Version 1
: Received: 21 December 2021 / Approved: 23 December 2021 / Online: 23 December 2021 (11:00:32 CET)
Version 2
: Received: 6 January 2022 / Approved: 10 January 2022 / Online: 10 January 2022 (11:52:04 CET)
Planat, M.; Amaral, M.M.; Fang, F.; Chester, D.; Aschheim, R.; Irwin, K. Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding. Current Issues in Molecular Biology 2022, 44, 1417–1433, doi:10.3390/cimb44040095.
Planat, M.; Amaral, M.M.; Fang, F.; Chester, D.; Aschheim, R.; Irwin, K. Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding. Current Issues in Molecular Biology 2022, 44, 1417–1433, doi:10.3390/cimb44040095.
Planat, M.; Amaral, M.M.; Fang, F.; Chester, D.; Aschheim, R.; Irwin, K. Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding. Current Issues in Molecular Biology 2022, 44, 1417–1433, doi:10.3390/cimb44040095.
Planat, M.; Amaral, M.M.; Fang, F.; Chester, D.; Aschheim, R.; Irwin, K. Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding. Current Issues in Molecular Biology 2022, 44, 1417–1433, doi:10.3390/cimb44040095.
Abstract
Transcription factors (TFs) are proteins that recognize specific DNA fragments in order to decode the genome and ensure its optimal functioning. TFs work at the local and global scales by specifying cell type, cell growth and death, cell migration, organization and timely tasks. We investigate the structure of DNA-binding motifs with the theory of finitely generated groups. The DNA ‘word’ in the binding domain -the motif- may be seen as the generator of a finitely generated group Fdna on four letters, the bases A, T, G and C. It is shown that, most of the time, the DNA-binding motifs have subgroup structure close to free groups of rank three or less, a property that we call ‘syntactical freedom’. Such a property is associated to the aperiodicity of the motif when it is seen as a substitution sequence. Examples are provided for the major families of TFs such as leucine zipper factors, zinc finger factors, homeo-domain factors, etc. We also discuss the exceptions to the existence of such a DNA syntactical rule and their functional role. This includes the TATA box in the promoter region of some genes, the single nucleotide markers (SNP) and the motifs of some genes of ubiquitous role in transcription and regulation.
Keywords
DNA transcription factors; genes; finitely-generated groups; free groups; aperiodic order
Subject
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Commenter: Michel Planat
Commenter's Conflict of Interests: Author
Commenter: Amina Daoui
The commenter has declared there is no conflict of interests.