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87 results for “RNA sequencing”
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Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection.
Molecular cell · 2026
Alternative polyadenylation (APA) generates transcript isoforms with distinct 3' ends, yet the repertoire of its protein regulators remains poorly defined. Using a large-scale tethered function screen, we profiled 879 human RNA-binding proteins (RBPs) and identified 63 high-confidence activators of poly(A) …
PMID 42361791 DOI ↗
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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<sup>1-11</sup>. Among these, alternative splicing has been shown to drive cell-type specificity and, when disrupted, is strongly linked to neurological disorders<sup>12-17</sup>. However, genome-wide measurements of mRNA translation with isoform …
PMID 41708856 DOI ↗
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Identification of RBP binding sites using RNA deaminases.
Methods in enzymology · 2025 · 713: 287-297
RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing. Identification of their binding sites has important implications for their physiological and disease-related functions. Crosslinking and immunoprecipitation, followed by sequencing (CLIP-seq) and its derivatives, are the most commonly …
PMID 40250958 DOI ↗
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Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression.
Cancer research · 2025
RNA-binding proteins (RBPs) are important regulators of post-transcriptional gene expression. Understanding which and how RBPs promote cancer progression is crucial for cancers that lack effective targeted therapies, such as triple negative breast cancer (TNBC). Here, we employed both in vitro …
PMID 41411621 DOI ↗
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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 ↗
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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 ↗
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Integrative CRISPR Screens and RNA-Omics Discover an Essential Role for PUF60-3' Splice Site Interactions in Cancer Progression.
bioRxiv : the preprint server for biology · 2025
RNA-binding proteins (RBPs) are important regulators of post-transcriptional gene expression. Understanding which and how RBPs promote cancer progression is crucial for cancers that lack effective targeted therapies such as triple negative breast cancer (TNBC). Here, we employ both <i>in vitro</i> …
PMID 40655003 DOI ↗
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Rational design yields RNA-binding zinc finger domains with altered sequence specificity.
RNA (New York, N.Y.) · 2025 · 31(2): 150-163
Targeting and manipulating endogenous RNAs in a sequence-specific manner is essential for both understanding RNA biology and developing RNA-targeting therapeutics. RNA-binding zinc fingers (ZnFs) are excellent candidates as designer proteins to expand the RNA-targeting toolbox, due to their compact size …
PMID 39658359 DOI ↗
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LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis.
bioRxiv : the preprint server for biology · 2025
Metabolic syndrome and excessive alcohol consumption result in liver injury and fibrosis, which is characterized by increased collagen production by activated Hepatic Stellate Cells (HSCs). LARP6, an RNA-binding protein, was shown to facilitate collagen production. However, LARP6 expression and functionality …
PMID 39868246 DOI ↗
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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 ↗
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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 ↗
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Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation.
Molecular cell · 2024 · 84(19): 3826-3842.e8
RNA interactome studies have revealed that hundreds of zinc-finger proteins (ZFPs) are candidate RNA-binding proteins (RBPs), yet their RNA substrates and functional significance remain largely uncharacterized. Here, we present a systematic multi-omics analysis of the DNA- and RNA-binding targets and …
PMID 39303722 DOI ↗
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Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion.
Nature biotechnology · 2024 · 42(9): 1429-1441
RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we developed tethered function luciferase-based splicing reporters that provide rapid, scalable and robust readouts of exon inclusion …
PMID 38168984 DOI ↗
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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 ↗
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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 ↗
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Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.
Nature communications · 2024 · 15(1): 875
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 38287010 DOI ↗
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FLARE: a fast and flexible workflow for identifying RNA editing foci.
BMC bioinformatics · 2023 · 24(1): 370
Fusion of RNA-binding proteins (RBPs) to RNA base-editing enzymes (such as APOBEC1 or ADAR) has emerged as a powerful tool for the discovery of RBP binding sites. However, current methods that analyze sequencing data from RNA-base editing experiments are vulnerable …
PMID 37784060 DOI ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients.
Cellular and molecular gastroenterology and hepatology · 2022 · 14(1): 35-53
Hyperbaric oxygen therapy (HBOT) is a promising treatment for moderate-to-severe ulcerative colitis. However, our current understanding of the host and microbial response to HBOT remains unclear. This study examined the molecular mechanisms underpinning HBOT using a multi-omic strategy. Pre- and …
PMID 35378331 DOI ↗
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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 ↗
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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 ↗
Datasets 22
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [scRNA-Seq]
GPL24676
Identification of islet-enriched long non-coding RNAs contributing to beta-cell failure in type 2 diabetes
Mus musculus · GPL9250
RNA sequencing of bone marrow CD34+ hematopoietic stem and progenitor cells from patients with myelodysplastic syndrome and healthy controls
Homo sapiens · GPL20301
Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome
Homo sapiens · GPL11154
RNA-Seq of CD8+ T cell subsets during LCMV infection III
Mus musculus · GPL17021
Transcriptional Survey of Ileal-Anal Pouch Immune Cells from Ulcerative Colitis
Homo sapiens · GPL20301
Developmental emergence of adult neural stem cells as revealed by single cell transcriptional profiling
Mus musculus · GPL19057
CRISPR/Cas9 screening of RNA binding proteins (RBPs) that regulate RUNX1 isoform production
Homo sapiens · GPL20301
A transcriptome-wide divergence in protein translation scales with LIN28B expression
Mus musculus · GPL20301
Epigenetics CRISPRi screen in mouse neuronal progenitor cells (NPCs)
Mus musculus · GPL21626
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (2)
Homo sapiens · GPL24676
RNA-seq in neurites and soma of primary hippocampal neurons isolated from P0 or P1 mice
Mus musculus · GPL19057
Molecular determinants and heterogeneity of circulating and tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing
Mus musculus · GPL21103
Direct RNA sequencing enables single-nucleotide m6A detection in endogenous transcript isoforms
Homo sapiens · GPL24106
FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci
Homo sapiens · GPL24676
Transcriptome analysis of diverse cell types infected with human cytomegalovirus [array]
Homo sapiens · GPL15106
Gene expression profiles at the single cell level of CD8+ T cells from the spleens of LCMV-Armstrong or LCMV-Clone 13 infected mice
Mus musculus · GPL19057
Early transcriptional and epigenetic regulation of CD8+ T cell differentiation revealed by single-cell RNA-seq
Mus musculus · GPL17021
Transcriptome analysis of diverse cell types infected with human cytomegalovirus [RNA-Seq]
Homo sapiens · GPL11154
Single Cell RNA-Seq of CD8+ T cell subsets responding to tumor
Mus musculus · GPL21103
The dsRBP and inactive editor, ADR-1, utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome
6239 · GPL9269
Analyses 8
GSE114922 · 7 steps · RNA-Seq · code_examples
Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms. (2022)
GSE65973 · 5 steps · RNA-Seq · code_examples
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)
GSE131847 · 5 steps · RNA-Seq · code_examples
Early precursors and molecular determinants of tissue-resident memory CD8<sup>+</sup> T lymphocytes revealed by single-cell RNA sequencing. (2020)
GSE132971 · 4 steps · RNA-Seq · code_examples
Direct RNA sequencing enables m<sup>6</sup>A detection in endogenous transcript isoforms at base-specific resolution. (2020)
GSE89036 · 3 steps · ChIP-Seq · code_examples
Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)
GSE89405 · 39 steps · RNA-Seq · code_examples
Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)
GSE95237 · 3 steps · ChIP-Seq · code_examples
Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)
GSE95238 · 3 steps · geo_data_processing
Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)