Analysis of nuclear organization and dosage compensation in Bombyx mori by Oligopaint FISH reveals divergent 3D architecture between moths and flies
Authors: Leah Rosin; Chen Dahong; Chen Yang; Elissa Lei
Affiliation: NIH
Keywords: i. dosage compensation; d. evolution of gene expression
Interphase genomes are organized into an intricate three-dimensional (3D) structure that facilitates accurate gene expression and maintains genome stability. This organization is largely conserved, yet how karyotype evolution influences 3D genome organization remains largely unexplored. Here, we use DNA Oligopaints to visualize autosomes and the Z sex chromosome (chZ) in B. mori (N=28) and compare our findings to D. melanogaster (N=4). We show that B. mori nuclei are highly compact, with nuclear volumes similar to D. melanogaster despite the B. mori genome being over three times larger. This discrepancy in nuclear size cannot be explained by differences in inter-chromosomal interactions or chromosome territory (CT) formation: both species harbor spatially separated CTs with minimal intermixing. Furthermore, CTs in both species are non-randomly organized, with gene-poor chromosomes being most peripheral. However, homologous chromosome copies share a single CT in D. melanogaster due to somatic homolog pairing, which does not occur in B. mori. Moreover, we find significant differences in intra-chromosomal interactions. Unlike loose chromosome folding observed in D. melanogaster, B. mori chromosomes are tightly folded within CTs, with nearly all tested chromosomes showing interactions between both telomere domains and the center of the chromosome.
Our first-time visual analysis of individual chromosomes further allowed us to address the outstanding question of how dosage compensation (DC) is achieved in B. mori, a ZW species. In B. mori males, both chZs are similar in size and shape and are more compact than autosomes or the female chZ, suggesting that both male chZs are partially and equally downregulated during DC. This mechanism contrasts with DC in D. melanogaster, where the single male chX is upregulated. Thus, B. mori DC is instead more similar to DC in the nematode C. elegans. Using both FISH and ATAC-seq, we find that the female chZ repositions toward the nuclear center and the chromatin becomes more open concomitant with increased Z-linked gene expression at the onset of DC. Together, these studies represent the first non-sequencing-based support for Ohno’s hypothesis for the evolution of dosage compensation. We uncover significant differences in chromosome folding between D. melanogaster and B. mori and intriguing similarities between DC in B. mori and C. elegans, despite these lineages harboring evolutionarily distinct sex chromosomes (ZW/XY). We propose a model where holocentricity may be more influential for interphase genome organization and DC than evolutionary relatedness.