Base pair resolution chromosome conformation capture reveals mechanistic insights into the nature of chromatin structure [Capture-C]

Chromatin structure is a key determinant of gene expression in eukaryotes but it has not previously been possible to define the full structure of regulatory elements at the scale of the proteins determining gene expression. Here we generate multidimensional chromosome conformation capture (3C) maps at single base-pair resolution using Micro Capture-C (MCC). This allows contacts between individual transcription factor binding sites within regulatory elements to be defined. Using degrons-we investigate the structural role of transcription factors and the Mediator complex. We show that the biophysical properties of nucleosomes and DNA can replicate the nanoscale chromatin structures observed with MCC using a detailed chemically specific, molecular dynamics approach. The ultra-high resolution 3C enable molecular dynamics approaches to be linked to larger scale nuclear architecture defined by super-resolution microscopy and allow us to propose a unified model to describe chromatin structure based on these orthogonal approaches. Overall design: MCC libraries were prepared from murine primary erythroid cells, embryonic stem cells or hematopoietic stem and progenitor cells. Micro-Capture-C-Ultra (MCCu) integrates Micro-Capture-C (MCC) library preparation with oligonucleotide capture enrichment to enable in-depth, targeted sequencing of chromatin interactions in specific regions of interest. Further information can be found in the Methods section of the paper.