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35 results for “Sequence analysis”

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  1. 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 ↗

  2. 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 ↗

  3. 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 ↗

  4. 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 ↗

  5. 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 ↗

  6. 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 ↗

  7. 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 ↗

  8. 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 ↗

  9. 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 ↗

  10. 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 ↗

  11. MECP2-related pathways are dysregulated in a cortical organoid model of myotonic dystrophy.

    Science translational medicine · 2022 · 14(651): eabn2375

    Myotonic dystrophy type 1 (DM1) is a multisystem, autosomal-dominant inherited disorder caused by CTG microsatellite repeat expansions (MREs) in the 3' untranslated region of the dystrophia myotonica-protein kinase (<i>DMPK</i>) gene. Despite its prominence as the most common adult-onset muscular dystrophy, …

    PMID 35767654 DOI ↗

  12. The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction.

    Scientific reports · 2022 · 12(1): 5077

    Throughout the COVID-19 pandemic, massive sequencing and data sharing efforts enabled the real-time surveillance of novel SARS-CoV-2 strains throughout the world, the results of which provided public health officials with actionable information to prevent the spread of the virus. However, …

    PMID 35332213 DOI ↗

  13. Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies.

    Nature communications · 2021 · 12(1): 6324

    Mutations in the cardiac splicing factor RBM20 lead to malignant dilated cardiomyopathy (DCM). To understand the mechanism of RBM20-associated DCM, we engineered isogenic iPSCs with DCM-associated missense mutations in RBM20 as well as RBM20 knockout (KO) iPSCs. iPSC-derived engineered heart …

    PMID 34732726 DOI ↗

  14. The <i>Thermus thermophilus</i> DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism.

    RNA (New York, N.Y.) · 2020 · 26(11): 1557-1574

    RNA helicases catalyze the ATP-dependent destabilization of RNA duplexes. DEAD-box helicases share a helicase core that mediates ATP binding and hydrolysis, RNA binding and unwinding. Most members of this family contain domains flanking the core that can confer RNA substrate …

    PMID 32669294 DOI ↗

  15. 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 ↗

  16. Heterogenous Populations of Tissue-Resident CD8<sup>+</sup> T Cells Are Generated in Response to Infection and Malignancy.

    Immunity · 2020 · 52(5): 808-824.e7

    Tissue-resident memory CD8<sup>+</sup> T cells (Trm) provide host protection through continuous surveillance of non-lymphoid tissues. Using single-cell RNA-sequencing (scRNA-seq) and genetic reporter mice, we identified discrete lineages of intestinal antigen-specific CD8<sup>+</sup> T cells, including a Blimp1<sup>hi</sup>Id3<sup>lo</sup> tissue-resident effector cell population …

    PMID 32433949 DOI ↗

  17. An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia.

    Nature cancer · 2020 · 1(4): 410-422

    Aggressive myeloid leukemias such as blast crisis chronic myeloid leukemia and acute myeloid leukemia remain highly lethal. Here we report a genome-wide in vivo CRISPR screen to identify new dependencies in this disease. Among these, RNA-binding proteins (RBPs) in general, …

    PMID 34109316 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. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.

    Nature communications · 2019 · 10(1): 1338

    Allele-specific protein-RNA binding is an essential aspect that may reveal functional genetic variants (GVs) mediating post-transcriptional regulation. Recently, genome-wide detection of in vivo binding of RNA-binding proteins is greatly facilitated by the enhanced crosslinking and immunoprecipitation (eCLIP) method. We developed …

    PMID 30902979 DOI ↗

  20. Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions.

    Methods (San Diego, Calif.) · 2017 · 126: 29-37

    Crosslinking and immunoprecipitation (CLIP) followed by high-throughput sequencing identifies the binding sites of RNA binding proteins on RNAs. The covalent RNA-amino acid adducts produced by UV irradiation can cause premature reverse transcription termination and deletions (referred to as crosslink-induced mutation …

    PMID 28790018 DOI ↗

  21. Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation.

    Molecular cell · 2017 · 67(1): 148-161.e5

    Alternative splicing (AS) generates isoform diversity for cellular identity and homeostasis in multicellular life. Although AS variation has been observed among single cells, little is known about the biological or evolutionary significance of such variation. We developed Expedition, a computational …

    PMID 28673540 DOI ↗

  22. Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions.

    Advances in experimental medicine and biology · 2016 · 907: 1-28

    After an RNA is transcribed, it undergoes a variety of processing steps that can change the encoded protein sequence (through alternative splicing and RNA editing), regulate the stability of the RNA, and control subcellular localization, timing, and rate of translation. …

    PMID 27256380 DOI ↗

  23. Pairing beyond the Seed Supports MicroRNA Targeting Specificity.

    Molecular cell · 2016 · 64(2): 320-333

    To identify endogenous miRNA-target sites, we isolated AGO-bound RNAs from Caenorhabditis elegans by individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP), which fortuitously also produced miRNA-target chimeric reads. Through the analysis of thousands of reproducible chimeras, pairing to the miRNA seed emerged as …

    PMID 27720646 DOI ↗

  24. SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.

    Molecular cell · 2016 · 64(2): 282-293

    RNA metabolism is controlled by an expanding, yet incomplete, catalog of RNA-binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull down …

    PMID 27720645 DOI ↗

  25. Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model.

    Genome medicine · 2016 · 8(1): 94

    Tuberous sclerosis complex (TSC) is a genetic disease characterized by benign tumor growths in multiple organs and neurological symptoms induced by mTOR hyperfunction. Because the molecular pathology is highly complex and the etiology poorly understood, we employed a defined human …

    PMID 27655340 DOI ↗

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Analyses 1

GSE9306 Processing Pipeline

GSE9306 · 2 steps · GSE · code_examples

RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. (2007)