Information thermodynamics of cytosine DNA methylation

Robersy Sanchez, Sally A. Mackenzie

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Cytosine DNA methylation (CDM) is a stable epigenetic modification to the genome and a widespread regulatory process in living organisms that involves multicomponent molecular machines. Genome-wide cytosine methylation patterning participates in the epigenetic reprogramming of a cell, suggesting that the biological information contained within methylation positions may be amenable to decoding. Adaptation to a new cellular or organismal environment also implies the potential for genome-wide redistribution of CDM changes that will ensure the stability of DNA molecules. This raises the question of whether or not we would be able to sort out the regulatory methylation signals from the CDM background ("noise") induced by thermal fluctuations. Here, we propose a novel statistical and information thermodynamic description of the CDM changes to address the last question. The physical basis of our statistical mechanical model was evaluated in two respects: 1) the adherence to Landauer's principle, according to which molecular machines must dissipate a minimum energy ε = kBTln2 at each logic operation, where kB is the Boltzmann constant, and T is the absolute temperature and 2) whether or not the binary stretch of methylation marks on the DNA molecule comprise a language of sorts, properly constrained by thermodynamic principles. The study was performed for genome-wide methylation data from 152 ecotypes and 40 trans-generational variations of Arabidopsis thaliana and 93 human tissues. The DNA persistence length, a basic mechanical property altered by CDM, was estimated with values from 39 to 66.9 nm. Classical methylome analysis can be retrieved by applying information thermodynamic modelling, which is able to discriminate signal from noise. Our finding suggests that the CDM signal comprises a language scheme properly constrained by molecular thermodynamic principles, which is part of an epigenomic communication system that obeys the same thermodynamic rules as do current human communication systems.

Original languageEnglish (US)
Article numbere0150427
JournalPloS one
Volume11
Issue number3
DOIs
StatePublished - Mar 2016

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cytosine
Cytosine
DNA methylation
DNA Methylation
Thermodynamics
thermodynamics
Methylation
methylation
Genes
Epigenomics
epigenetics
Genome
genome
communications technology
DNA
Communication systems
Striae Distensae
Language
Communication
Ecotype

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Information thermodynamics of cytosine DNA methylation. / Sanchez, Robersy; Mackenzie, Sally A.

In: PloS one, Vol. 11, No. 3, e0150427, 03.2016.

Research output: Contribution to journalArticle

Sanchez, Robersy ; Mackenzie, Sally A. / Information thermodynamics of cytosine DNA methylation. In: PloS one. 2016 ; Vol. 11, No. 3.
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