The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos

Abstract

Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a significant genome-wide correlation between pairing, transcription during zygotic genome activation, and binding of the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered a century ago in Drosophila. Finally, we demonstrate the versatility of our haplotype-resolved approach by applying it to mammalian embryos.

Global chromatin conformation differences in the Drosophila dosage compensated chromosome X

“…As the male chrX is the only chromosome without a paired homologue, we asked if this male chrX peculiarity may affect the observed differences in the interaction decay profile. To this concern, recent independent studies presenting haplotype-resolved Hi-C data show that the ratio of inter-homologous interactions vs cis -interactions increases at mid-/long-range distances 38,39 . Thus, the lack of a homologous chromosome may result in less mid-/long-range contacts being detected, i.e.…”

“…Homologous pairing (between the two copies of chromosome 3R and, in the female-like situation, between the two copies of chromosome X) was accounted for by first initially forcing the homologous polymers to occupy the same position in the simulation box and then, in the rest of the simulation, by forcing some homologous beads to stay in contact. We randomly selected these forced beads so that the proportion of homologous loci in close contact, for every epigenetic classes, is the one observed by Abed et al 38 using Hi-C (~100% for active, ~75% for PcG, ~50% for inactive and ~50% for heterochromatin). In the male-like situation (unpaired Xs), the two X copies started from different locations and no forcing was imposed.…”

Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin

“…Oligopaint probes and AAGAG probe. Embryo FISH with both Oligopaint and AAGAG (for bulk heterochromatin) LNA probe followed [105], except for staining nuclei with DAPI and resuspension in Prolong Gold Antifade (Life Technologies).…”

Fine-Mapping Complex Inversion Breakpoints and Investigating Somatic Pairing in theAnopheles gambiaeSpecies Complex Using Proximity-Ligation Sequencing

“…This suggests that maternal and paternal chromosomes are almost equally likely to contact each other as to contact themselves in the region 2 Mb from inversion breakpoints and that inversion breakpoints present little barrier to somatic pairing despite different chromosome structures in intermediate to large distances away from breakpoint positions along the genome [similar to inversions in D. melanogaster (Golic and Golic 1996)]. Recent work using Hi-C to study somatic pairing in Drosophila embryos uncovered a highly regulated and "ondiagonal" structure of pairing between homologs (Erceg et al 2019), our result appears approximately consistent, but suggest slightly more diffuse contacts between homologs in An. coluzzi.…”