Characterization of DNA methylation as a function of biological complexity via dinucleotide inter-distances

TL;DR

This study analyzes the distribution of dinucleotide distances in DNA across various organisms, revealing unique patterns in mammals linked to DNA methylation and providing a potential method for organism classification based on methylation features.

Contribution

It introduces a statistical approach to characterize DNA methylation by analyzing dinucleotide inter-distances across different species, highlighting differences related to biological complexity.

Findings

Mammalian CG dinucleotide distributions show exponential tails.

Non-mammalian organisms exhibit more heterogeneous CG distributions.

Dinucleotide distance patterns can classify organisms by methylation roles.

Abstract

We perform a statistical study of the distances between successive occurrencies of a given dinucleotide in the DNA sequence for a number of organisms of different complexity. Our analysis highlights peculiar features of the dinucleotide CG 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 dinucleotides CG provides useful insights in characterizing and classifying organisms in terms of methylation functionalities.