Topological isolation of developmental regulators in mammalian genomes

Abstract

Precise control of mammalian gene expression is facilitated through epigenetic mechanisms and nuclear organization. In particular, insulated chromosome structures are important for regulatory control, but the phenotypic consequences of their boundary disruption on developmental processes are complex and remain insufficiently understood. Here, we generated deeply sequenced Hi-C data for human pluripotent stem cells (hPSCs) that allowed us to identify CTCF loop domains that have highly conserved boundary CTCF sites and show a notable enrichment of individual developmental regulators. Importantly, perturbation of such a boundary in hPSCs interfered with proper differentiation through deregulated distal enhancer-promoter activity. Finally, we found that germline variations affecting such boundaries are subject to purifying selection and are underrepresented in the human population. Taken together, our findings highlight the importance of developmental gene isolation through chromosomal folding structures as a mechanism to ensure their proper expression.

Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism

“…The stability across cell types and evolutionary conservation of the TAD boundary that separates GPR101 from centromeric CREs underscores the tight regulation of the normal GPR101 regulatory unit, as has been reported for other topologically isolated genes with roles in development. 53 Stable boundaries are more intolerant of disruption by structural variants than unique ones, 54 implying that the X-LAG locus is under strong selection. The severity of the clinical effects of gigantism in X-LAG and its extreme rarity (40 individuals described) combine to support a hypothesis that GPR101 and its surrounding regulatory environment are tightly regulated.…”

Dynamic network-guided CRISPRi screen reveals CTCF loop-constrained nonlinear enhancer-gene regulatory activity in cell state transitions

“…Hi-C datafile ENCFF080DPJ.hic 56 for K562 was downloaded from encodeproject.org. Hi-C .hic datafiles for HUES64 and differentiated to (EC, MS, EN) were downloaded from NCBI GEO accession GSE130085 67 . Contact frequency .bedpe files were generated from Juicer Tools version 1.22.01 or 2.13.05 (K562).…”

Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes

“…We find ∼12% of the ∼2,400 TADs found in several mouse cell types contained only a single gene that were collectively enriched in developmental GO-terms ( Figure S6 A; Eden et al., 2009 ). Thus, as previously suggested, a fraction of developmental loci are isolated alone within dedicated mono-gene TAD regulatory landscapes ( Wu et al., 2021 ). Nevertheless, ∼88% of TADs contained multiple genes which we classified into ubiquitous (Ubiq.)…”

“…TADs are frequently described as stable and conserved structural scaffolds that ensure transmission of enhancer activities to promoters found within a domain’s boundaries ( Andrey and Mundlos, 2017 ). In this simple model, genes with similar functions can be controlled together in a shared TAD, whereas those requiring divergent regulation must be placed alone in separated domains ( Wu et al., 2021 ). However, we find most TADs in the genome contain multiple independently regulated developmental genes as seen in previous studies of specific loci (e.g., the essential Hox genes) ( Andrey et al., 2013 ; Huang et al., 2017 ; Noordermeer et al., 2011 ; Palstra et al., 2003 ; Soshnikova and Duboule, 2009 ).…”