title: Characterization of DNA methylation as a function of biological complexity via dinucleotide inter-distances.
abstract: We perform a statistical study of the distances between successive occurrences of a given dinucleotide in the DNA sequence for a number of organisms of different complexity. Our analysis highlights peculiar features of the CG dinucleotide distribution in mammalian DNA, pointing towards a connection with the role of such dinucleotide in DNA methylation. While the CG distributions of mammals exhibit exponential tails with comparable parameters, the picture for the other organisms studied (e.g. fish, insects, bacteria and viruses) is more heterogeneous, possibly because in these organisms DNA methylation has different functional roles. Our analysis suggests that the distribution of the distances between CG dinucleotides provides useful insights into characterizing and classifying organisms in terms of methylation functionalities.
authors: Department of Physics and Astronomy, University of Bologna, Viale B. Pichat 6/2, Bologna 40127, Italy.
authors: Giulia
authors: 0000-0003-0565-4356
authors: G
authors: Paci
authors: Department of Mathematics, University of Bologna, Piazza di Porta S. Donato 5, Bologna 40126, Italy.
authors: Giampaolo
authors: 0000-0003-4601-8575
authors: G
authors: Cristadoro
authors: Department of Pharmacy and Biotechnology, University of Bologna, Via S. Donato 15, Bologna 40127, Italy.
authors: Barbara
authors: 0000-0003-0330-482X
authors: B
authors: Monti
authors: Department of Mathematics, University of Bologna, Piazza di Porta S. Donato 5, Bologna 40126, Italy Bologna Unit, INFN, Viale B. Pichat 6/2, Bologna 40127, Italy.
authors: Marco
authors: 0000-0002-4283-7488
authors: M
authors: Lenci
authors: Department of Mathematics, University of Bologna, Piazza di Porta S. Donato 5, Bologna 40126, Italy.
authors: Mirko
authors: 0000-0003-0316-3449
authors: M
authors: Degli Esposti
authors: Department of Physics and Astronomy, University of Bologna, Viale B. Pichat 6/2, Bologna 40127, Italy Bologna Unit, INFN, Viale B. Pichat 6/2, Bologna 40127, Italy.
authors: Gastone C
authors: 0000-0003-4892-925X
authors: GC
authors: Castellani
authors: Department of Physics and Astronomy, University of Bologna, Viale B. Pichat 6/2, Bologna 40127, Italy Bologna Unit, INFN, Viale B. Pichat 6/2, Bologna 40127, Italy daniel.remondini@unibo.it.
authors: Daniel
authors: 0000-0003-3185-7456
authors: D
authors: Remondini
mesh_terms: D000818:Animals; D019175:DNA Methylation; D006801:Humans; D008957:Models, Genetic; D009711:Nucleotides / Q000235:genetics*
chemical_list: D009711:Nucleotides
keywords: DNA sequence; first return times; stochastic processes