Gene expression isn’t just a linear process. 3-D genome architecture brings together distant regulatory elements and plays a critical role in the regulation of gene expression. With almost three meters of DNA packaged in a nucleus ~6 microns in diameter in specific human cells, the 3-D architectural structure of the genome is deliberate, dynamic, and hierarchical in nature. DNA wraps around histone proteins form nucleosomes, the basic building block of chromatin. Chromatin is then packed in ever increasing hierarchical structures including functional features such as loops, topologically associating domains (TADs), A/B compartments and chromosome territories, which all play a role in gene expression by mediating contacts between regulatory elements that are otherwise separated by large distances.¹

Chromatin conformation capture (3C) exploits proximity ligation chemistry and is considered the gold-standard method for unlocking access to 3-D genome architecture. Hi-C pairs chromatin conformation capture with standard next-generation sequencing (NGS), and can be used to map genome-wide contacts. Hi-C data facilitates the assembly of complete genomes for your species of interest, delivers novel insights into the role of 3-D genome architecture in gene expression, and can provide mechanism-of-action for disease initiation and progression that can only be seen in 3-D.

New to Hi-C? Dovetail® makes it easy! The five-step process begins with intact cells or cell nuclei. The chromatin is first crosslinked in vivo to stabilize the in situ chromatin structure, preserving the physical 3-D orientation. Sequence independent fragmentation followed by proximity ligation is performed to ligate DNA fragments found in close proximity within the scaffold to capture short, medium, and long-range associations reflective of the 3-D architecture of the original chromatin. Crosslinks are reversed, DNA purified, and ligation containing fragments are selectively pulled down. A sequencing library is then prepared for standard paired-end sequencing. Simple, right?

Want to take your ChIP-seq data to a whole new dimension? Just add a ChIP step in between the fragmentation and ligation step to investigate protein-directed chromatin architecture.

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1. Three-dimensional chromatin packing and positioning of plant genomes, Doğan ES and Liu C. Nature Plants. 2018,4(8):521-9.