The common origin of symmetry and structure in genetic sequences

Abstract

When exploring statistical properties of genetic sequences two main features stand out: the existence of non-random structures at various scales (e.g., long-range correlations) and the presence of symmetries (e.g., Chargaff parity rules). In the last decades, numerous studies investigated the origin and significance of each of these features separately. Here we show that both symmetry and structure have to be considered as the outcome of the same biological processes, whose cumulative effect can be quantitatively measured on extant genomes. We present a novel analysis (based on a minimal model) that not only explains and reproduces previous observations but also predicts the existence of a nested hierarchy of symmetries emerging at different structural scales. Our genome-wide analysis of H. Sapiens confirms the theoretical predictions.

Tracking evolutionary trends towards increasing complexity: a case study in Cyanobacteria

“…This information is an elusive but crucial component of the genome, whose study as a whole deserves deeper attention because it holds clues to answer many biological questions, particularly those of an evolutionary nature. The genome has distinct layers of information encoded in DNA sequences (Dekker et al ., 2017; Cristadoro et al ., 2018). The most well-known of these are those involved in biological function, such as the typical genome division into coding and non-coding parts or, within genes, the differential conservation shown by distinct codon positions due to the differential evolutionary constraints acting on them (Ikemura, 1985; Sueoka, 1992; Bernardi, 2004).…”

“…Such strand asymmetries are less directly related to biological function, but this alphabet has been useful to uncover long-range correlations and analyze the evolution of fractal structure in the genomes (Li and Kaneko, 1992; Peng et al ., 1992; Voss, 1992). Recently, a connection has been found between strand symmetry and the repetitive action of transposable elements during evolution (Cristadoro et al ., 2018; see also Koonin, 2016a and his concept of ‘fuzzy meaning’ of sequences). The partition given by SCC KM , to our knowledge, has not been associated to any biological function.…”

Hidden patterns of codon usage bias across kingdoms

“…One of the basic features of statistical mechanics is that it can derive useful and universal laws from macroscopic descriptions of systems containing many intractable microscopic interactions. Previous examples of application in biology include scaling laws [34], spatial genome structures [35] and evolutionary processes [36,37] to name but a few. Common to all applications of statistical mechanics is that a large number of difficult, or indeed intractable behaviours can, when considered at the right level, lead to simple macroscopic behaviours.…”

DNA energy constraints shape biological evolutionary trajectories

“…After fifty years from the discovery of Chargaff's second parity rule, there is not a generally accepted justification for its emergence, although several explanations have been proposed based on different models and hypothesis, such as: statistical 7,20,21 , stem-loops 22 , tandem duplications 23 , duplication followed by inversions 24 , inverted transpositions 25,26 , and non-uniform substitutions 27 . Notably, these explanations, although very promising, do not have predictive power, i.e.…”