Chromosome Conformation Capture for Large Genomes.

Abstract

The gigantic 32Gb Axolotl genome inspires fascinating questions such as: how such a big genome is organized and packed in nuclei and how regulation of gene transcription can happen over such large genomic distances. Currently, there are many technical challenges when we investigate chromatin architecture in axolotl. For example, probing promoter-enhancer interactions in such a large genome. Chromatin capture methods (e.g., Chromatin Conformation Capture) have been used in a variety of species. The large size of the axolotl nuclei and its genome requires the adaptation of such methods. Here, we describe a detailed protocol for high-throughput genome-wide conformation capture (Hi-C) using axolotl limb cells. This Hi-C library preparation protocol can also be used to prepare libraries from other nonmodel organisms such as Lungfish and Cephalopods. We believe that our protocol could be useful for a variety of animal systems including other salamanders.