A high-resolution map of Drosophila hybrid pairing connects BLACK heterochromatin to pairing loss, reproductive incompatibility, and DNA underreplication
Authors: James Baldwin-Brown; Nitin Phadnis
Affiliation: University of Utah
Keywords: Speciation & hybridization
Homologous chromosome pairing is essential to all eukaryotes, but we do not fully understand the molecular mechanisms underlying pairing. Although pairing is often associated with meiosis, it also occurs in somatic cells. Complete somatic pairing is the wild type state in Drosophila and other dipterans. More that 80 years ago, researchers studying Drosophila between-species hybrids discovered that somatic chromosome pairing broke down in hybrid individuals, with no explanation as to which regions were breaking down or why. Because pairing machinery exists in all eukaryotes, finding the genomic elements that drive this non-pairing will help us understand the drivers of pairing generally.
Technical hurdles to measuring pairing rates genome-wide have prevented most investigation into hybrid pairing breakdown. In the past few years, however, new technologies, principally Hi-C, have allowed for high-resolution measurement of pairing across the genome by directly measuring physical contacts between chromosomes. To find the mechanistic basis of hybrid pairing breakdown, we used Hi-C in hybrids of D. melanogaster and D. simulans to measure pairing rates with unprecedentedly high resolution across the genome. Compared to within-species crosses, this hybrid Hi-C shows dramatic regions of high and low pairing. Contrary with expectations, pairing rates did not correlate with sequence similarity. Instead, they correlated with the presence of BLACK chromatin. This has important implications for understanding speciation: chromatin state, rather than sequence, drives loss of pairing between species.
To better understand the effect of tissue on pairing, we repeated our pairing measurements in multiple tissues. Contrary to expectations, we found that hybrid pairing loss uniquely affects polytene nuclei but not diploid nuclei. This raises the possibility that DNA overreplication influences pairing breakdown, a hypothesis bolstered by the fact that BLACK chromatin is the last chromatin to replicate during mitosis. Our results suggest rapid evolution of genomic regions that alter chromatin state and replication timing may contribute to hybrid dysfunction. We also hypothesize a connection between polytene pairing breakdown and hybrid incompatibility genes in D. melanogaster and D. simulans, as pairing breakdown is substantially reduced by knockout of incompatibility genes. Our current work focuses on the consequences of pairing breakdown on gene expression through the phenomenon of transvection (a process where cis-regulators can act in trans when paired). Together, these studies tease apart whether hybrid pairing breakdown is a cause or an effect of reproductive incompatibility. Here, I describe our insights into fundamental evolutionary phenomena at the intersection of chromosome pairing, reproductive isolation, gene expression, and chromatin state evolution.