For more details, please refer to our bioRxiv preprint. We would welcome any questions and feedback as we envision that this approach will be applicable for uncovering the regulatory logic for replication-coupled chromatin re-assembly across various cell types and species. (13/x)

Meanwhile, at highly transcribed TSSs, we observe that high levels of chromatin accessibility are retained and/or rapidly restored within minutes of fork passage, suggesting that nucleosome-free regions are tightly coordinated with the replisome. (12/x)

At CTCF-binding sites, CTCF protein and nascent nucleosomes (both recycled and de novo) compete with one another for binding, resulting in reduced CTCF occupancy and consequently decreased accessibility upon replication. (11/x)

Leveraging the ability of long-read sequencing to detect nucleosome spacing within intact chromatin fibers, we find that newly replicated DNA is also enriched for irregularly spaced nucleosomes. (8/x)

We believe this transient hyperaccessibility arises at two levels: nascent chromatin more often comprises partially unwrapped nucleosomes and/or subnucleosomes (e.g. hexasomes, missing an H2A-H2B dimer) than mature fibers. (7/x)

First, we show that that newly replicated chromatin fibers, in mouse and human cells, are ‘hyperaccessible’. That is, within the same cell type, nascent chromatin is more accessible to methyltransferase footprinting than steady-state fibers (those not labeled with BrdU). (6/x)

In brief, we have developed the experimental and computational tools needed to non-destructively and simultaneously measure replication status and protein-DNA interactions on individual chromatin fibers in vivo. (4/x)

We, in the Ramani Lab, have engineered a series of PacBio methyltransferase footprinting approaches (SAMOSA, SAMOSA-ChAAT, and SAMOSA-Tag). Now, we present Replication-Aware Single-molecule Accessibility Mapping (or RASAM, for short). (3/x)

In brief, we have developed the experimental and computational tools needed to non-destructively and simultaneously measure replication status and protein-DNA interactions on individual chromatin fibers in vivo. (4/x)