title: Effects of cytosine methylation on DNA morphology: An atomic force microscopy study.
abstract: Methylation is one of the most important epigenetic mechanisms in eukaryotes. As a consequence of cytosine methylation, the binding of proteins that are implicated in transcription to gene promoters is severely hindered, which results in gene regulation and, eventually, gene silencing. To date, the mechanisms by which methylation biases the binding affinities of proteins to DNA are not fully understood; however, it has been proposed that changes in double-strand conformations, such as stretching, bending, and over-twisting, as well as local variations in DNA stiffness/flexibility may play a role. The present work investigates, at the single molecule level, the morphological consequences of DNA methylation in vitro. By tracking the atomic force microscopy images of single DNA molecules, we characterize DNA conformations pertaining to two different degrees of methylation. In particular, we observe that methylation induces no relevant variations in DNA contour lengths, but produces measurable incremental changes in persistence lengths. Furthermore, we observe that for the methylated chains, the statistical distribution of angles along the DNA coordinate length is characterized by a double exponential decay, in agreement with what is predicted for polyelectrolytes. The results reported herein support the claim that the biological consequences of the methylation process, specifically difficulties in protein-DNA binding, are at least partially due to DNA conformation modifications.
authors.affiliation: Health Science Department, University of Milano-Bicocca, Via Cadore 48, 20900 Monza (MB), Italy. Electronic address: valeria.cassina@unimib.it.
authors.forename: V
authors.initials: V
authors.lastname: Cassina
authors.affiliation: Laboratoire de Physique Théorique, Université Paul Sabatier, CNRS, 118 route de Narbonne, 31062 Toulouse, France.
authors.forename: M
authors.initials: M
authors.lastname: Manghi
authors.affiliation: Health Science Department, University of Milano-Bicocca, Via Cadore 48, 20900 Monza (MB), Italy.
authors.forename: D
authors.initials: D
authors.lastname: Salerno
authors.affiliation: LENS-Department of Physics and Astronomy, University of Florence, via Sansone 1, 50019 Sesto Fiorentino (FI), Italy.
authors.forename: A
authors.initials: A
authors.lastname: Tempestini
authors.affiliation: Health Science Department, University of Milano-Bicocca, Via Cadore 48, 20900 Monza (MB), Italy.
authors.forename: V
authors.initials: V
authors.lastname: Iadarola
authors.affiliation: Health Science Department, University of Milano-Bicocca, Via Cadore 48, 20900 Monza (MB), Italy.
authors.forename: L
authors.initials: L
authors.lastname: Nardo
authors.affiliation: Health Science Department, University of Milano-Bicocca, Via Cadore 48, 20900 Monza (MB), Italy.
authors.forename: S
authors.initials: S
authors.lastname: Brioschi
authors.affiliation: Health Science Department, University of Milano-Bicocca, Via Cadore 48, 20900 Monza (MB), Italy.
authors.forename: F
authors.initials: F
authors.lastname: Mantegazza
mesh_terms: D003596:Cytosine / Q000378:metabolism*; D019175:DNA Methylation; D018625:Microscopy, Atomic Force / Q000379:methods*; D009690:Nucleic Acid Conformation
chemical_list: D003596:Cytosine
keywords: Atomic force microscopy (AFM); DNA methylation; Persistence length