Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications

Author:

Giniūnaitė Rasa12,Sharma Rahul3,Maddocks John H.3,Kriaučionis Skirmantas4ORCID,Petkevičiūtė-Gerlach Daiva1ORCID

Affiliation:

1. Department of Applied Mathematics, Kaunas University of Technology

2. Institute of Applied Mathematics, Vilnius University

3. Institut de Mathématiques, École Polytechnique Fédérale de Lausanne, EPFL SB MATH LCVMM

4. Ludwig Institute for Cancer Research Ltd, University of Oxford, Nuffield Department of Medicine, Old Road Campus Research Building, Roosevelt Drive

Abstract

The majority of vertebrate promoters have a distinct DNA composition, known as a CpG island. Cytosine methylation in promoter CpG islands is associated with a substantial reduction of transcription initiation. We hypothesise that both atypical sequence composition, and epigenetic base modifications may affect the mechanical properties of DNA in CpG islands, influencing the ability of proteins to bind and initiate transcription. In this work, we model two scalar measures of the sequence-dependent propensity of DNA to wrap into nucleosomes: the energy of DNA required to assume a particular nucleosomal configuration and a measure related to the probability of linear DNA spontaneously reaching the nucleosomal configuration. We find that CpG density and modification state can alter DNA mechanics by creating states more or less compatible with nucleosome formation.

Publisher

eLife Sciences Publications, Ltd

Reference64 articles.

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3. Modulation of the helical properties of DNA : next-to-nearest neighbour effects and beyond;Nucleic Acids Res,2019

4. The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function;PLOS Comput Biol,2021

5. Structural Mechanics of DNA Wrapping in the Nucleosome;J Mol Biol,2010

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