ArticleInternational journal of molecular sciences2022
Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters.
Article in International journal of molecular sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Structural Features of DNA in TATA-Containing and TATA-Less Core Promoters of RNA Polymerase II Differ.International journal of molecular sciences · 2026Article
- Structural Features of DNA in tRNA Genes and Their Upstream Sequences.International journal of molecular sciences · 2024Article
- Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks.International journal of molecular sciences · 2024Article
- Research Topics of the Bioinformatics of Gene Regulation.International journal of molecular sciences · 2023Article
- Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs.International journal of molecular sciences · 2023Article
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Authors and funding
3 authors.
Funding
Abstract
Eukaryotic and archaeal RNA polymerase II (POL II) machinery is highly conserved, regardless of the extreme changes in promoter sequences in different organisms. The goal of our work is to find the cause of this conservatism. The representative sets of aligned promoter sequences of fifteen organisms belonging to different evolutional stages were studied. Their textual profiles, as well as profiles of the indexes that characterize the secondary structure and the mechanical and physicochemical properties, were analyzed. The evolutionarily stable, extremely heterogeneous special secondary structure of POL II core promoters was revealed, which includes two singular regions-hexanucleotide "INR" around TSS and octanucleotide "TATA element" of about -28 bp upstream. Such structures may have developed at some stage of evolution. It turned out to be so well matched for the pre-initiation complex formation and the subsequent initiation of transcription for POL II machinery that in the course of evolution there were selected only those nucleotide sequences that were able to reproduce these structural properties. The individual features of specific sequences representing the singular region of the promoter of each gene can affect the kinetics of DNA-protein complex formation and facilitate strand separation in double-stranded DNA at the TSS position.
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