The impact of chromosomal fusions on 3D genome folding and recombination in the germ line

Covadonga Vara,Laia Marín-Gual,Andreu Paytuví-Gallart,Jeremy B Searle,François Le Dily,Rosa Ana Sanchéz-Guillén,Marc A Marti-Renom,Jacint Ventura,Laia Capilla,Beatriu Florit-Sabater,Yasmina Cuartero,Zaida Sarrate,Aurora Ruiz-Herrera,Francisca Garcia,Riccardo Aiese Cigliano,Lucía Álvarez-González,Walter Sanseverino

doi:10.1038/s41467-021-23270-1

Abstract

The spatial folding of chromosomes inside the nucleus has regulatory effects on gene expression, yet the impact of genome reshuffling on this organization remains unclear. Here, we take advantage of chromosome conformation capture in combination with single-nucleotide polymorphism (SNP) genotyping and analysis of crossover events to study how the higher-order chromatin organization and recombination landscapes are affected by chromosomal fusions in the mammalian germ line. We demonstrate that chromosomal fusions alter the nuclear architecture during meiosis, including an increased rate of heterologous interactions in primary spermatocytes, and alterations in both chromosome synapsis and axis length. These disturbances in topology were associated with changes in genomic landscapes of recombination, resulting in detectable genomic footprints. Overall, we show that chromosomal fusions impact the dynamic genome topology of germ cells in two ways: (i) altering chromosomal nuclear occupancy and synapsis, and (ii) reshaping landscapes of recombination.

Highlights

The spatial folding of chromosomes inside the nucleus has regulatory effects on gene expression, yet the impact of genome reshuffling on this organization remains unclear
We conducted an integrative approach that combined the cytological mapping of CO events directly in male germ cells (Figs. 1, 2 and Supplementary Fig. 1) together with estimates of linkage disequilibrium based on singlenucleotide polymorphism (SNP) genotyping (Supplementary Fig. 2)
Our results show that chromosomal fusions pose important mechanistic constraints in the nuclear architecture of germ cells, affecting heterologous interactions, chromosomal synapsis, and meiotic recombination

Summary

Introduction

The spatial folding of chromosomes inside the nucleus has regulatory effects on gene expression, yet the impact of genome reshuffling on this organization remains unclear. Germ cells are a unique cell model to test the genome-wide impact of chromosomal fusions—they have sequential developmental stages that involve dramatic and tightly regulated chromosomal movements and chromatin remodeling These include changes in intra-/interchromosomal interaction ratios, distancedependent interaction frequencies, genomic compartments, TADs, occupancy of insulator proteins (CTCF and cohesins), and gene expression[13,14,15,16]. This system is characterized by the presence of different Rb fusions distributed in nongeographically coincident clines, leading to a progressive reduction in diploid numbers toward the center of the range[23] This natural model permits interrogation of the impact that Rb fusions have on chromatin remodeling and fine-scale recombination in the germ line. We studied how chromosomal fusions alter the nuclear architecture at different hierarchical levels in meiotic (i.e., primary spermatocytes) and postmeiotic cells (i.e., round spermatids), and discuss the implications for evolution and fertility

Methods

Results

Conclusion