Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding

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.

Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding

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.

Quasi-isometric rigidity for graphs of virtually free groups with two-ended edge groups

We study the quasi-isometric rigidity of a large family of finitely generated groups that split as graphs of groups with virtually free vertex groups and two-ended edge groups. Let G be a group that is one-ended, hyperbolic relative to virtually abelian subgroups, and has JSJ decomposition over two-ended subgroups containing only virtually free vertex groups that are not quadratically hanging. Our main result is that any group quasi-isometric to G is abstractly commensurable to G. In particular, our result applies to certain “generic” HNN extensions of a free group over cyclic subgroups.

Hierarchy for groups acting on hyperbolic ℤn-spaces

In [A.-P. Grecianu, A. Kvaschuk, A. G. Myasnikov and D. Serbin, Groups acting on hyperbolic [Formula: see text]-metric spaces, Int. J. Algebra Comput. 25(6) (2015) 977–1042], the authors initiated a systematic study of hyperbolic [Formula: see text]-metric spaces, where [Formula: see text] is an ordered abelian group, and groups acting on such spaces. The present paper concentrates on the case [Formula: see text] taken with the right lexicographic order and studies the structure of finitely generated groups acting on hyperbolic [Formula: see text]-metric spaces. Under certain constraints, the structure of such groups is described in terms of a hierarchy (see [D. T. Wise, The Structure of Groups with a Quasiconvex Hierarchy[Formula: see text][Formula: see text]AMS-[Formula: see text], Annals of Mathematics Studies (Princeton University Press, 2021)]) similar to the one established for [Formula: see text]-free groups in [O. Kharlampovich, A. G. Myasnikov, V. N. Remeslennikov and D. Serbin, Groups with free regular length functions in [Formula: see text], Trans. Amer. Math. Soc. 364 (2012) 2847–2882].

Computability of finite quotients of finitely generated groups

We systematically study groups whose marked finite quotients form a recursive set. We give several definitions, and prove basic properties of this class of groups, and in particular emphasize the link between the growth of the depth function and solvability of the word problem. We give examples of infinitely presented groups whose finite quotients can be effectively enumerated. Finally, our main result is that a residually finite group can fail to be recursively presented and still have computable finite quotients, and that, on the other hand, it can have solvable word problem but not have computable finite quotients.

The relative exponential growth rate of subgroups of acylindrically hyperbolic groups

We introduce a new invariant of finitely generated groups, the ambiguity function, and we prove that every finitely generated acylindrically hyperbolic group has a linearly bounded ambiguity function. We use this result to prove that the relative exponential growth rate lim n → ∞ ⁡ | B H X ⁢ ( n ) | n \lim_{n\to\infty}\sqrt[n]{\lvert\vphantom{1_{1}}{B^{X}_{H}(n)}\rvert} of a subgroup 𝐻 of a finitely generated acylindrically hyperbolic group 𝐺 exists with respect to every finite generating set 𝑋 of 𝐺 if 𝐻 contains a loxodromic element of 𝐺. Further, we prove that the relative exponential growth rate of every finitely generated subgroup 𝐻 of a right-angled Artin group A Γ A_{\Gamma} exists with respect to every finite generating set of A Γ A_{\Gamma} .

Condensed groups in product varieties

A finitely generated group 𝐺 is said to be condensed if its isomorphism class in the space of finitely generated marked groups has no isolated points. We prove that every product variety U ⁢ V \mathcal{UV} , where 𝒰 (respectively, 𝒱) is a non-abelian (respectively, a non-locally finite) variety, contains a condensed group. In particular, there exist condensed groups of finite exponent. As an application, we obtain some results on the structure of the isomorphism and elementary equivalence relations on the set of finitely generated groups in U ⁢ V \mathcal{UV} .