SciTech Daily January 6, 2023
Diverse DNA-deforming processes are impacted by the local mechanical and structural properties of DNA, which in turn depend on local sequence and epigenetic modifications.
Deciphering the mechanical code which impacts the diverse deforming processes has been a challenge. Utilizing high-throughput measurements of DNA bendability an international team of researchers (UK, USA – Johns Hopkins University, Howard Hughes Medical Institute, Spain) quantitatively established how the occurrence and spatial distribution of dinucleotides, tetranucleotides and methylated CpG impact DNA bendability. They used the measurements to develop a physical model for the sequence and methylation dependence of DNA bendability. The model was validated by performing loop-seq on mouse genomic sequences around transcription start sites and CTCF-binding sites. They applied the model to test the predictions of all-atom molecular dynamics simulations and demonstrated that sequence and epigenetic modifications can mechanically encode regulatory information in diverse contexts…read more. TECHNICAL ARTICLE
a) Mean propeller twist as a function of position averaged over those 50 bp DNA fragments in the random library…Credit: Nature Structural & Molecular Biology volume 29, pages1178–1187 (2022)