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Series GSE156271 Query DataSets for GSE156271
Status Public on Dec 07, 2020
Title Core transcription regulatory circuitry orchestrates stratified epithelial homeostasis (RNA-seq)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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 the corneal epithelial identity and homeostasis. RUNX1 or SMAD3 depletion inhibits PAX6 and induces LSCs to differentiate into epidermal-like type. 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 the establishment of stem cell identity and lineage commitment, and provides comprehensive regulatory principles for human stratified epithelial homeostasis and pathogenesis.
Overall design RNA-seq for wildtype LSCs and skin epithelial stem cells (SESCs). RNA-seq for scrambled shRNA- and shRUNX1-treated LSCs. RNA-seq for scrambled shRNA- and shSMAD3-treated LSCs.
Citation(s) 33462242, 35277509, 36652264
Submission date Aug 14, 2020
Last update date Feb 06, 2023
Contact name Mingsen Li
Organization name Sun Yat-sen University
Department Zhongshan Ophthalmic Center
Street address No. 7 Jinsui road Tianhe district
City Guanzhou
ZIP/Postal code 510060
Country China
Platforms (1)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (12)
GSM4728051 LSC_scramble_R_rep1
GSM4728052 LSC_scramble_R_rep2
GSM4728053 LSC_shRUNX1_rep1
This SubSeries is part of SuperSeries:
GSE156273 Core transcription regulatory circuitry orchestrates stratified epithelial homeostasis
BioProject PRJNA657250
SRA SRP277533

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE156271_LSC_vs_SESC_TPM.xlsx 3.4 Mb (ftp)(http) XLSX
GSE156271_LSC_vs_SESC_differential_genes.xlsx 294.0 Kb (ftp)(http) XLSX
GSE156271_shRUNX1_vs_scramble_TPM.xlsx 3.5 Mb (ftp)(http) XLSX
GSE156271_shRUNX1_vs_scramble_differential_genes.xlsx 163.1 Kb (ftp)(http) XLSX
GSE156271_shSMAD3_vs_scramble_TPM.xlsx 3.4 Mb (ftp)(http) XLSX
GSE156271_shSMAD3_vs_scramble_differential_genes.xlsx 133.4 Kb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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