Abstract
BackgroundStatistical approaches to genetic sequences have revealed helpful to gain deeper insight into biological and structural functionalities, using ideas coming from information theory and stochastic modelling of symbolic sequences. In particular, previous analyses on CG dinucleotide position along the genome allowed to highlight its epigenetic role in DNA methylation, showing a different distribution tail as compared to other dinucleotides.In this paper we extend the analysis to the whole CG distance distribution over a selected set of higher-order organisms. Then we apply the best fitting probability density function to a large range of organisms (>4400) of different complexity (from bacteria to mammals) and we characterize some emerging global features.ResultsWe find that the Gamma distribution is optimal for the selected subset as compared to a group of several distributions, chosen for their physical meaning or because recently used in literature for similar studies. The parameters of this distribution, when applied to our larger set of organisms, allows to highlight some biologically relavant features for the considered organism classes, that can be useful also for classification purposes.ConclusionsThe quantification of statistical properties of CG dinucleotide positioning along the genome is confirmed as a useful tool to characterize broad classes of organisms, spanning the whole range of biological complexity.
Highlights
Statistical approaches to genetic sequences have revealed helpful to gain deeper insight into biological and structural functionalities, using ideas coming from information theory and stochastic modelling of symbolic sequences
An extended analysis was performed on a dataset composed of 4425 genomes, selected among 7 of the 11 categories represented on the NCBI database: bacteria, fungi, invertebrates, plants, protozoa, mammal vertebrates and non-mammal vertebrates
Goodness-of-fit parameters showed that gamma distribution (Eq 6) is the function that best describes CG interdistance distribution for the 9 mammal subset
Summary
Statistical approaches to genetic sequences have revealed helpful to gain deeper insight into biological and structural functionalities, using ideas coming from information theory and stochastic modelling of symbolic sequences. In a previous paper [4], we higlighted a peculiar feature of mammals CG dinucleotides: the tail of CG interdistance distributions showed an exponential decay, at difference with non CG’s which had a heavier tail more similar to a power law This might be due to the specific role that CGs play inside mammals genomes, since they are the preferential sites of methylation, a fundamental epigenetic mechanism involved in gene regulation [6,7,8,9,10] and structural conformation of chromatine [11, 12]. We have extended the study to CG interdistance distributions from 4425 genomes, belonging to a wide range of organism categories
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