Filling the gap: Micro-C accesses the nucleosomal fiber at 100-1000 bp resolution

Abstract

The fine three-dimensional structure of the nucleosomal fiber has remained elusive to genome-wide chromosome conformation capture (3C) approaches. A new study mapping contacts at the single nucleosome level (Micro-C) reveals topological interacting domains along budding yeast chromosomes. These domains encompass one to five consecutive genes and are delimited by highly active promoters.

Fig. 1

a Schematic representation of the differences between Micro-C and Hi-C contacts. Top: snapshot from a physical simulation of the yeast chromosomes as a brush of polymers (white beads) tethered by their centromeres (yellow spheres). The large structure on the right represents the nucleolus (see also [6]). Chromosomes 3 and 11 are highlighted in red and cyan. Each bead represents three nucleosomes. Bottom: expanded view of four nucleosomes (purple circles). Contacts, from frequent to rare, are highlighted on both representations in red, orange and yellow. b Models of the chromosomal fiber with 167-bp nucleosomal repeat length (built using the three angle model described in Riposo and Mozziconacci [9]). c Number of contacts in parts per million (ppm) obtained through a Micro-C experiment at various genomic distances (schematic representation of the results presented in Figure S3 of Hsieh et al. [5]). The first bump corresponds to contacts between nucleosome n and n + 1, and the second bump to contacts between n and n + 2. Only reads in the same orientation were used to avoid self-ligation artifacts