Status
Public on Mar 12, 2025
Title
Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [scRNA-Seq and scATAC-Seq]
Experiment type
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary
Aire, a transcriptional regulator whose defect results in the development of autoimmunity, controls the transcriptome in the bulk of medullary thymic epithelial cells (mTECs) including the genes for self-antigens. Mechanisms for this process, however, remained incompletely understood, especially regarding the effects of Aire in each subpopulation in mTECs. Here, we combined single-cell multi-omics (scMulti-seq) technologies by which gene expression and open chromatin were simultaneously profiled from the same cell and deeper single-cell sequencing by RamDA-seq which enabled profiling of the minimum dropout. scMulti-seq effectively demonstrated the subpopulations among mTECs associated with diverse transcription factor activities which are affected by Aire and developmental stages, while RamDA-seq revealed the different modes of gene regulations by Aire in different subpopulations. Aire is not only essential for the development of a specific population in which Aire induces a set of genes in a stochastic manner but also promotes the development of multiple subpopulations in which Aire enhances the expressions of genes in a coordinated manner. The former group of Aire-induced genes was characterized by enhanced H3K27me3 chromatin modifications and Aire seems to unleash these silenced genes by deactivating polycomb repressive complex 2 (PRC2). We also found unique gene signatures for the neonatal stage such as high expression of chemokines and expression of cortical TEC (cTEC)-like genes in TECs, which were Aire-independent. Our approach has illuminated the multilayered transcriptional control in mTECs governing the multiple subpopulations organizing the thymic microenvironment.
Overall design
single cell multiome ATAC + gene expression analysis of FACS-sorted mouse thymic epithelial cells (TECs, CD45-EpCAM+) from wild-type and Aire knockout (KO) mice
Submission date
Jun 06, 2022
Last update date
Apr 23, 2025
Contact name
Hideyuki Yoshida
Organization name
RIKEN IMS
Street address
1-7-22 Suehiro-cho
City
Tsurumi-ku, Yokohama
State/province
Kanagawa
ZIP/Postal code
230-0045
Country
Japan
This SubSeries is part of SuperSeries:
GSE205411
Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations
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Format
Supplementary file
Size
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File type/resource
Raw data are available in SRA
Processed data provided as supplementary file