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11 results for “RNA regulatory elements”

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  1. High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay.

    Cell reports · 2026 · 45(5): 117348

    The CCR4-NOT complex is a central regulator of gene expression, orchestrating mRNA turnover through interactions with RNA-binding proteins (RBPs) and the microRNA (miRNA)-induced silencing complex. However, identifying which RBP- and miRNA-associated RNA elements recruit CCR4-NOT remains challenging, due in part …

    PMID 42154591 DOI ↗

  2. 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 ↗

  3. 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 ↗

  4. A large-scale binding and functional map of human RNA-binding proteins.

    Nature · 2020 · 583(7818): 711-719

    Many proteins regulate the expression of genes by binding to specific regions encoded in the genome<sup>1</sup>. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part …

    PMID 32728246 DOI ↗

  5. Expanded encyclopaedias of DNA elements in the human and mouse genomes.

    Nature · 2020 · 583(7818): 699-710

    The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded …

    PMID 32728249 DOI ↗

  6. 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 ↗

  7. 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 ↗

  8. The <i>C. elegans</i> neural editome reveals an ADAR target mRNA required for proper chemotaxis.

    eLife · 2017 · 6

    ADAR proteins alter gene expression both by catalyzing adenosine (A) to inosine (I) RNA editing and binding to regulatory elements in target RNAs. Loss of ADARs affects neuronal function in all animals studied to date. <i>Caenorhabditis elegans</i> lacking ADARs exhibit …

    PMID 28925356 DOI ↗

  9. 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 ↗

  10. 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 ↗

  11. Inference of splicing regulatory activities by sequence neighborhood analysis.

    PLoS genetics · 2006 · 2(11): e191

    Sequence-specific recognition of nucleic-acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood Inference (NI) that predicts sequences with activity in regulating a biochemical process based on the local density of known …

    PMID 17121466 DOI ↗

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