Measuring DNA mechanics on the genome scale

Mechanical deformations of DNA such as bending are ubiquitous and have been implicated in diverse cellular functions(1). However, the lack of high-throughput tools to measure the mechanical properties of DNA has limited our understanding of how DNA mechanics influence chromatin transactions across the genome. Here we develop 'loop-seq'-a high-throughput assay to measure the propensity for DNA looping-and determine the intrinsic cyclizabilities of 270,806 50-base-pair DNA fragments that span Saccharomyces cerevisiae chromosome V, other genomic regions, and random sequences. We found sequence-encoded regions of unusually low bendability within nucleosome-depleted regions upstream of transcription start sites (TSSs). Low bendability of linker DNA inhibits nucleosome sliding into the linker by the chromatin remodeller INO80, which explains how INO80 can define nucleosome-depleted regions in the absence of other factors(2). Chromosome-wide, nucleosomes were characterized by high DNA bendability near dyads and low bendability near linkers. This contrast increases for deeper gene-body nucleosomes but disappears after random substitution of synonymous codons, which suggests that the evolution of codon choice has been influenced by DNA mechanics around gene-body nucleosomes. Furthermore, we show that local DNA mechanics affect transcription through TSS-proximal nucleosomes. Overall, this genome-scale map of DNA mechanics indicates a 'mechanical code' with broad functional implications. A high-throughput, chromosome-wide analysis of DNA looping reveals its contribution to the organization of chromatin, and provides insight into how nucleosomes are deposited and organised de novo.

Automated summary

Mechanical deformations of DNA, such as bending, are common and have been implicated in various cellular functions. A high-throughput assay called 'loop-seq' was developed to measure DNA looping propensity and intrinsic cyclizabilities of DNA fragments across different genomic regions. The study found regions of low bendability in nucleosome-depleted regions, which affects nucleosome sliding and gene transcription. Overall, the study shows that local DNA mechanics have broad functional implications on chromatin organization and transcription.