The Common Origin of Symmetry and Structure in Genetic Sequences

Overview

Journal Sci Rep

Specialty Science

Date 2018 Oct 27

PMID 30361485

Citations 4

Authors

Giampaolo Cristadoro

Mirko Degli Esposti

Eduardo G Altmann

Affiliations

Soon will be listed here.

Abstract

Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On the other hand, single-strand symmetry has been scrutinised using neutral models in which correlations are not considered or irrelevant, contrary to empirical evidence. Different studies investigated these two statistical features separately, reaching minimal consensus despite sustained efforts. Here we unravel previously unknown symmetries in genetic sequences, which are organized hierarchically through scales in which non-random structures are known to be present. These observations are confirmed through the statistical analysis of the human genome and explained through a simple domain model. These results suggest that domain models which account for the cumulative action of mobile elements can explain simultaneously non-random structures and symmetries in genetic sequences.

Citing Articles

Generalised interrelations among mutation rates drive the genomic compliance of Chargaff's second parity rule.

Pflughaupt P, Sahakyan A Nucleic Acids Res. 2023; 51(14):7409-7423.

PMID: 37293966 PMC: 10415130. DOI: 10.1093/nar/gkad477.

A role for circular code properties in translation.

Giannerini S, Gonzalez D, Goracci G, Danielli A Sci Rep. 2021; 11(1):9218.

PMID: 33911089 PMC: 8080828. DOI: 10.1038/s41598-021-87534-y.

Driven progressive evolution of genome sequence complexity in Cyanobacteria.

Moya A, Oliver J, Verdu M, Delaye L, Arnau V, Bernaola-Galvan P Sci Rep. 2020; 10(1):19073.

PMID: 33149190 PMC: 7643063. DOI: 10.1038/s41598-020-76014-4.

DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule.

Fariselli P, Taccioli C, Pagani L, Maritan A Brief Bioinform. 2020; 22(2):2172-2181.

PMID: 32266404 PMC: 7986665. DOI: 10.1093/bib/bbaa041.

References

Chargaff E . Structure and function of nucleic acids as cell constituents. Fed Proc. 1951; 10(3):654-9. View

Mitchell D, Bridge R . A test of Chargaff's second rule. Biochem Biophys Res Commun. 2005; 340(1):90-4. DOI: 10.1016/j.bbrc.2005.11.160. View

Bogachev M, Kayumov A, Bunde A . Universal internucleotide statistics in full genomes: a footprint of the DNA structure and packaging?. PLoS One. 2014; 9(12):e112534. PMC: 4249851. DOI: 10.1371/journal.pone.0112534. View

Tavares A, Pinho A, M Silva R, Rodrigues J, Bastos C, Ferreira P . DNA word analysis based on the distribution of the distances between symmetric words. Sci Rep. 2017; 7(1):728. PMC: 5428789. DOI: 10.1038/s41598-017-00646-2. View

Peng C, Buldyrev S, Goldberger A, Havlin S, Sciortino F, Simons M . Long-range correlations in nucleotide sequences. Nature. 1992; 356(6365):168-70. DOI: 10.1038/356168a0. View

Karlin S, Brendel V . Patchiness and correlations in DNA sequences. Science. 1993; 259(5095):677-80. DOI: 10.1126/science.8430316. View

Yam P . Noisy nucleotides. DNA sequences show fractal correlations. Sci Am. 1992; 267(3):23-4, 27. View

Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G . The mosaic genome of warm-blooded vertebrates. Science. 1985; 228(4702):953-8. DOI: 10.1126/science.4001930. View

Lobry J, Lobry C . Evolution of DNA base composition under no-strand-bias conditions when the substitution rates are not constant. Mol Biol Evol. 1999; 16(6):719-23. DOI: 10.1093/oxfordjournals.molbev.a026156. View

10.

Zhang S, Huang Y . Limited contribution of stem-loop potential to symmetry of single-stranded genomic DNA. Bioinformatics. 2009; 26(4):478-85. DOI: 10.1093/bioinformatics/btp703. View

11.

Rudner R, KARKAS J, Chargaff E . Separation of B. subtilis DNA into complementary strands, I. Biological properties. Proc Natl Acad Sci U S A. 1968; 60(2):630-5. PMC: 225093. DOI: 10.1073/pnas.60.2.630. View

12.

Bell S, Forsdyke D . Accounting units in DNA. J Theor Biol. 1999; 197(1):51-61. DOI: 10.1006/jtbi.1998.0857. View

13.

Amato I . DNA shows unexplained patterns writ large. Science. 1992; 257(5071):747. DOI: 10.1126/science.1496395. View

14.

Li W . The study of correlation structures of DNA sequences: a critical review. Comput Chem. 1997; 21(4):257-71. DOI: 10.1016/s0097-8485(97)00022-3. View

15.

Bell S, Forsdyke D . Deviations from Chargaff's second parity rule correlate with direction of transcription. J Theor Biol. 1999; 197(1):63-76. DOI: 10.1006/jtbi.1998.0858. View

16.

Nikolaou C, Almirantis Y . Deviations from Chargaff's second parity rule in organellar DNA Insights into the evolution of organellar genomes. Gene. 2006; 381:34-41. DOI: 10.1016/j.gene.2006.06.010. View

17.

Prabhu V . Symmetry observations in long nucleotide sequences. Nucleic Acids Res. 1993; 21(12):2797-800. PMC: 309655. DOI: 10.1093/nar/21.12.2797. View

18.

Baisnee P, Hampson S, Baldi P . Why are complementary DNA strands symmetric?. Bioinformatics. 2002; 18(8):1021-33. DOI: 10.1093/bioinformatics/18.8.1021. View

19.

Bryce R, Sprague K . Revisiting detrended fluctuation analysis. Sci Rep. 2012; 2:315. PMC: 3303145. DOI: 10.1038/srep00315. View

20.

Albrecht-Buehler G . Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions. Proc Natl Acad Sci U S A. 2006; 103(47):17828-33. PMC: 1635160. DOI: 10.1073/pnas.0605553103. View