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16 results for “Intronic”

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  1. ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses.

    The Journal of experimental medicine · 2021 · 218(9)

    Cytosolic double-stranded RNA (dsRNA) initiates type I IFN responses. Endogenous retroelements, notably Alu elements, constitute a source of dsRNA. Adenosine-to-inosine (A-to-I) editing by ADAR induces mismatches in dsRNA and prevents recognition by MDA5 and autoinflammation. To identify additional endogenous dsRNA …

    PMID 34297039 DOI ↗

  2. Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.

    Genome medicine · 2020 · 12(1): 112

    Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions …

    PMID 33287884 DOI ↗

  3. 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 ↗

  4. 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 ↗

  5. 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 ↗

  6. 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 ↗

  7. 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 ↗

  8. 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 ↗

  9. Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses.

    Nature communications · 2016 · 7: 12143

    The RNA-binding protein (RBP) TAF15 is implicated in amyotrophic lateral sclerosis (ALS). To compare TAF15 function to that of two ALS-associated RBPs, FUS and TDP-43, we integrate CLIP-seq and RNA Bind-N-Seq technologies, and show that TAF15 binds to ∼4,900 RNAs …

    PMID 27378374 DOI ↗

  10. 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 ↗

  11. 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 ↗

  12. Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs.

    Nature neuroscience · 2012 · 15(11): 1488-97

    FUS/TLS (fused in sarcoma/translocated in liposarcoma) and TDP-43 are integrally involved in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. We found that FUS/TLS binds to RNAs from >5,500 genes in mouse and human brain, primarily through a GUGGU-binding motif. We …

    PMID 23023293 DOI ↗

  13. Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43.

    Nature neuroscience · 2011 · 14(4): 459-68

    We used cross-linking and immunoprecipitation coupled with high-throughput sequencing to identify binding sites in 6,304 genes as the brain RNA targets for TDP-43, an RNA binding protein that, when mutated, causes amyotrophic lateral sclerosis. Massively parallel sequencing and splicing-sensitive junction …

    PMID 21358643 DOI ↗

  14. Alternative splicing in stem cell self-renewal and diferentiation.

    Advances in experimental medicine and biology · 2010 · 695: 92-104

    This chapter provides a review of recent advances in understanding the importance of alternative pre-messenger RNA splicing in stem cell biology. The majority of transcribed pre-mRNAs undergo RNA splicing where introns are excised and exons are juxtaposed to form mature …

    PMID 21222201 DOI ↗

  15. Alternative splicing events identified in human embryonic stem cells and neural progenitors.

    PLoS computational biology · 2007 · 3(10): 1951-67

    Human embryonic stem cells (hESCs) and neural progenitor (NP) cells are excellent models for recapitulating early neuronal development in vitro, and are key to establishing strategies for the treatment of degenerative disorders. While much effort had been undertaken to analyze …

    PMID 17967047 DOI ↗

  16. Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements.

    PLoS genetics · 2007 · 3(5): e85

    Knowledge of the functional cis-regulatory elements that regulate constitutive and alternative pre-mRNA splicing is fundamental for biology and medicine. Here we undertook a genome-wide comparative genomics approach using available mammalian genomes to identify conserved intronic splicing regulatory elements (ISREs). Our …

    PMID 17530930 DOI ↗

Datasets 3

GSE138197 GSE · GEO

Alternative polyadenylation mediates genetic regulation of gene expression

Homo sapiens · GPL18573

GSE113193 GSE · GEO

Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9

Homo sapiens · GPL18573

GSE224998 GSE · GEO

RPS19 binding with and without Diamond-Blackfan anemia variants

Homo sapiens · GPL24676

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