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Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation
Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Vascular Biology.
Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
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2014 (English)In: Epigenetics, ISSN 1559-2294, E-ISSN 1559-2308, Vol. 9, no 12, 1604-1612 p.Article in journal (Refereed) Published
Abstract [en]

We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding.

Place, publisher, year, edition, pages
2014. Vol. 9, no 12, 1604-1612 p.
Keyword [en]
DNA methylation, epigenetics, indirect readout, molecular dynamics, recognition, AFM, Atomic Force Microscopy, DDD, Dickerson-Drew Dodecamer, DFT, Density Functional Theory, DNA, Deoxyribonucleic Acid, DNMT, DNA Methyltransferase, LINEs, Long Interspred Transposable Elements, MD, MeCP, Methylated CpG-binding proteins, MM, Molecular Mechanics, PBC, Periodic Boundary Conditions, QM, Quantum Mechanics, RDF, Radial Distribution Functions, RESP, Restrained Electrostatic Potentials Model, SINEs, Short Interspred Transposable Elements, SPME, Smooth Particle-Mesh Ewald, TET, Translocation Proteins, WT, Wild Type
National Category
Medical Genetics Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-247344DOI: 10.4161/15592294.2014.988043ISI: 000349364000006PubMedID: 25625845OAI: oai:DiVA.org:uu-247344DiVA: diva2:796924
Funder
Swedish National Infrastructure for Computing (SNIC), 25/2-10
Available from: 2015-03-20 Created: 2015-03-17 Last updated: 2017-12-04Bibliographically approved

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Carvalho, Alexandra T. P.Gouveia, LeonorKamerlin, Lynn Shina Caroline

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Science for Life Laboratory, SciLifeLabStructure and Molecular BiologyVascular BiologyDepartment of Cell and Molecular Biology
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