Ultra-high resolution mapping of 3d genome structure using region capture micro-c

A method comprising:

• (a) crosslinking genomic DNA in cells with at least two crosslinking agents to form a composition comprising crosslinked genomicDNA (cG-DNA);
• (b) fragmenting the cG-DNA creating a plurality of crosslinked fragments (CFs);
• (c) repairing ends of the plurality of the CFs, followed by fragment end labelling, by contacting the plurality of the crosslinked fragments with labelled nucleotides to form labelled crosslinked fragments;
• (d) ligating the 1-CFs and removing labelled nucleotides from unligated fragment ends;
• (e) obtaining a purified dinucleosome-sized DNA fraction in a series of steps that comprise:
• (i) de-crosslinking the crosslinked fragments to obtain a mix of DNA fragments,
• (ii) isolating dinucleosome-sized DNA fragments in a method comprising separation of de-crosslinked DNA fragments by size, and
• (iii) isolating ligated and labelled DNA fragments in a method comprising contacting the de-crosslinked dinucleosome-sized DNA fragments with a binding partner for the label on labelled ligated fragments,
• wherein each isolated dinucleosome-sized DNA fragments comprise a first and a second DNA region ligated to each other;
• (f) preparing a sequencing library from the dinucleosome-sized DNA fraction and optionally amplifying the purified fragments;
• and
• (g) performing tiling region capture of a region of interest.