{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T05:16:37Z","timestamp":1788498997941,"version":"build-2803163510"},"reference-count":34,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T00:00:00Z","timestamp":1787875200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Nucleotide motifs in the core promoters of eukaryotic protein-coding genes transcribed by RNA polymerase II (Pol II) play an important role in the transcription process. We analyzed the role of an octanucleotide located in the TATA box position. Depending on whether this octanucleotide can form a complex with the TATA-binding protein (TBP), the promoter is classified as either TATA-containing or TATA-less. We analyzed the differences in the primary and spatial structures, as well as their dynamics, in TATA-containing and TATA-less promoters of mammals and plants. We divided the complete promoter sets of six organisms (H. sapiens, M. musculus, C. familiaris, A. thaliana, Z. mays, and H. vulgare) from the EPDnew database into TATA-containing and TATA-less fractions. The sizes of the TATA-containing promoter fractions are significantly smaller than those of the TATA-less fractions in all studied organisms, except in A. thaliana, where the sizes of both fractions are approximately equal. We characterized promoter architecture using variation profiles of various base-pair step parameters, minor-groove width, and the conformational dynamics of native DNA. The architectures of TATA-containing and TATA-less promoters differ significantly. The possible mechanistic influence of DNA structural features on the formation of the pre-initiation complex (PIC) in both types of promoters is discussed.<\/jats:p>","DOI":"10.3390\/ijms27177735","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T09:48:36Z","timestamp":1788256116000},"page":"7735","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Structural Features of DNA in TATA-Containing and TATA-Less Core Promoters of RNA Polymerase II Differ"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-9874-8873","authenticated-orcid":false,"given":"Ekaterina A.","family":"Savina","sequence":"first","affiliation":[{"name":"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow 119991, Russia"},{"name":"Department of Information and Internet Technologies, Institute of Digital Biodesign and Artificial Intelligence in Medicine, Sechenov University, 8-2 Trubetskaya Str., Moscow 119991, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Olga D.","family":"Soldatenkova","sequence":"additional","affiliation":[{"name":"Department of Information and Internet Technologies, Institute of Digital Biodesign and Artificial Intelligence in Medicine, Sechenov University, 8-2 Trubetskaya Str., Moscow 119991, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"visualization","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1763-300X","authenticated-orcid":false,"given":"Anastasia A.","family":"Anashkina","sequence":"additional","affiliation":[{"name":"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow 119991, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"project-administration","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8172-243X","authenticated-orcid":false,"given":"Irina A.","family":"Il\u2019icheva","sequence":"additional","affiliation":[{"name":"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow 119991, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/s41580-018-0028-8","article-title":"Eukaryotic Core Promoters and the Functional Basis of Transcription Initiation","volume":"19","author":"Haberle","year":"2018","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1016\/j.bbagrm.2015.04.003","article-title":"The Core Promoter: At the Heart of Gene Expression","volume":"1849","author":"Danino","year":"2015","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Sloutskin, A., Shir-Shapira, H., Freiman, R.N., and Juven-Gershon, T. (2021). The Core Promoter Is a Regulatory Hub for Developmental Gene Expression. Front. Cell Dev. Biol., 9.","DOI":"10.3389\/fcell.2021.666508"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1002\/wdev.21","article-title":"Perspectives on the RNA Polymerase II Core Promoter","volume":"1","author":"Kadonaga","year":"2012","journal-title":"Wiley Interdiscip. Rev. Dev. Biol."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Il\u2019icheva, I.A., Khodikov, M.V., Poptsova, M.S., Nechipurenko, D.Y., Nechipurenko, Y.D., and Grokhovsky, S.L. (2016). Structural Features of DNA That Determine RNA Polymerase II Core Promoter. BMC Genom., 17.","DOI":"10.1186\/s12864-016-3292-z"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Melikhova, A.V., Anashkina, A.A., and Il\u2019icheva, I.A. (2022). Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms231810873"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"3217","DOI":"10.1101\/gad.13.24.3217","article-title":"TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved throughout Evolution","volume":"13","author":"Patikoglou","year":"1999","journal-title":"Genes Dev."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/ng1789","article-title":"Genome-Wide Analysis of Mammalian Promoter Architecture and Evolution","volume":"38","author":"Carninci","year":"2006","journal-title":"Nat. Genet."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1002\/2211-5463.12166","article-title":"DNA Structural Features of Eukaryotic TATA-Containing and TATA-Less Promoters","volume":"7","author":"Yella","year":"2017","journal-title":"FEBS Open Bio"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"D51","DOI":"10.1093\/nar\/gkw1069","article-title":"The Eukaryotic Promoter Database in Its 30th Year: Focus on Non-Vertebrate Organisms","volume":"45","author":"Dreos","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"D37","DOI":"10.1093\/nar\/gkn597","article-title":"DiProDB: A Database for Dinucleotide Properties","volume":"37","author":"Friedel","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1423","DOI":"10.1098\/rsta.2004.1390","article-title":"The Structural Basis of DNA Flexibility","volume":"362","author":"Travers","year":"2004","journal-title":"Philos. Trans. A Math. Phys. Eng. Sci."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"5108","DOI":"10.1093\/nar\/gkg680","article-title":"3DNA: A Software Package for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic Acid Structures","volume":"31","author":"Lu","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"6144","DOI":"10.1093\/nar\/gkh954","article-title":"The Relative Flexibility of B-DNA and A-RNA Duplexes: Database Analysis","volume":"32","author":"Noy","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"R263","DOI":"10.1186\/gb-2007-8-12-r263","article-title":"Determining Promoter Location Based on DNA Structure First-Principles Calculations","volume":"8","author":"Torrents","year":"2007","journal-title":"Genome Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1038\/333824a0","article-title":"DNA Sequence Determinants of CAP-Induced Bending and Protein Binding Affinity","volume":"333","author":"Gartenberg","year":"1988","journal-title":"Nature"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.bpj.2010.10.052","article-title":"Sequence-Specific Ultrasonic Cleavage of DNA","volume":"100","author":"Grokhovsky","year":"2011","journal-title":"Biophys. J."},{"key":"ref_18","unstructured":"Grokhovsky, S.L., Il\u2019icheva, I.A., Golovkin, M.V., Nechipurenko, Y.D., Nechipurenko, D.Y., Panchenko, L.A., and Polozov, R.V. (2013). Mechanochemical Cleavage of DNA by Ultrasound. Ultrasonics: Theory, Techniques and Practical Applications, Nova Science Publishers, Inc."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Grokhovsky, S., Il\u2019icheva, I., Nechipurenko, D., Golovkin, M., Taranov, G., Panchenko, L., Polozov, R., and Nechipurenko, Y. (2012). Quantitative Analysis of Electrophoresis Data-Application to Sequence-Specific Ultrasonic Cleavage of DNA. Gel Electrophoresis-Principles and Basics, InTech.","DOI":"10.5772\/37686"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"149803","DOI":"10.1016\/j.ijbiomac.2025.149803","article-title":"Sequence-Specific Cleavage of DNA under Ultrasound Is Due to Intramolecular Dynamics","volume":"338","author":"Kovaleva","year":"2026","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1038\/332464a0","article-title":"Structure Refined to 2A of a Nicked DNA Octanucleotide Complex with DNase I","volume":"332","author":"Suck","year":"1988","journal-title":"Nature"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1016\/0022-2836(92)91064-V","article-title":"X-Ray Structure of the DNase I-d(GGTATACC)2 Complex at 2.3 A Resolution","volume":"226","author":"Weston","year":"1992","journal-title":"J. Mol. Biol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1002\/jmr.300070203","article-title":"DNA Recognition by DNase I","volume":"7","author":"Suck","year":"1994","journal-title":"J. Mol. Recognit."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"6376","DOI":"10.1073\/pnas.1216822110","article-title":"Probing DNA Shape and Methylation State on a Genomic Scale with DNase I","volume":"110","author":"Lazarovici","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1016\/S0092-8674(04)00205-3","article-title":"Identification and Distinct Regulation of Yeast TATA Box-Containing Genes","volume":"116","author":"Basehoar","year":"2004","journal-title":"Cell"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1093\/nar\/gkg041","article-title":"PlantProm: A Database of Plant Promoter Sequences","volume":"31","author":"Shahmuradov","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Molina, C., and Grotewold, E. (2005). Genome Wide Analysis of Arabidopsis Core Promoters. BMC Genom., 6.","DOI":"10.1186\/1471-2164-6-25"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1038\/365512a0","article-title":"Crystal Structure of a Yeast TBP\/TATA-Box Complex","volume":"365","author":"Kim","year":"1993","journal-title":"Nature"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1038\/365520a0","article-title":"Co-Crystal Structure of TBP Recognizing the Minor Groove of a TATA Element","volume":"365","author":"Kim","year":"1993","journal-title":"Nature"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1038\/nsb0994-638","article-title":"1.9 A Resolution Refined Structure of TBP Recognizing the Minor Groove of TATAAAAG","volume":"1","author":"Kim","year":"1994","journal-title":"Nat. Struct. Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"13850","DOI":"10.1074\/jbc.270.23.13850","article-title":"Evidence for Functional Binding and Stable Sliding of the TATA Binding Protein on Nonspecific DNA","volume":"270","author":"Coleman","year":"1995","journal-title":"J. Biol. Chem."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"724","DOI":"10.1038\/373724a0","article-title":"Pre-Bending of a Promoter Sequence Enhances Affinity for the TATA-Binding Factor","volume":"373","author":"Parvin","year":"1995","journal-title":"Nature"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1006\/jmbi.1999.2947","article-title":"TATA Box DNA Deformation with and without the TATA Box-Binding Protein","volume":"291","author":"Davis","year":"1999","journal-title":"J. Mol. Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"e00448-17","DOI":"10.1128\/MCB.00448-17","article-title":"Mechanistic Differences in Transcription Initiation at TATA-Less and TATA-Containing Promoters","volume":"38","author":"Donczew","year":"2018","journal-title":"Mol. Cell. Biol."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/17\/7735\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T04:27:41Z","timestamp":1788496061000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/17\/7735"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,28]]},"references-count":34,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ijms27177735"],"URL":"https:\/\/doi.org\/10.3390\/ijms27177735","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,28]]}}}