5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells

Abstract

Mammalian genomes contain several dozens of large (>0.5 Mbp) lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs) in these loci remain poorly understood. TADs are principle units of the genome folding and represents the DNA regions within which DNA interacts more frequently and less frequently across the TAD boundary. Here, we used Chromatin Conformation Capture Carbon Copy (5C) technology to characterize spatial chromatin interaction network in the 3.1 Mb Epidermal Differentiation Complex (EDC) locus harbouring 61 functionally related genes that show lineage-specific activation during terminal keratinocyte differentiation in the epidermis. 5C data validated by 3D-FISH demonstrate that the EDC locus is organized into several TADs showing distinct lineage-specific chromatin interaction networks based on their transcription activity and the gene-rich or gene-poor status. Correlation of the 5C results with genome-wide studies for enhancer-specific histone modifications (H3K4me1 and H3K27ac) revealed that the majority of spatial chromatin interactions that involves the gene-rich TADs at the EDC locus in keratinocytes include both intra- and inter-TAD interaction networks, connecting gene promoters and enhancers. Compared to thymocytes in which the EDC locus is mostly transcriptionally inactive, these interactions were found to be keratinocyte-specific. In keratinocytes, the promoter-enhancer anchoring regions in the gene-rich transcriptionally active TADs are enriched for the binding of chromatin architectural proteins CTCF, Rad21 and chromatin remodeler Brg1. In contrast to gene-rich TADs, gene-poor TADs show preferential spatial contacts with each other, do not contain active enhancers and show decreased binding of CTCF, Rad21 and Brg1 in keratinocytes. Thus, spatial interactions between gene promoters and enhancers at the multi-TAD EDC locus in skin epithelial cells are cell type-specific and involve extensive contacts within TADs as well as between different gene-rich TADs, forming the framework for lineage-specific transcription.

Epigenetic control in skin development, homeostasis and injury repair

“…Epidermal‐specific regulatory enhancer 923 was found to interact with the epidermal gene promoters within EDC for lineage specification . Recently, a chromatin conformation capture carbon copy (5C) technique was developed to investigate long‐range enhancer‐promoter interactions . Comparing 5C results with other genome studies within enhancer‐promoter interacting regions in EDC, H3K4me1 and H3K27ac were enriched and BRG1 were bound near these regions for proper epidermal‐specific gene activation .…”

“…Recently, a chromatin conformation capture carbon copy (5C) technique was developed to investigate long‐range enhancer‐promoter interactions . Comparing 5C results with other genome studies within enhancer‐promoter interacting regions in EDC, H3K4me1 and H3K27ac were enriched and BRG1 were bound near these regions for proper epidermal‐specific gene activation . Unlike typical enhancers (TE), super‐enhancers (SE) are clusters of closely associated enhancers that provide binding sites for transcription factors involved in cell fate choice or cell identity .…”

Alu retrotransposons modulate Nanog expression through dynamic changes in regional chromatin conformation via aryl hydrocarbon receptor

“…These changes in Nanog expression and in the levels of other pluripotency regulators involve epigenetic modifications of their loci, as observed in several differentiation models [18][19][20][21][22][23]. Under stem cell differentiating conditions, chromatin folding is altered, the chromatin of topologically associated domains (TADs) is reordered and the whole transcriptome of the cell rewired [24][25][26][27][28]. Nevertheless, we are still far from a comprehensive view of the molecular events that comprise cellular differentiation and on the functions of specific regulators of pluripotency.…”

Cohesin mediates Esco2-dependent transcriptional regulation in zebrafish regenerating fin model of Roberts syndrome

“…Extensive research provides fascinating evidence that cohesin functions beyond sister chromatid cohesion ( trans -tethering that brings together two DNA molecules). Cohesins (often in combination with CTCF) also participate in various cis -tethering events including transcriptional regulation via looping and chromosome condensation through intramolecular looping such that cohesins can associate with DNA throughout the genome and in a site-specific manner ( Kang et al, 2015 ; Poterlowicz et al, 2017 ; Phillips-Cremins et al, 2013 ; Rao et al, 2014 ; de Wit et al, 2015 ; Guo et al, 2015 ; Tang et al, 2015 ; Hansen et al, 2017 ; Dorsett, 2016 ; Kawauchi et al, 2016 ; Watrin et al, 2016 ). Formation of both cis- and trans -DNA tethers throughout the cell cycle has hampered efforts to understand the molecular etiology of cohesinopathies.…”