Characterization of enhancers and the role of the transcription factor KLF7 in regulating corneal epithelial differentiation

• Published in: The Journal of biological chemistry Vol. 292; no. 46; pp. 18937 - 18950
• Main Authors: Klein, Rachel Herndon, Hu, William, Kashgari, Ghaidaa, Lin, Ziguang, Nguyen, Tuyen, Doan, Michael, Andersen, Bogi
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 17-11-2017; American Society for Biochemistry and Molecular Biology
• Subjects: Acetylation; Cell Differentiation; Cell Line; cell proliferation; chromatin; Chromatin Immunoprecipitation; Corneal Diseases - genetics; Corneal Diseases - metabolism; corneal epithelium; Enhancer Elements, Genetic; epithelial cell; Epithelium, Corneal - cytology; Epithelium, Corneal - metabolism; eye; Gene Expression Regulation; Gene Regulation; Histones - metabolism; Humans; KLF7; Kruppel-like factor 4 (KLF4); Kruppel-Like Transcription Factors - genetics; Kruppel-Like Transcription Factors - metabolism; Polymorphism, Single Nucleotide; Stem Cells - cytology; Stem Cells - metabolism; superenhancer; eye; KLF7; cell proliferation; gene regulation; superenhancer; chromatin; epithelial cell; Kruppel-like factor 4 (KLF4); corneal epithelium
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M117.793117

During tissue development, transcription factors bind regulatory DNA regions called enhancers, often located at great distances from the genes they regulate, to control gene expression. The enhancer landscape during embryonic stem cell differentiation has been well characterized. By contrast, little is known about the shared and unique enhancer regulatory mechanisms in different ectodermally derived epithelial cells. Here we use ChIP sequencing (ChIP-seq) to identify domains enriched for the histone marks histone H3 lysine 4 trimethylation, histone H3 lysine 4 monomethylation, and histone H3 lysine 27 acetylation (H3K4me3, H3K4me1, and H3K27ac) and define, for the first time, the super enhancers and typical enhancers active in primary human corneal epithelial cells. We show that regulatory regions are often shared between cell types of the ectodermal lineage and that corneal epithelial super enhancers are already marked as potential regulatory domains in embryonic stem cells. Kruppel-like factor (KLF) motifs were enriched in corneal epithelial enhancers, consistent with the important roles of KLF4 and KLF5 in promoting corneal epithelial differentiation. We now show that the Kruppel family member KLF7 promotes the corneal progenitor cell state; on many genes, KLF7 antagonized the corneal differentiation–promoting KLF4. Furthermore, we found that two SNPs linked previously to corneal diseases, astigmatism, and Stevens-Johnson syndrome fall within corneal epithelial enhancers and alter their activity by disrupting transcription factor motifs that overlap these SNPs. Taken together, our work defines regulatory enhancers in corneal epithelial cells, highlights global gene-regulatory relationships shared among different epithelial cells, identifies a role for KLF7 as a KLF4 antagonist in corneal epithelial cell differentiation, and explains how two SNPs may contribute to corneal diseases.