Core transcription regulatory circuitry orchestrates corneal epithelial homeostasis

Mingsen Li,Chenxi He,Jiafeng Liu,Tao Xu,Nan Cao,Jin Yuan,Liqiong Zhu,Junjun Ding,Lingyu Li,Hong Ouyang,Yizhi Liu,Kang Zhang,Huaxing Huang,Fei Lan,Huizhen Guo,Jingxin Liu,Siqi Wu,Zhen Mao,Li Wang

doi:10.1038/s41467-020-20713-z

Abstract

Adult stem cell identity, plasticity, and homeostasis are precisely orchestrated by lineage-restricted epigenetic and transcriptional regulatory networks. Here, by integrating super-enhancer and chromatin accessibility landscapes, we delineate core transcription regulatory circuitries (CRCs) of limbal stem/progenitor cells (LSCs) and find that RUNX1 and SMAD3 are required for maintenance of corneal epithelial identity and homeostasis. RUNX1 or SMAD3 depletion inhibits PAX6 and induces LSCs to differentiate into epidermal-like epithelial cells. RUNX1, PAX6, and SMAD3 (RPS) interact with each other and synergistically establish a CRC to govern the lineage-specific cis-regulatory atlas. Moreover, RUNX1 shapes LSC chromatin architecture via modulating H3K27ac deposition. Disturbance of RPS cooperation results in cell identity switching and dysfunction of the corneal epithelium, which is strongly linked to various human corneal diseases. Our work highlights CRC TF cooperativity for establishment of stem cell identity and lineage commitment, and provides comprehensive regulatory principles for human stratified epithelial homeostasis and pathogenesis.

Highlights

Adult stem cell identity, plasticity, and homeostasis are precisely orchestrated by lineagerestricted epigenetic and transcriptional regulatory networks
Similar to H3K27ac and H3K4me[1] occupancy, the ATAC peaks were mainly located at intron and intergenic regions with a small fraction at proximal promoters, which was distinct from the H3K4me[3]
We map the epigenetic landscape of limbal stem/progenitor cells (LSCs) and identify an RPS-mediated chromatin-regulatory networks required for corneal epithelial identity and homeostasis (Fig. 7)

Summary

Introduction

Plasticity, and homeostasis are precisely orchestrated by lineagerestricted epigenetic and transcriptional regulatory networks. By integrating superenhancer and chromatin accessibility landscapes, we delineate core transcription regulatory circuitries (CRCs) of limbal stem/progenitor cells (LSCs) and find that RUNX1 and SMAD3 are required for maintenance of corneal epithelial identity and homeostasis. Our work highlights CRC TF cooperativity for establishment of stem cell identity and lineage commitment, and provides comprehensive regulatory principles for human stratified epithelial homeostasis and pathogenesis. Limbal stem/progenitor cells (LSCs) segregated in the basal layer of limbus undergo self-renewal and differentiation throughout life to maintain corneal epithelial homeostasis and regeneration[9,10], which is orchestrated by lineage-specific regulators[11,12,13]. Using the corneal epithelium as a model tissue, we characterize the SE-mediated regulatory landscape of LSCs and reveal a CRC TF interconnected auto-regulation network. We show that RUNX1, PAX6, and SMAD3 (RPS) proteins interact physically and establish an enhancer especially SE repertoire, conferring corneal epithelial function and identity

Methods

Results

Conclusion