Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs
RNA polymerase II (POL II) is responsible for the transcription of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs). Previously, we have shown the evolutionary invariance of the structural features of DNA in the POL II core promoters of the precursors of mRNAs. In this work, we have analyze...
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MDPI AG
2023-05-01
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| Online Access: | https://www.mdpi.com/1422-0067/24/9/8199 |
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| author | Ekaterina A. Savina Tatiana G. Shumilina Vladimir G. Tumanyan Anastasia A. Anashkina Irina A. Il’icheva |
| author_facet | Ekaterina A. Savina Tatiana G. Shumilina Vladimir G. Tumanyan Anastasia A. Anashkina Irina A. Il’icheva |
| author_sort | Ekaterina A. Savina |
| collection | DOAJ |
| description | RNA polymerase II (POL II) is responsible for the transcription of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs). Previously, we have shown the evolutionary invariance of the structural features of DNA in the POL II core promoters of the precursors of mRNAs. In this work, we have analyzed the POL II core promoters of the precursors of lncRNAs in <i>Homo sapiens</i> and <i>Mus musculus</i> genomes. Structural analysis of nucleotide sequences in positions −50, +30 bp in relation to the TSS have shown the extremely heterogeneous 3D structure that includes two singular regions - hexanucleotide “INR” around the TSS and octanucleotide “TATA-box” at around ~−28 bp upstream. Thus, the 3D structure of core promoters of lncRNA resembles the architecture of the core promoters of mRNAs; however, textual analysis revealed differences between promoters of lncRNAs and promoters of mRNAs, which lies in their textual characteristics; namely, the informational entropy at each position of the nucleotide text of lncRNA core promoters (by the exception of singular regions) is significantly higher than that of the mRNA core promoters. Another distinguishing feature of lncRNA is the extremely rare occurrence in the TATA box of octanucleotides with the consensus sequence. These textual differences can significantly affect the efficiency of the transcription of lncRNAs. |
| first_indexed | 2024-03-11T04:16:25Z |
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| id | doaj.art-ae7f52c5ab1e464fa2df8db375b5d7d1 |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T04:16:25Z |
| publishDate | 2023-05-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-ae7f52c5ab1e464fa2df8db375b5d7d12023-11-17T23:06:20ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-05-01249819910.3390/ijms24098199Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAsEkaterina A. Savina0Tatiana G. Shumilina1Vladimir G. Tumanyan2Anastasia A. Anashkina3Irina A. Il’icheva4Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova, 32, Moscow 119991, RussiaDepartment of Information and Internet Technologies of the Institute of Digital Medicine, Sechenov University, 8-2 Trubetskaya str., Moscow 119991, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova, 32, Moscow 119991, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova, 32, Moscow 119991, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova, 32, Moscow 119991, RussiaRNA polymerase II (POL II) is responsible for the transcription of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs). Previously, we have shown the evolutionary invariance of the structural features of DNA in the POL II core promoters of the precursors of mRNAs. In this work, we have analyzed the POL II core promoters of the precursors of lncRNAs in <i>Homo sapiens</i> and <i>Mus musculus</i> genomes. Structural analysis of nucleotide sequences in positions −50, +30 bp in relation to the TSS have shown the extremely heterogeneous 3D structure that includes two singular regions - hexanucleotide “INR” around the TSS and octanucleotide “TATA-box” at around ~−28 bp upstream. Thus, the 3D structure of core promoters of lncRNA resembles the architecture of the core promoters of mRNAs; however, textual analysis revealed differences between promoters of lncRNAs and promoters of mRNAs, which lies in their textual characteristics; namely, the informational entropy at each position of the nucleotide text of lncRNA core promoters (by the exception of singular regions) is significantly higher than that of the mRNA core promoters. Another distinguishing feature of lncRNA is the extremely rare occurrence in the TATA box of octanucleotides with the consensus sequence. These textual differences can significantly affect the efficiency of the transcription of lncRNAs.https://www.mdpi.com/1422-0067/24/9/8199eukaryoteslong non-coding RNAslong intergenic non-coding RNAsantisense RNAsRNAP II transcription apparatusRNAP II core promoter |
| spellingShingle | Ekaterina A. Savina Tatiana G. Shumilina Vladimir G. Tumanyan Anastasia A. Anashkina Irina A. Il’icheva Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs International Journal of Molecular Sciences eukaryotes long non-coding RNAs long intergenic non-coding RNAs antisense RNAs RNAP II transcription apparatus RNAP II core promoter |
| title | Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs |
| title_full | Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs |
| title_fullStr | Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs |
| title_full_unstemmed | Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs |
| title_short | Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs |
| title_sort | core promoter regions of antisense and long intergenic non coding rnas |
| topic | eukaryotes long non-coding RNAs long intergenic non-coding RNAs antisense RNAs RNAP II transcription apparatus RNAP II core promoter |
| url | https://www.mdpi.com/1422-0067/24/9/8199 |
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