Tough Tissue Hi-C

Abstract

The ability to decipher the three-dimensional chromosome folding in many eukaryotes is a major asset in molecular biology. It is not only required to study the biological relevance of chromosome folding in cellular processes but also for the de novo assembly of genomes of nonmodel species. With lowering DNA sequencing costs, the latter has recently become interesting to many scientists, ranging from molecular biologists that aim to establish new model organisms, to evolutionary biologists and ecologists, interested in genome evolution and diversity. Hi-C is regarded as the method of choice to characterize three-dimensional genome folding and, thus, also has been integrated as a standard method in assembly pipelines. However, Hi-C is a demanding molecular biology technique, and its application can be considerably challenged by the tissue used. Hi-C relies on efficient and pure nuclei isolation, which is, especially in many plant species, inhibited by the tough nature of plant tissues and cell walls. The Hi-C protocol presented here has been optimized for such tissues and has been shown to generate Hi-C samples of sufficient quality in various plant and animal tissues.

Keywords: 3D chromosome folding; Genome assembly; Hi-C; Nonmodel species; Tough tissues.