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144 results for “Regulation”

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  1. 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 ↗

  2. How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms.

    Molecular cell · 2020 · 78(1): 9-29

    RNA-binding proteins (RBPs) comprise a large class of over 2,000 proteins that interact with transcripts in all manner of RNA-driven processes. The structures and mechanisms that RBPs use to bind and regulate RNA are incredibly diverse. In this review, we …

    PMID 32243832 DOI ↗

  3. The mRNA Decay Factor CAR-1/LSM14 Regulates Axon Regeneration via Mitochondrial Calcium Dynamics.

    Current biology : CB · 2020 · 30(5): 865-876.e7

    mRNA decay factors regulate mRNA turnover by recruiting non-translating mRNAs and targeting them for translational repression and mRNA degradation. How mRNA decay pathways regulate cellular function in vivo with specificity is poorly understood. Here, we show that C. elegans mRNA …

    PMID 31983639 DOI ↗

  4. 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 ↗

  5. 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 ↗

  6. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription.

    Cell · 2019 · 178(1): 107-121.e18

    Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA-binding proteins (RBPs). Although multiple RBPs have been implicated in transcription control, it has remained unclear how extensively RBPs directly act on …

    PMID 31251911 DOI ↗

  7. 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 ↗

  8. 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 ↗

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

    PLoS genetics · 2019 · 15(3): e1007948

    Glial cells regulate multiple aspects of synaptogenesis. In the absence of Schwann cells, a peripheral glial cell, motor neurons initially innervate muscle but then degenerate. Here, using a genetic approach, we show that neural activity-regulated negative factors produced by muscle …

    PMID 30870413 DOI ↗

  10. 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 ↗

  11. RBP-Maps enables robust generation of splicing regulatory maps.

    RNA (New York, N.Y.) · 2019 · 25(2): 193-204

    Alternative splicing of pre-messenger RNA transcripts enables the generation of multiple protein isoforms from the same gene locus, providing a major source of protein diversity in mammalian genomes. RNA binding proteins (RBPs) bind to RNA to control splice site choice …

    PMID 30413564 DOI ↗

  12. 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 ↗

  13. A Transcriptome-wide Translational Program Defined by LIN28B Expression Level.

    Molecular cell · 2019 · 73(2): 304-313.e3

    LIN28 RNA binding proteins are dynamically expressed throughout mammalian development and during disease. However, it remains unclear how changes in LIN28 expression define patterns of post-transcriptional gene regulation. Here we show that LIN28 expression level is a key variable that …

    PMID 30527666 DOI ↗

  14. An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys.

    RNA (New York, N.Y.) · 2018 · 24(9): 1255-1265

    During terminal erythropoiesis, the splicing machinery in differentiating erythroblasts executes a robust intron retention (IR) program that impacts expression of hundreds of genes. We studied IR mechanisms in the <i>SF3B1</i> splicing factor gene, which expresses ∼50% of its transcripts in …

    PMID 29959282 DOI ↗

  15. Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS.

    Acta neuropathologica · 2018 · 136(3): 405-423

    Sporadic amyotrophic lateral sclerosis (sALS) is the most common form of ALS, however, the molecular mechanisms underlying cellular damage and motor neuron degeneration remain elusive. To identify molecular signatures of sALS we performed genome-wide expression profiling in laser capture microdissection-enriched …

    PMID 29881994 DOI ↗

  16. 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 ↗

  17. Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels.

    Molecular cell · 2018 · 69(6): 1005-1016.e7

    RNA binding proteins (RBPs) interact with primary, precursor, and mature microRNAs (miRs) to influence mature miR levels, which in turn affect critical aspects of human development and disease. To understand how RBPs contribute to miR biogenesis, we analyzed human enhanced …

    PMID 29547715 DOI ↗

  18. 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 ↗

  19. 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 ↗

  20. 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 ↗

  21. 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 ↗

  22. 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 ↗

  23. 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 ↗

  24. MicroRNA-101 Regulates Multiple Developmental Programs to Constrain Excitation in Adult Neural Networks.

    Neuron · 2016 · 92(6): 1337-1351

    A critical feature of neural networks is that they balance excitation and inhibition to prevent pathological dysfunction. How this is achieved is largely unknown, although deficits in the balance contribute to many neurological disorders. We show here that a microRNA …

    PMID 27939580 DOI ↗

  25. Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.

    Neuron · 2016 · 92(4): 780-795

    HnRNPA2B1 encodes an RNA binding protein associated with neurodegeneration. However, its function in the nervous system is unclear. Transcriptome-wide crosslinking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ∼2,500 hnRNP A2/B1 binding sites and an unexpected role …

    PMID 27773581 DOI ↗

Datasets 25+

GSE302600 GSE · GEO

Zfp697/ZNF697 is an RNA-binding protein that modulates TGF-β1 2 signaling and hepatic inflammation in liver disease

Mus musculus · GPL30172

GSE254209 GSE · GEO

Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (eCLIP).

Homo sapiens · GPL24676

GSE254208 GSE · GEO

Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS (RNA-Seq).

Homo sapiens · Illumina

GSE328331 GSE · GEO

Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [RIP-Seq]

Homo sapiens · Illumina

GSE290625 GSE · GEO

Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [eclip]

Homo sapiens · Illumina

GSE290765 GSE · GEO

Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [cutnrun]

Homo sapiens · Illumina

GSE290755 GSE · GEO

Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [rna-seq]

Homo sapiens · Illumina

GSE290248 GSE · GEO

Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [PAS-seq]

Homo sapiens · Illumina

GSE290282 GSE · GEO

Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [RNA-Seq]

Homo sapiens · Illumina

GSE290281 GSE · GEO

Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [eCLIP]

Homo sapiens · Illumina

GSE313324 GSE · GEO

PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [CRISPR]

GPL24676

GSE280898 GSE · GEO

PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [eCLIP]

GPL24676

GSE280897 GSE · GEO

PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [RNA-seq]

GPL24676

GSE247544 GSE · GEO

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

GPL24247

GSE92602 GSE · GEO

Identification of islet-enriched long non-coding RNAs contributing to beta-cell failure in type 2 diabetes

Mus musculus · GPL9250

GSE55727 GSE · GEO

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

Mus musculus · GPL9115

GSE65973 GSE · GEO

RNA sequencing of mice expressing NLS-hTDP-43

Mus musculus · GPL9250

GSE56504 GSE · GEO

Loss of nuclear TDP-43 in ALS causes altered expression of splicing machinery and widespread dysregulation of RNA splicing in motor neurons

Mus musculus · GPL5188

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

GSE138197 GSE · GEO

Alternative polyadenylation mediates genetic regulation of gene expression

Homo sapiens · GPL18573

GSE202881 GSE · GEO

Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling

Homo sapiens · GPL24676

GSE206674 GSE · GEO

SerRS mediates translational readthrough of through engagement of the selenocysteine incorporation machinery

Homo sapiens · GPL30173

GSE215251 GSE · GEO

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

Homo sapiens · GPL16791

GSE104949 GSE · GEO

RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination

Homo sapiens · GPL15520

Showing first 25 dataset results.

Analyses 25+

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)

GSE249245 Processing Pipeline

GSE249245 · 5 steps · OTHER · code_examples

Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)

GSE249246 Processing Pipeline

GSE249246 · 3 steps · RIP-Seq · code_examples

Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)

GSE249247 Processing Pipeline

GSE249247 · 5 steps · GSE · code_examples

Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)

GSE268963 Processing Pipeline

GSE268963 · 1 step · OTHER · code_examples

Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)

GSE277047 Processing Pipeline

GSE277047 · 2 steps · OTHER · code_examples

Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)

GSE277160 Processing Pipeline

GSE277160 · 8 steps · RNA-Seq · code_examples

Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)

GSE277161 Processing Pipeline

GSE277161 · 4 steps · RNA-Seq · code_examples

Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)

GSE138197 Processing Pipeline

GSE138197 · 6 steps · RNA-Seq · code_examples

Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites. (2023)

GSE56504 Processing Pipeline

GSE56504 · 2 steps · GSE · code_examples

Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)

GSE113947 Processing Pipeline

GSE113947 · 4 steps · RNA-Seq · code_examples

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)

GSE118347 Processing Pipeline

GSE118347 · 10 steps · OTHER · code_examples

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)

GSE175885 Processing Pipeline

GSE175885 · 5 steps · RNA-Seq · code_examples

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)

GSE175886 Processing Pipeline

GSE175886 · 4 steps · GSE · code_examples

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)

GSE176045 Processing Pipeline

GSE176045 · 4 steps · RNA-Seq · code_examples

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)

GSE176060 Processing Pipeline

GSE176060 · 3 steps · OTHER · code_examples

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)

GSE178259 Processing Pipeline

GSE178259 · 6 steps · RNA-Seq · code_examples

Non-microRNA binding competitively inhibits LIN28 regulation. (2021)

GSE157048 Processing Pipeline

GSE157048 · 14 steps · RNA-Seq · code_examples

AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation. (2020)

GSE157049 Processing Pipeline

GSE157049 · 14 steps · RNA-Seq · code_examples

AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation. (2020)

GSE157050 Processing Pipeline

GSE157050 · 6 steps · RNA-Seq · code_examples

AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation. (2020)

GSE157051 Processing Pipeline

GSE157051 · 14 steps · GSE · code_examples

AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation. (2020)

GSE55727 Processing Pipeline

GSE55727 · 5 steps · RNA-Seq · code_examples

Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program. (2020)

GSE107867 Processing Pipeline

GSE107867 · 14 steps · RNA-Seq · code_examples

Widespread RNA editing dysregulation in brains from autistic individuals. (2019)

Showing first 25 analysis results.