Analysis of chromatin accessibility in human epidermis identifies putative barrier dysfunction-sensing enhancers

Abstract

To identify putative gene regulatory regions that respond to epidermal injury, we mapped chromatin dynamics in a stratified human epidermis during barrier maturation and disruption. Engineered skin substitutes (ESS) cultured at the air-liquid interface were used as a model of developing human epidermis with incomplete barrier formation. The epidermal barrier stabilized following engraftment onto immunocompromised mice, and was compromised again upon injury. Modified formaldehyde-assisted isolation of regulatory elements (FAIRE) was used to identify accessible genomic regions characteristic of monolayer keratinocytes, ESS in vitro, grafted ESS, and tape-stripped ESS graft. We mapped differentiation- and maturation-associated changes in transcription factor binding sites enriched at each stage and observed overrepresentation of AP-1 gene family motifs in barrier-deficient samples. Transcription of TSLP, an important effector of immunological memory in response to allergen exposure, was dramatically elevated in our barrier-deficient samples. We identified dynamic DNA elements that correlated with TSLP induction and may contain enhancers that regulate TSLP. Two dynamic regions were located near the TSLP promoter and overlapped with allergy-associated SNPs rs17551370 and rs2289877, strongly implicating these loci in the regulation of TSLP expression in allergic disease. Additional dynamic chromatin regions ~250kb upstream of the TSLP promoter were found to be in high linkage disequilibrium with allergic disease SNPs. Taken together, these results define dynamic chromatin accessibility changes during epidermal development and dysfunction.

Functional interactions between Mi-2β and AP1 complexes control response and recovery from skin barrier disruption

“…While our effort to confirm the relevance of this work in mice to human skin was confined to studies in vitro, it is noteworthy that a study of newly accessible chromatin sites in xenografted human skin equivalents after TS also identified AP1 as a likely regulator of the barrier disruption response (Lander et al, 2017). In addition, microarray analysis of gene expression changes in human skin after barrier disruption is consistent with the results reported here (Sextius et al, 2010).…”

“…In the adult skin, Mi-2β represses genes supporting basal keratinocyte activation, mobilization, and immune cell function ( Kashiwagi et al, 2017 ). Many of the same genes are also induced by physiological challenge to the skin, such as wounding or barrier disruption ( Keyes et al, 2016 ; Lander et al, 2017 ; Sextius et al, 2010 ), suggesting that suppression of Mi-2β activity may be a mechanism by which environmental challenges mobilize the skin’s stress responses.…”

Triangulating molecular evidence to prioritise candidate causal genes at established atopic dermatitis loci

“…We also looked at variant overlap within different regulatory regions: insulator[77], promoter-enhancer interactions[78],[79],[80],[81],[82],[83],[84],[85],[86], regulatory non-coding RNAs[87],[88],[89],[90],[91], topologically associating domains (TADs)[92],[93],[79],[94],[81],[95], and CTCF binding sites[96] culled from various publications, using giggle[97] search engine. Independently, we looked for overlap inside Roadmap regions classified as containing active chromatin state (states 1-8)[63] and FAIRE-Seq-determined regions of accessible chromatin in human epidermis during barrier maturation and disruption[98]. Cell-type specific regulatory elements[99] were also annotated based on histone marks and chromatin state.…”

Skin epigenetics

“…The epigenetics of epidermal differentiation, whereby epidermal stem cells give rise to differentiated cells of the epidermis, has been extensively studied. The data indicate that multiple mechanisms are important, including DNA methylation, 9 activating and repressive histone modifications, [10][11][12][13][14] chromatin accessibility, [15][16][17][18][19][20][21][22] 3D chromatin regulation [23][24][25][26] and long non-coding RNAs. 27 In this issue, Johann Bauer and colleagues provide a broad review of epigenetic and metabolic regulatory mechanisms in epidermal homeostasis.…”