Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters
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...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-09-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/18/10873 |
| _version_ | 1797487026492145664 |
|---|---|
| author | Anastasia V. Melikhova Anastasia A. Anashkina Irina A. Il’icheva |
| author_facet | Anastasia V. Melikhova Anastasia A. Anashkina Irina A. Il’icheva |
| author_sort | Anastasia V. Melikhova |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T23:42:49Z |
| format | Article |
| id | doaj.art-565b16e08a0741dab3164fbb2376f4ac |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T23:42:49Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-565b16e08a0741dab3164fbb2376f4ac2023-11-23T16:49:34ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-09-0123181087310.3390/ijms231810873Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core PromotersAnastasia V. Melikhova0Anastasia A. Anashkina1Irina A. Il’icheva2V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, RussiaV.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, RussiaV.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, RussiaEukaryotic 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.https://www.mdpi.com/1422-0067/23/18/10873eukaryotestranscription apparatuscore promoter DNA local structureultrasonic cleavageDNase I cleavageevolutionary invariant local structure of RNAP II core promoter |
| spellingShingle | Anastasia V. Melikhova Anastasia A. Anashkina Irina A. Il’icheva Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters International Journal of Molecular Sciences eukaryotes transcription apparatus core promoter DNA local structure ultrasonic cleavage DNase I cleavage evolutionary invariant local structure of RNAP II core promoter |
| title | Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters |
| title_full | Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters |
| title_fullStr | Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters |
| title_full_unstemmed | Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters |
| title_short | Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters |
| title_sort | evolutionary invariant of the structure of dna double helix in rnap ii core promoters |
| topic | eukaryotes transcription apparatus core promoter DNA local structure ultrasonic cleavage DNase I cleavage evolutionary invariant local structure of RNAP II core promoter |
| url | https://www.mdpi.com/1422-0067/23/18/10873 |
| work_keys_str_mv | AT anastasiavmelikhova evolutionaryinvariantofthestructureofdnadoublehelixinrnapiicorepromoters AT anastasiaaanashkina evolutionaryinvariantofthestructureofdnadoublehelixinrnapiicorepromoters AT irinaailicheva evolutionaryinvariantofthestructureofdnadoublehelixinrnapiicorepromoters |