Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis

Abstract

Mammalian sex is determined by an opposing networks of ovarian and testicular genes that are well characterized. However, its epigenetic regulation is still largely unknown, thus limiting our understanding of a fundamental process for species propagation. Here we explore the 3D chromatin landscape of sex determination in vivo, by profiling FACS-sorted embryonic mouse gonadal populations, prior and after sex determination, in both sexes. We integrate Hi-C with ChIP-seq experiments using METALoci, a novel genome spatial auto-correlation analysis that identifies 3D enhancer hubs across the genome. We uncover a prominent rewiring of chromatin interactions during sex determination, affecting the enhancer hubs of hundreds of genes that display temporal- and sex-specific expression. Moreover, the identification of the 3D enhancer hubs allows the reconstruction of regulatory networks, revealing key transcription factors involved in sex determination. By combining predictive approaches and validations in transgenic mice we identify a novel Fgf9 regulatory hub, deletion of which results in male-to-female sex reversal with the upregulation of ovarian-specific markers and the initiation of meiosis. Thus, spatial auto-correlation analysis is an effective strategy to identify regulatory networks associated to biological processes and to further characterize the functional role of the 3D genome.

Transposable elements acquire time- and sex-specific transcriptional and epigenetic signatures along mouse fetal gonad development

“…These three TEs are contained within the 306 kb locus previously identified as an Fgf9 enhancer-containing locus using 3D genome enhancer hub prediction tool. Deletion of the 306 kb region causes partial to complete male-to-female sex reversal (Mota-Gómez et al 2022). Finally, the last group contains TEs showing none of the investigated histone marks (9,367 out of 31,534).…”

Transposable elements acquire time- and sex-specific transcriptional and epigenetic signatures along mouse fetal gonad development

“…These three TEs are contained within the 306 kb locus previously identified as an Fgf9 enhancer-containing locus using the 3D genome enhancer hub prediction tool. The deletion of the 306-kb region causes partial to complete male-to-female sex reversal (Mota-Gómez et al, 2022). The last group contains TEs showing none of the investigated histone marks (9,367 out of 31,534).…”

The genome in space and time comes of age

“…By studying changes in chromatin organization during sex differentiation in mammalian gonads, Marc A. Marti-Renom (Barcelona, Spain) and his team and collaborators indeed observed moderate changes in A/B chromatin compartment and topological associated domains (TADs) between bipotential and differentiated stages. Nonetheless, by introducing METALoci, a computational approach to integrate Hi-C and ‘omics data for an unbiased quantification of the regulatory environment around each gene in the genome, they identified prominent rewiring of 3D enhancer hubs specifically during male sex differentiation [ 9 ]. Such rewiring suggests that even if nuclear compartmentalization is largely stable, individual genes can move from a repressive to a permissive environment in response to cellular cues.…”