Lander Julie M, Supp Dorothy M, He Hua, Martin Lisa J, Chen Xiaoting, Weirauch Matthew T, Boyce Steven T, Kopan Raphael
Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.
Research Department, Shriners Hospitals for Children, Cincinnati, Ohio, United States of America.
PLoS One. 2017 Sep 27;12(9):e0184500. doi: 10.1371/journal.pone.0184500. eCollection 2017.
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.
为了识别对表皮损伤有反应的假定基因调控区域，我们绘制了分层人类表皮在屏障成熟和破坏过程中的染色质动态变化。在气液界面培养的工程皮肤替代物（ESS）被用作人类表皮发育且屏障形成不完全的模型。将其移植到免疫受损小鼠身上后，表皮屏障得以稳定，而在受伤后又会再次受损。采用改良的甲醛辅助调控元件分离法（FAIRE）来识别单层角质形成细胞、体外ESS、移植的ESS以及胶带剥离的ESS移植样本所特有的可及基因组区域。我们绘制了在每个阶段富集的转录因子结合位点的分化和成熟相关变化，并观察到在屏障缺陷样本中AP - 1基因家族基序的过度表达。TSLP是一种在接触过敏原时免疫记忆的重要效应因子，其转录在我们的屏障缺陷样本中显著升高。我们鉴定出与TSLP诱导相关的动态DNA元件，其可能包含调控TSLP的增强子。两个动态区域位于TSLP启动子附近，并与过敏相关单核苷酸多态性rs17551370和rs2289877重叠，强烈表明这些位点参与过敏性疾病中TSLP表达的调控。在TSLP启动子上游约250kb处发现的其他动态染色质区域与过敏性疾病单核苷酸多态性处于高度连锁不平衡状态。综上所述，这些结果定义了表皮发育和功能障碍过程中动态染色质可及性的变化。
