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4 results for “RNA secondary structure”

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  1. 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 ↗

  2. Crosstalk between CRISPR-Cas9 and the human transcriptome.

    Nature communications · 2022 · 13(1): 1125

    CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 …

    PMID 35236841 DOI ↗

  3. fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.

    STAR protocols · 2021 · 2(3): 100762

    Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) structure probing techniques characterize the secondary structure of RNA molecules, which influence their functions and interactions. A variation of SHAPE, footprinting SHAPE (fSHAPE), probes RNA in the presence and absence of protein …

    PMID 34485935 DOI ↗

  4. 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 ↗

Datasets 2

GSE145805 GSE · GEO

RNA secondary structome of different cell lines

Homo sapiens, Mus musculus · GPL20795, GPL21273

GSE167466 GSE · GEO

Crosstalk between CRISPR-Cas9 and the human transcriptome

Homo sapiens · GPL20301

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