Measuring DNA mechanics on the genome scale

Mechanical deformations of DNA such as bending are ubiquitous and implicated in diverse cellular functions. However, the lack of high-throughput tools to measure the mechanical properties of DNA limits our understanding of whether and how DNA sequences modulate DNA mechanics and associated chromatin transactions genome-wide. We developed an assay called loop-seq to measure the intrinsic cyclizability of DNA - a proxy for DNA bendability - in high throughput. We measured the intrinsic cyclizabilities of 270,806 50 bp DNA fragments that span the entire length of S. cerevisiae chromosome V and other genomic regions, and also include random sequences. We discovered sequence-encoded regions of unusually low bendability upstream of Transcription Start Sites (TSSs). These regions disfavor the sharp DNA bending required for nucleosome formation and are co-centric with known Nucleosome Depleted Regions (NDRs). We show biochemically that low bendability of linker DNA about 40 bp away from a nucleosome edge inhibits nucleosome sliding into the linker by the chromatin remodeler INO80. It explains how INO80 can create promoter-proximal nucleosomal arrays in the absence of any other factors by reading the DNA mechanical landscape. At the chromosome scale, sequence-dependent mechanical modulations make DNA around nucleosomal dyads significantly more bendable than linker DNAs, and this contrast increases for nucleosomes deeper into gene bodies. It suggests that DNA mechanics plays a previously unappreciated role in organizing nucleosomes far from the influence of remodelers that operate near TSSs. Altering gene sequences by randomly selecting synonymous codons does not preserve this contrast, suggesting that evolutionary selection among synonymous codons has been impacted by the way sequence modulates mechanics. Finally, we provide evidence that transcription through the TSS-proximal nucleosomes is impacted by local DNA mechanics. Overall, this first genome-scale map of DNA mechanics hints at a mechanical code with broad functional implications.