Probing Short-Range Chromatin Fiber Folding and Nucleosome Occupancy with a Minimally Invasive Approach

The architecture of chromatin at the scale of nucleosomes is thought to regulate DNA-based processes, including transcription, by controlling the access of proteins to their binding sites on DNA. This level of chromatin architecture remains incompletely understood despite extensive study because of the dynamic and highly dense nature of chromatin in the nucleus. Methods for probing chromatin architecture and nucleosome occupancy have produced at times conflicting results because of the need to fix, isolate, or enzymatically process chromatin in order to assay its conformation [1]. To address these problems, we have developed radiation-induced spatially correlated cleavage with sequencing (RICC-seq), an approach for probing DNA-DNA contacts in folded chromatin within intact cells using ionizing radiation [2]. RICC-seq does not require cell permeabilization or the diffusion of enzymatic probes into chromatin. Using this new method, we show that tri-nucleosome contacts consistent with a zig-zag compaction of the chromatin fiber are enhanced in H3K9me-marked chromatin domains of human fibroblasts. We also use RICC-seq to analyze nucleosome occupancy at transcription start sites and CTCF motifs in mouse embryonic stem cells. In both cases, we identify a depletion of nucleosome occupancy that correlates with gene expression level and CTCF occupancy, respectively.

References:

1. Lai, W. K. M., & Pugh, B. F. (2017). Understanding nucleosome dynamics and their links to gene expression and DNA replication. Nature Reviews. Molecular Cell Biology, 18(9), 548-562.

2. Risca, V. I., Denny, S. K., Straight, A. F., & Greenleaf, W. J. (2017). Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping. Nature, 541(7636), 237-241.