Exploring the role of nuclear organization in zebrafish development with hichip using histone mark antibodies

Abstract

Animal development requires the precise transciptional regulation of thousands of genes in every cell of the embryo. Interestingly, transcriptional regulation in metazoans seems to be heavily influenced by the 3D organization of the genome in several ways. On the one side, active and inactive chromatin regions tend to cluster together in the nucleus forming the so called A and B compartments. Some developmental genes are known to switch from one compartment to another while getting activated or repressed. On the other side, developmental genes are often controlled by large sets of enhancers that activate them in a spatio-temporal specific manner during embryogenesis. In order to regulate the transcription from a promoter, enhancers need to be close to them. Specific 3D structures named chromatin loops can facilitate the interaction in space between enhancers and their target promoters, even though they might lay far apart in the linear sequence. In the same way, undesired interactions between enhancers and promoters can also be prevented at the structural level. Chromatin conformation capture techniques, such as HiC, have been key to understand these roles of the 3D configuration of the genome in gene regulation. In short, HiC experiments provide the frequency of interactions between every two pair of loci in the genome. It has been shown recently that by coupling the regular HiC protocol with a step of chromatin selection with a given antibody it is possible to sample only those interactions involving a protein of interest, such as CTCF or cohesin. In this work, we perform HiChIP experiments in 24hpf zebrafish embryos using antibodies against three histone marks: H3K4me3 (marking active promoters), H3K27ac (marking active promoters and enhancers), and H3K27me3 (marking polycomb repression) reaching 5kb resolution with a moderate sequencing effort. We provide evidence that the HiChIP experiments using H3K4me3 and H3K27ac antibodies are sufficient to predict active promoters and enhancers at 24 hpf stage and assign these predicted enhancers to their targets promoters, all at once. In addition, HiChIP using the H3K27me3 antibody confirmed that the presence of polycomb mediated repressive interactions, such as those taking place between the HoxD and Dlx1-2 gene clusters in mouse, are conserved in zebrafish. Compartments A and B are also readily identified using this approach.