Version 1
: Received: 29 June 2023 / Approved: 30 June 2023 / Online: 3 July 2023 (14:06:15 CEST)
Version 2
: Received: 19 October 2023 / Approved: 23 October 2023 / Online: 23 October 2023 (11:16:53 CEST)
Planat M, Amaral M, Chester D, Fang F, Aschheim R, Irwin K. Group Theory of Messenger RNA Metabolism and Disease. Gene Expr. Published online: Jan 31, 2024. doi: 10.14218/GE.2023.00079.
Planat M, Amaral M, Chester D, Fang F, Aschheim R, Irwin K. Group Theory of Messenger RNA Metabolism and Disease. Gene Expr. Published online: Jan 31, 2024. doi: 10.14218/GE.2023.00079.
Planat M, Amaral M, Chester D, Fang F, Aschheim R, Irwin K. Group Theory of Messenger RNA Metabolism and Disease. Gene Expr. Published online: Jan 31, 2024. doi: 10.14218/GE.2023.00079.
Planat M, Amaral M, Chester D, Fang F, Aschheim R, Irwin K. Group Theory of Messenger RNA Metabolism and Disease. Gene Expr. Published online: Jan 31, 2024. doi: 10.14218/GE.2023.00079.
Abstract
Our recent work has focused on the application of infinite group theory and related algebraic geometric tools in the context of transcription factors and microRNAs. We were able to differentiate between “healthy" nucleotide sequences and disrupted sequences that may be associated with various diseases. In this paper, we extend our efforts to the study of messenger RNA metabolism, showcasing the power of our approach. We investigate (i) mRNA translation in prokaryotes and eukaryotes, (ii) polyadenylation in eukaryotes, which is crucial for nuclear export, translation, stability, and splicing of mRNA, (iii) miRNAs involved in RNA silencing and post-transcriptional regulation of gene expression, and (iv) the identification of disrupted sequences that could lead to potential illnesses. To achieve this, we employ (a) infinite (finitely generated) groups fp, with generators representing the r+1 distinct nucleotides and a relation between them [e.g., the consensus sequence in the mRNA translation (i), the poly(A) tail in item (ii), and the miRNA seed in item (iii)], (b) aperiodicity theory, which connects “healthy groups" fp to free groups Fr of rank r and their profinite completion F^r, and (c) the representation theory of groups fp over the space-time-spin group SL2(C), highlighting the role of surfaces with isolated singularities in the character variety. Our approach could potentially contribute to the understanding of the molecular mechanisms underlying various diseases and help develop new diagnostic or therapeutic strategies.
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.
Received:
23 October 2023
Commenter:
Michel Planat
Commenter's Conflict of Interests:
Author
Comment:
The paper was submitted to Biomedicines but was rejected. Then it was submitted to Gene Expression. We did many changes following the suggestion of one referee.
This is our response to Reviewer 2 after submission of our paper to Gene Expression.
We acknowledege Reviewer 2 for his reading of the paper and the suggestions he made.
1) Yes, we wrote that the subject of subsection 2.3 is \lq deep and complex' but we also wrote that \lq it can be skipped without affecting the comprehension of the rest of the paper'.
2) Concerning his remark that \lq the conciseness may pose challenges for readers', we added more material and more references in few places. (i) We summarized our quantum approach of the genetic code with finite groups and added the references. (ii) We added a section on chemical modifications of RNA: this is announced in the introduction and detailed through a new subsection of the discussion. Table 2 is added as well. (iii) We put in context our algebraic approach in subsection 2.4 and add references to our previous work.
3) About describing 'how the work advances the existing body of knowledge', we find that the paper speaks for itself since our methods have not been employed elsewhere. In the introduction we write that \lq it has npo been done before'.
4) We also attempted to reduce the similarity of some sentences to previous papers of ours as much as possible. The highest similarity is in item 1 (which includes the name and address of authors, keywords and some necessary introduction to mathematical concepts).
Commenter: Michel Planat
Commenter's Conflict of Interests: Author
This is our response to Reviewer 2 after submission of our paper to Gene Expression.
We acknowledege Reviewer 2 for his reading of the paper and the suggestions he made.
1) Yes, we wrote that the subject of subsection 2.3 is \lq deep and complex' but we also wrote that \lq it can be skipped without affecting the comprehension of the rest of the paper'.
2) Concerning his remark that \lq the conciseness may pose challenges for readers', we added more material and more references in few places.
(i) We summarized our quantum approach of the genetic code with finite groups and added the references.
(ii) We added a section on chemical modifications of RNA: this is announced in the introduction and detailed through a new subsection of the discussion. Table 2 is added as well.
(iii) We put in context our algebraic approach in subsection 2.4 and add references to our previous work.
3) About describing 'how the work advances the existing body of knowledge', we find that the paper speaks for itself since our methods have not been employed elsewhere.
In the introduction we write that \lq it has npo been done before'.
4) We also attempted to reduce the similarity of some sentences to previous papers of ours as much as possible. The highest similarity is in item 1 (which includes the name and address of authors,
keywords and some necessary introduction to mathematical concepts).