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

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 1,847 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.

Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation

“…When looking into the TFs that mediate estradiol's effects in XYM for potential male-biased regulation in adipose tissue, we found matches with 13 of the top 20 TFs from the Anderson et al ( 2020) human adipose study. These included AR, CTCF, SMC1A, EZH2, ESR1, RAD21, and TP63, and many were also consistent in additional mouse Matthews and Waxman 2020) and human studies including GTEx Oliva et al 2020).…”

Characterization of a strain-specific CD-1 reference genome reveals potential inter- and intra-strain functional variability

“…To determine whether the non-uniform SNPs can result in variations in TF binding between CD-1 individuals, we used a CTCF ChIP-seq dataset that was taken from the liver of four male and four female CD-1 individuals [5]. Upon examination, replicate 4 of the male, and replicate 4 of the female, appeared globally to be of lower quality than the other replicates (Additional file 1: Figure S2A); thus, these two replicates were removed from consideration.…”

“…We then determined peaks that were ir-reproducible between the remaining replicates (Additional file 1: Figure S2B; see Methods) and took these as candidates for regions where there could be variability in Ctcf binding between individuals. The study that generated these ChIP-seq datasets identified regions of sexual dimorphism in Ctcf binding [5], and these were excluded from the set of considered ir-reproducible peaks. We reasoned that it was possible that not all sexually dimorphic regions were identified.…”

“…Genomic DNA sequencing and ATAC-seq data that support the findings of this study have been deposited in NCBI GEO with the accession code GSE209816 (token: unszskikljozril). All previously published data analyzed in this study are available at the NCBI GEO repository at the following locations: CTCF ChIP-seq, GSE102997 and GSE130908 [5]; WGBS, GSE149302. All custom scripts used to process and analyze the data and to obtain the results described in this 30 paper have been deposited in the GitHub repository (https://github.com/ikremsky/Scripts-for-Characterization-of-a-strain-specific-CD-1-reference-genome...-).…”

Advances in sex disparities for cancer immunotherapy: unveiling the dilemma of Yin and Yang

“…The sex bias in the mutation burden of the cancer genomes was associated with decreased gene expression in DNA mismatch repair [ 44 ], suggesting that lower efficiency of genome repair mechanisms might underlie sex differences in the frequency of mutations [ 47 , 48 ]. Moreover, recent studies are showing that two main regulators of genome topology (i.e., CTCF and COHESIN) bind chromatin in a sex-specific manner [ 49 , 50 ] and that mutations at CTCF binding sites can act as tumor drivers [ 51 ]. Sex-specific chromatin conformations might, therefore, affect the efficiency with which DNA damage is repaired, providing a further mechanistic explanation for sex differences in tumor development.…”