Wouter de Laat, PhD
Group Leader
Hubrecht Institute
Cooperative and non-cooperative spatial regulatory chromatin interactions uncovered by Multi-Contact 4C (MC-4C)
Spatial chromatin organization is increasingly recognized as a regulator of nuclear processes such as gene activity. Most methods developed to unravel three-dimensional (3D) chromatin conformation analyze pair-wise chromatin contacts, but are incapable of identifying simultaneous associations among multiple loci. Yet, exactly this type of ‘beyond two-way’ contact information will provide the insights required to start composing a more complete picture of 3D genome organization at the level of the individual allele.
We describe a novel chromatin conformation capture technology that allows direct identification of multi-way chromatin contacts. Multi-Contact 4C (MC-4C) applies third-generation long-read single molecule real time (SMRT) sequencing technology to an intermediate product of the conventional chromatin conformation capture (3C) protocol. For a given allele of interest, MC-4C can easily identify 4 to 8 spatial neighbors, based on proximity-ligation events. With many thousands of identified multi-way (>3) contacts per targeted locus, MC-4C presents a unique and promising new technology to distinguish co-operative from mutually exclusive 3D chromatin structures. Data will be presented that show the existence of regulatory hubs and mutually exclusive contacts between regulatory sites.
Amin Allahyar, Carlo Vermeulen, Britta Bouwman, Peter Krijger, Benjamin Rowland, Elzo de Wit, Jeroen de Ridder, Wouter de Laat.
