Genome-Wide Chromatin Structure Changes During Caste Differentiation in Honeybees

Three-dimensional (3D) chromatin architecture is an important transcription regulator which is linked to gene expression regulation and correct developmental programs, yet little is known that the 3D chromatin architecture within honeybees and how it influences gene expression and methylation in caste differentiation. Here, we report that larvae at 96 h after hatching (L5) contain the highest number of known caste differentiation genes, and that constitutes the critical window determining the final phenotypic outcomes. We also show that DNA methylation pattern is conserved and gene body methylation is thought to contribute to phenotypic plasticity. Then, we determine the 3D organization of honey bee chromosomes at 5 kb resolution. Although almost 87% regions remained in the same compartments, TAD boundary insulation increased during larvae development, especially in worker larvae at 96 h after hatching (WL5). The insulator protein, CP190, CTCF-L and vtd/Rad21 appear to be indispensable in defining these topologically associating domain boundaries. Furthermore, Mrjp1, a member of the MRJP/yellow family, is also involved in regulating larval development. These results provide key insights into caste differentiation and establish a fundamental dataset for the future in-depth characterization of epigenetic features.