3D chromosomal capture of X. laevis

To determine 3D chromosomal structure in differentating ectoderm of the frog Xenopus laevis, we performed tethered conformation capture (TCC) (PMID: 22198700) on wild-type dissected ectoderm and ectoderm injected with multicilin. We used these data to investigate possible differences between these conditions (we found very few) and also to determine the positions of topologically-associated domains (TADs). These data were also used to facilitate chromosome-level assembly of the X. laevis genome. Some embryos were harvested as wild-types (stage 10). In other experiments, we injected some embryos with mRNAs encoding an inducible form of multicilin (mcidas-HGR). After injecting, we isolated ectoderm surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested chromatin at 9 hours after induction (roughly stage 18) and performed tethered conformation capture on all harvested tissues (PMID: 22198700). We then sequenced these libraries, aligned the reads to the X. laevis genome (version 9.1 to interrogate 3D structure and the more fragmented genome version 7.1 to assist with chromosome assembly). TADs were called with HOMER, and chromosomes were assembled with both Lachesis (PMID: 24185095) and HighRise (arXiv:1502.05331).