High resolution maps of nucleosome position and interactions

Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a novel proximity-tagging method which assigns unique DNA barcodes to molecules that associate in 3D space. Using this method – termed Proximity Copy Paste (PCP) – we mapped the connectivity of individual nucleosomes in Saccharomyces cerevisiae. We show that chromatin is predominantly organized into regularly spaced nucleosome arrays. The properties of the arrays differs according to transcriptional activity with short delocalized arrays dominating the most highly transcribed genes. Additionally, by mapping long-range, multi-way interactions we provide evidence for the longstanding hypothesis that metaphase chromosomes are compacted by arrayed cohesin hubs. Using single-molecule nuclease footprinting data we define distinct chromatin states within a mixed population to show that noncanonical nucleosomes are a stable feature of chromatin. PCP is a versatile method allowing the connectivity of individual molecules to be mapped at high-resolution PCP experiment in synchronized cells in G1 or in G2/M. Asynchronous cells in control conidion or after depletion of chromatin remodelers RSC (sth1) and SWI/SNF (snf2)