Effects of cytosine methylation on DNA morphology: An atomic force microscopy study

• Published in: Biochimica et biophysica acta Vol. 1860; no. 1; pp. 1 - 7
• Main Authors: Cassina, V., Manghi, M., Salerno, D., Tempestini, A., Iadarola, V., Nardo, L., Brioschi, S., Mantegazza, F.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.01.2016; Elsevier
• Subjects: atomic force microscopy; Atomic force microscopy (AFM); binding capacity; binding proteins; Biological Physics; Cytosine - metabolism; DNA; DNA conformation; DNA Methylation; electrolytes; epigenetics; eukaryotic cells; gene silencing; genes; Microscopy, Atomic Force - methods; Nucleic Acid Conformation; Persistence length; Physics; transcription (genetics); DNA methylation; Persistence length; Atomic force microscopy (AFM)
• ISSN: 0304-4165; 0006-3002; 1872-8006
• DOI: 10.1016/j.bbagen.2015.10.006

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. •Atomic force microscopy on single molecules of DNA at different degree of methylation.•Quantitative characterization of DNA stiffness by means of persistence length measure.•From Worm Like Chain model to an improved theoretical model for DNA conformation•Development of tracking procedure for quantitative AFM images analysis