosage-sensitive <i>RBFOX2</i> autoregulation promotes cardiomyocyte differentiation by maturing the transcriptome.

    bioRxiv : the preprint server for biology · 2025

    Haploinsufficiency of the RNA splicing regulator, <i>RBFOX2</i> , is linked to congenital heart disease (CHD), yet its pathogenic mechanisms remain unclear. Here, we demonstrate that RBFOX2 is essential for progressing cardiomyocyte (CM) differentiation by shifting exon usage profiles to more …

    PMID 41280054 DOI ↗

  5. 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 ↗

  6. Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO.

    bioRxiv : the preprint server for biology · 2025

    RNA-binding proteins (RBPs) play important roles in mRNA transcription, processing, and translation. Chemical tools are lacking for RBPs, which has hindered efforts to perturb and understand RBP function in cells. We recently reported a chloroacetamide compound ( <i>R</i> )-SKBG-1 that …

    PMID 40661397 DOI ↗

  7. 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 ↗

  8. Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner.

    Science immunology · 2025 · 10(106): eadn1894

    Tissue-resident memory CD8 T (T<sub>RM</sub>) cells serve as a front-line defense against microbial pathogens in barrier and mucosal tissues. Accurately predicting the roles of tissue-specific transcription factors (TFs) that regulate T<sub>RM</sub> biology remains a challenge. Here, by applying integrated transcriptomic …

    PMID 40215325 DOI ↗

  9. Stratification of enterochromaffin cells by single-cell expression analysis.

    eLife · 2025 · 12

    Dynamic interactions between gut mucosal cells and the external environment are essential to maintain gut homeostasis. Enterochromaffin (EC) cells transduce both chemical and mechanical signals and produce 5-hydroxytryptamine to mediate disparate physiological responses. However, the molecular and cellular basis for …

    PMID 40184163 DOI ↗

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

    Nature · 2025 · 639(8054): 483-492

    Tissue-resident memory CD8 T (T<sub>RM</sub>) cells provide protection from infection at barrier sites. In the small intestine, T<sub>RM</sub> cells are found in at least two distinct subpopulations: one with higher expression of effector molecules and another with greater memory potential<sup>1</sup>. …

    PMID 39843748 DOI ↗

  11. 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 ↗

  12. Stratification of enterochromaffin cells by single-cell expression analysis.

    bioRxiv : the preprint server for biology · 2025

    Dynamic interactions between gut mucosal cells and the external environment are essential to maintain gut homeostasis. Enterochromaffin (EC) cells transduce both chemical and mechanical signals and produce 5-hydroxytryptamine (5-HT) to mediate disparate physiological responses. However, the molecular and cellular basis …

    PMID 37662229 DOI ↗

  13. Decoding protein-RNA interactions using CLIP-based methodologies.

    Nature reviews. Genetics · 2024 · 25(12): 879-895

    Protein-RNA interactions are central to all RNA processing events, with pivotal roles in the regulation of gene expression and cellular functions. Dysregulation of these interactions has been increasingly linked to the pathogenesis of human diseases. High-throughput approaches to identify RNA-binding …

    PMID 38982239 DOI ↗

  14. 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 ↗

  15. Transcriptome regulation by PARP13 in basal and antiviral states in human cells.

    iScience · 2024 · 27(4): 109251

    The RNA-binding protein PARP13 is a primary factor in the innate antiviral response, which suppresses translation and drives decay of bound viral and host RNA. PARP13 interacts with many proteins encoded by interferon-stimulated genes (ISG) to activate antiviral pathways including …

    PMID 38495826 DOI ↗

  16. 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 ↗

  17. Functional Diversity of Memory CD8 T Cells is Spatiotemporally Imprinted.

    bioRxiv : the preprint server for biology · 2024

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

    PMID 38585842 DOI ↗

  18. Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment.

    Current opinion in biotechnology · 2024 · 85: 103048

    Complex networks of cell-cell interactions (CCIs) within the tumor microenvironment (TME) play a crucial role in cancer persistence. These communication axes represent prime targets for therapeutic intervention, but our incomplete understanding of the cellular heterogeneity and interacting partners within the …

    PMID 38142648 DOI ↗

  19. 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 ↗

  20. 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 ↗

  21. 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 ↗

  22. 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 ↗

  23. Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP.

    Nature methods · 2023 · 20(1): 65-69

    Ultraviolet crosslinking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites of RNA-binding proteins (RBPs). Despite improvements in the library preparation of RNA fragments, the enhanced CLIP (eCLIP) protocol requires 4 days of hands-on time and lacks the …

    PMID 36550273 DOI ↗

  24. 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<sup>EX</sup> …

    PMID 36510111 DOI ↗

  25. 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 ↗

Datasets 25+

GSE302651 GSE · GEO

Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay

GPL18573

GSE302649 GSE · GEO

Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [miRNA-Seq]

GPL18573

GSE302648 GSE · GEO

Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [RIP-Seq]

GPL18573

GSE68618 GSE · GEO

Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved insulin secretion by pancreatic β cells

Mus musculus · GPL13112

GSE98869 GSE · GEO

The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis

6239 · GPL19757

GSE125490 GSE · GEO

Glial cells maintain synapses by inhibiting an activity-dependent retrograde protease signal

Mus musculus · GPL13112

GSE95156 GSE · GEO

Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression

Mus musculus · GPL17021

GSE69889 GSE · GEO

Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk

Mus musculus · GPL17021

GSE55727 GSE · GEO

Integrative Genomic Analysis Reveals Widespread Enhancer Regulation by p53 in Response to DNA Damage

Mus musculus · GPL9115

GSE152033 GSE · GEO

RNA-targeting Cas9 corrects molecular and physiological features in pre-clinical model of myotonic dystrophy type 1

Mus musculus · GPL21103

GSE90963 GSE · GEO

Transcriptome-wide Profiling of Multiple RNA Modifications Simultaneously at Single-base Resolution

Homo sapiens · GPL15520

GSE122649 GSE · GEO

Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia [motor cortex]

Homo sapiens · GPL18573

GSE121569 GSE · GEO

ALS implicated protein TDP-43 sustains levels of STMN2 a mediator of motor neuron growth and repair

Homo sapiens · GPL11154

GSE124439 GSE · GEO

Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia

Homo sapiens · GPL16791

GSE147005 GSE · GEO

Loss of canonical splicing factor SRSF1 in hepatocytes results in acute liver injury and regeneration

Mus musculus · GPL21103

GSE179634 GSE · GEO

Splicing Factor SRSF1 Deficiency in the Liver Triggers NASH-like Pathology via R-Loop Induced DNA Damage and Cell Death

Mus musculus · GPL21103

GSE198212 GSE · GEO

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

Homo sapiens · GPL24676

GSE202051 GSE · GEO

Refined molecular taxonomy and treatment remodeling of pancreatic cancer using single-cell resolution

Homo sapiens · GPL20301

GSE215251 GSE · GEO

Transcriptome Regulation by PARP13 in Basal and Antiviral States in Human Cells

Homo sapiens · GPL16791

GSE106493 GSE · GEO

Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking

Homo sapiens · GPL11154

GSE230097 GSE · GEO

Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

Homo sapiens · GPL24676

GSE240014 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP]

Mus musculus · GPL24247

GSE240521 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [eCLIP-seq ]

Mus musculus · GPL21103

GSE263371 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isSTAMP]

Mus musculus · GPL30172

GSE210263 GSE · GEO

Transcriptomic profiles of muscular dystrophy with myositis (mdm) in extensor digitorum longus, psoas, and soleus muscles from mice

Mus musculus · GPL19057

Showing first 25 dataset results.

Analyses 25+

GSE299099 Processing Pipeline

GSE299099 · 3 steps · RNA-Seq · code_examples

Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO. (2026)

GSE302648 Data Processing

GSE302648 · 3 steps · geo_data_processing

High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)

GSE302649 eCLIP Data Processing

GSE302649 · 11 steps · eCLIP · geo_data_processing

High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)

GSE302651 Data Processing

GSE302651 · 3 steps · geo_data_processing

High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)

GSE125970 Processing Pipeline

GSE125970 · 4 steps · RNA-Seq · code_examples

Stratification of enterochromaffin cells by single-cell expression analysis. (2025)

GSE104949 Processing Pipeline

GSE104949 · 9 steps · RIP-Seq · code_examples

Transcriptome regulation by PARP13 in basal and antiviral states in human cells. (2024)

GSE106493 Processing Pipeline

GSE106493 · 4 steps · RIP-Seq · code_examples

Transcriptome regulation by PARP13 in basal and antiviral states in human cells. (2024)

GSE215251 Processing Pipeline

GSE215251 · 5 steps · GSE · code_examples

Transcriptome regulation by PARP13 in basal and antiviral states in human cells. (2024)

GSE240014 Processing Pipeline

GSE240014 · 6 steps · RNA-Seq · code_examples

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)

GSE240325 Processing Pipeline

GSE240325 · 7 steps · RNA-Seq · code_examples

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)

GSE240326 Processing Pipeline

GSE240326 · 6 steps · GSE · code_examples

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)

GSE240521 Processing Pipeline

GSE240521 · 9 steps · RIP-Seq · code_examples

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)

GSE248461 Processing Pipeline

GSE248461 · 6 steps · RNA-Seq · code_examples

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)

GSE263371 Processing Pipeline

GSE263371 · 6 steps · OTHER · code_examples

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)

GSE263870 Processing Pipeline

GSE263870 · 9 steps · OTHER · code_examples

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)

GSE122425 Processing Pipeline

GSE122425 · 5 steps · RNA-Seq · code_examples

Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP. (2023)

GSE198212 Processing Pipeline

GSE198212 · 7 steps · RIP-Seq · code_examples

Remodeling oncogenic transcriptomes by small molecules targeting NONO. (2023)

GSE198419 Processing Pipeline

GSE198419 · 7 steps · RNA-Seq · code_examples

Remodeling oncogenic transcriptomes by small molecules targeting NONO. (2023)

GSE205536 Processing Pipeline

GSE205536 · 13 steps · OTHER · code_examples

Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP. (2023)

GSE222216 Processing Pipeline

GSE222216 · 4 steps · RNA-Seq · code_examples

Remodeling oncogenic transcriptomes by small molecules targeting NONO. (2023)

GSE222217 Processing Pipeline

GSE222217 · 7 steps · GSE · code_examples

Remodeling oncogenic transcriptomes by small molecules targeting NONO. (2023)

GSE167466 Processing Pipeline

GSE167466 · 18 steps · RIP-Seq · code_examples

Crosstalk between CRISPR-Cas9 and the human transcriptome. (2022)

GSE180686 Processing Pipeline

GSE180686 · 20 steps · RIP-Seq · code_examples

Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq. (2022)

GSE55887 Processing Pipeline

GSE55887 · 5 steps · ChIP-Seq · code_examples

Crosstalk between CRISPR-Cas9 and the human transcriptome. (2022)

GSE90963 Processing Pipeline

GSE90963 · 35 steps · RNA-Seq · code_examples

Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. (2022)

Showing first 25 analysis results.