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87 results for “RNA sequencing”
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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 ↗
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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 ↗
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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 ↗
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Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9.
Nucleic acids research · 2018 · 46(14): 7323-7338
Adenosine DeAminases acting on RNA (ADAR) catalyzes adenosine-to-inosine (A-to-I) conversion within RNA duplex structures. While A-to-I editing is often dynamically regulated in a spatial-temporal manner, the mechanisms underlying its tissue-selective restriction remain elusive. We have previously reported that transcripts of …
PMID 29733375 DOI ↗
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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 ↗
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Advances and challenges in the detection of transcriptome-wide protein-RNA interactions.
Wiley interdisciplinary reviews. RNA · 2018 · 9(1)
RNA binding proteins (RBPs) play key roles in determining cellular behavior by manipulating the processing of target RNAs. Robust methods are required to detect the numerous binding sites of RBPs across the transcriptome. RNA-immunoprecipitation followed by sequencing (RIP-seq) and crosslinking …
PMID 28853213 DOI ↗
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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 ↗
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Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP).
Methods in molecular biology (Clifton, N.J.) · 2017 · 1648: 177-200
Profiling of RNA binding protein targets in vivo provides critical insights into the mechanistic roles they play in regulating RNA processing. The enhanced crosslinking and immunoprecipitation (eCLIP) methodology provides a framework for robust, reproducible identification of transcriptome-wide protein-RNA interactions, with …
PMID 28766298 DOI ↗
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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 ↗
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Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing.
Nature immunology · 2017 · 18(4): 422-432
During microbial infection, responding CD8<sup>+</sup> T lymphocytes differentiate into heterogeneous subsets that together provide immediate and durable protection. To elucidate the dynamic transcriptional changes that underlie this process, we applied a single-cell RNA-sequencing approach and analyzed individual CD8<sup>+</sup> T lymphocytes …
PMID 28218746 DOI ↗
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CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins.
Methods (San Diego, Calif.) · 2017 · 118-119: 50-59
Identification of in vivo direct RNA targets for RNA binding proteins (RBPs) provides critical insight into their regulatory activities and mechanisms. Recently, we described a methodology for enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP) using antibodies against endogenous …
PMID 28003131 DOI ↗
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iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.
Stem cell reports · 2017 · 8(4): 1086-1100
Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 …
PMID 28410642 DOI ↗
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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 ↗
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Tethered Function Assays as Tools to Elucidate the Molecular Roles of RNA-Binding Proteins.
Advances in experimental medicine and biology · 2016 · 907: 61-88
Dynamic regulation of RNA molecules is critical to the survival and development of cells. Messenger RNAs are transcribed in the nucleus as intron-containing pre-mRNAs and bound by RNA-binding proteins, which control their fate by regulating RNA stability, splicing, polyadenylation, translation, …
PMID 27256382 DOI ↗
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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 ↗
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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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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 ↗
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Applications of Cas9 as an RNA-programmed RNA-binding protein.
BioEssays : news and reviews in molecular, cellular and developmental biology · 2015 · 37(7): 732-9
The Streptococcus pyogenes CRISPR-Cas system has gained widespread application as a genome editing and gene regulation tool as simultaneous cellular delivery of the Cas9 protein and guide RNAs enables recognition of specific DNA sequences. The recent discovery that Cas9 can …
PMID 25880497 DOI ↗
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RNA-binding proteins in neurodegeneration: Seq and you shall receive.
Trends in neurosciences · 2015 · 38(4): 226-36
As critical players in gene regulation, RNA binding proteins (RBPs) are taking center stage in our understanding of cellular function and disease. In our era of bench-top sequencers and unprecedented computational power, biological questions can be addressed in a systematic, …
PMID 25765321 DOI ↗
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Nxf1 natural variant E610G is a semi-dominant suppressor of IAP-induced RNA processing defects.
PLoS genetics · 2015 · 11(4): e1005123
Endogenous retroviruses and retrotransposons contribute functional genetic variation in animal genomes. In mice, Intracisternal A Particles (IAPs) are a frequent source of both new mutations and polymorphism across laboratory strains. Intronic IAPs can induce alternative RNA processing choices, including alternative …
PMID 25835743 DOI ↗
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Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development.
Circulation · 2015 · 131(14): 1278-1290
Long noncoding RNAs (lncRNAs) have emerged as critical epigenetic regulators with important functions in development and disease. Here, we sought to identify and functionally characterize novel lncRNAs critical for vertebrate development. By relying on human pluripotent stem cell differentiation models, …
PMID 25739401 DOI ↗
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The dsRBP and inactive editor ADR-1 utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome.
Cell reports · 2014 · 6(4): 599-607
Inadequate adenosine-to-inosine editing of noncoding regions occurs in disease but is often uncorrelated with ADAR levels, underscoring the need to study deaminase-independent control of editing. C. elegans have two ADAR proteins, ADR-2 and the theoretically catalytically inactive ADR-1. Using high-throughput …
PMID 24508457 DOI ↗
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Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges.
Nature structural & molecular biology · 2013 · 20(12): 1434-42
Alternative splicing (AS) enables programmed diversity of gene expression across tissues and development. We show here that binding in distal intronic regions (>500 nucleotides (nt) from any exon) by Rbfox splicing factors important in development is extensive and is an …
PMID 24213538 DOI ↗
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Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling.
The Journal of biological chemistry · 2013 · 288(49): 35372-86
Diabetic cardiomyopathy is one of the complications of diabetes that eventually leads to heart failure and death. Aberrant activation of PKC signaling contributes to diabetic cardiomyopathy by mechanisms that are poorly understood. Previous reports indicate that PKC is implicated in …
PMID 24151077 DOI ↗
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LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.
Molecular cell · 2012 · 48(2): 195-206
LIN28 is a conserved RNA-binding protein implicated in pluripotency, reprogramming, and oncogenesis. It was previously shown to act primarily by blocking let-7 microRNA (miRNA) biogenesis, but here we elucidate distinct roles of LIN28 regulation via its direct messenger RNA (mRNA) …
PMID 22959275 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)