Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver

Bryan J Matthews,David J Waxman

doi:10.1186/s13072-020-00350-y

Abstract

Several thousand sex-differential distal enhancers have been identified in mouse liver; however, their links to sex-biased genes and the impact of any sex-differences in nuclear organization and chromatin interactions are unknown. To address these issues, we first characterized 1847 mouse liver genomic regions showing significant sex differential occupancy by cohesin and CTCF, two key 3D nuclear organizing factors. These sex-differential binding sites were primarily distal to sex-biased genes but rarely generated sex-differential TAD (topologically associating domain) or intra-TAD loop anchors, and were sometimes found in TADs without sex-biased genes. A substantial subset of sex-biased cohesin-non-CTCF binding sites, but not sex-biased cohesin-and-CTCF binding sites, overlapped sex-biased enhancers. Cohesin depletion reduced the expression of male-biased genes with distal, but not proximal, sex-biased enhancers by >10-fold, implicating cohesin in long-range enhancer interactions regulating sex-biased genes. Using circularized chromosome conformation capture-based sequencing (4C-seq), we showed that sex differences in distal sex-biased enhancer–promoter interactions are common. Intra-TAD loops with sex-independent cohesin-and-CTCF anchors conferred sex specificity to chromatin interactions indirectly, by insulating sex-biased enhancer–promoter contacts and by bringing sex-biased genes into closer proximity to sex-biased enhancers. Furthermore, sex-differential chromatin interactions involving sex-biased gene promoters, enhancers, and lncRNAs were associated with sex-biased binding of cohesin and/or CTCF. These studies elucidate how 3D genome organization impacts sex-biased gene expression in a non-reproductive tissue through both direct and indirect effects of cohesin and CTCF looping on distal enhancer interactions with sex-differentially expressed genes.

Highlights

Sex differences in gene expression are found in several non-reproductive tissues, including the brain [1], immune system [2], kidney [3] and liver [4]
A higher fraction of malebiased than female-biased Lone CCCTC-binding factor (CTCF) sites contained a CTCF motif (66% vs 48%, Additional file 1: Figure S2C), but there was no significant sex difference in normalized ChIP signal or motif score (Fig. 2a, Additional file 1: Figure S2C). The latter sex differences may be driven by additional factors, such as the inhibitory effect of DNA methylation on CTCF binding [56, 57], where the same sequence motif in male and female liver could be preferentially bound in males due to the hypermethylation of DNA seen in female compared to male mouse liver [58]
We investigated sex differences in autosomal 3D genome organization in the mouse liver model, focusing on sexbased differences in chromatin binding and interactions involving cohesin and CTCF, which mediate long-range DNA looping interactions that segment mammalian genomes into megabase-scale Topologically Associating Domains (TADs) domains and their shorter intra-TAD domains

Summary

Introduction

Sex differences in gene expression are found in several non-reproductive tissues, including the brain [1], immune system [2], kidney [3] and liver [4]. Transcriptomic and epigenetic sex differences in the transcriptome are best characterized in mouse liver, where more than 1000 genes [8], including many lncRNA genes [9, 10] and miRNAs [11], exhibit sex-biased expression regulated by the sex-differential temporal patterns of pituitary growth hormone secretion [12]. Sex differences in the epigenome are widespread, and frequently are associated with sex Matthews and Waxman Epigenetics & Chromatin (2020) 13:30 differences in gene distal, but not gene proximal, regulatory elements, which show characteristic sex-differential patterns of histone marks and chromatin accessibility (DNase hypersensitive sites, DHS) [13, 14]. When degradation of the cohesin loading factor Nipbl is induced in adult mouse liver, a dose-dependent loss of both cohesin binding and virtually all focal DNA looping is seen without major hepatocyte toxicity [21]. CTCF and cohesin are both required for DNA looping

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