Measuring the Physical Properties of DNA on a Genomic Scale

The physical properties of DNA have been extensively measured. However, relatively little is known on how DNA sequence modulates DNA flexibility, and how sequence mutations affect downstream biological processes by altering DNA flexibility. To address these questions, we have developed an assay to create a genome-wide map of DNA flexibility. An input library of thousands of short DNA molecules representing nucleosomal sequences from S. Cerevisiae is end modified to permit each molecule to form a loop. A selection condition is imposed whereby stiffer molecules that fail to loop after various amounts of time are digested. The surviving molecules are sequenced at various time points, and individual kinetic curves for DNA cyclization is constructed for each sequence. Our measurements indicate that +1 nucleosomes have asymmetric cyclization rates, with the promoter proximal half more cyclizable than the distal half. We compare our data with existing biochemical and genome-wide NET-seq data to understand how nucleosomal flexibility asymmetry affects polymerase translocation through the nucleosome. We also find that CpG and TpA content have a marked effect on DNA cyclization rate. Our assay provides a platform for understanding how sequence features modulate DNA flexibility, and more broadly, how physical forces may have shaped the evolution of genomes.