ArticleNucleic acids research2020
Structural transitions in the RNA 7SK 5' hairpin and their effect on HEXIM binding.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- ARNy plotter: A comprehensive web server for RNA ensemble structural analysis and visualization.PLoS computational biology · 2026Article
- Decoding RNA Structural Ensembles: Energy Landscape Exploration of the TAR Stemloop.Journal of chemical theory and computation · 2026Article
- Critical structural perturbations of ribozyme active sites induced by 2'-O-methylation commonly used in structural studies.Nucleic acids research · 2026Article
- Solution structure determination and biophysical characterization studies of 7SK RNP and 7SL SRP RNAs.RNA (New York, N.Y.) · 2025Article
- The role of structure in regulatory RNA elements.Bioscience reports · 2024Review
- Assessing RNA atomistic force fields via energy landscape explorations in implicit solvent.Biophysical reviews · 2024Review
- Clinical phenotype and genetic function analysis of a family with hypomyelinating leukodystrophy-7 caused by POLR3A mutation.Scientific reports · 2024Article
- RNA folding pathways from all-atom simulations with a variationally improved history-dependent bias.Biophysical journal · 2023Article
- Progress in 7SK ribonucleoprotein structural biology.Frontiers in molecular biosciences · 2023Review
- A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA.Communications biology · 2022Article
- Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP.Molecular cell · 2022Article
- Investigating the structural changes due to adenosine methylation of the Kaposi's sarcoma-associated herpes virus ORF50 transcript.PLoS computational biology · 2022Article
- The Energy Landscape Perspective: Encoding Structure and Function for Biomolecules.Frontiers in molecular biosciences · 2022Article
- Computer-aided comprehensive explorations of RNA structural polymorphism through complementary simulation methods.QRB discovery · 2022Review
- RNA modifications detection by comparative Nanopore direct RNA sequencing.Nature communications · 2021Article
- An alternative D. melanogaster 7SK snRNP.BMC molecular and cell biology · 2021Article
- A high-efficiency method for site-directed mutagenesis of large plasmids based on large DNA fragment amplification and recombinational ligation.Scientific reports · 2021Article
- RNA Modeling with the Computational Energy Landscape Framework.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Different views of the dynamic landscape covered by the 5'-hairpin of the 7SK small nuclear RNA.RNA (New York, N.Y.) · 2020Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
7SK RNA, as part of the 7SK ribonucleoprotein complex, is crucial to the regulation of transcription by RNA-polymerase II, via its interaction with the positive transcription elongation factor P-TEFb. The interaction is induced by binding of the protein HEXIM to the 5' hairpin (HP1) of 7SK RNA. Four distinct structural models have been obtained experimentally for HP1. Here, we employ computational methods to investigate the relative stability of these structures, transitions between them, and the effects of mutations on the observed structural ensembles. We further analyse the results with respect to mutational binding assays, and hypothesize a mechanism for HEXIM binding. Our results indicate that the dominant structure in the wild type exhibits a triplet involving the unpaired nucleotide U40 and the base pair A43-U66 in the GAUC/GAUC repeat. This conformation leads to an open major groove with enough potential binding sites for peptide recognition. Sequence mutations of the RNA change the relative stability of the different structural ensembles. Binding affinity is consequently lost if these changes alter the dominant structure.
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