SRP353090 PRJNA793580 GSE192871 Transcriptional regulation of the thymus master regulator Foxn1 [RNAseq_dev_HFC] FOXN1 is a transcription factor critical for the development of both thymic epithelial cell (TEC) and hair follicle cell (HFC) compartments. However, mechanisms controlling its expression remain poorly understood. To address this question, we performed thorough analyses of the conservation and chromatin status of the Foxn1 locus in different tissues and states, and identified several putative cis-regulatory regions unique to TEC vs. HFC. Furthermore, experiments using genetically modified mice with specific deletions in the Foxn1 locus and additional bioinformatic analyses helped us identify key regions and transcription factors involved in either positive or negative regulation of Foxn1 in both TEC and HFC. Specifically, we identified SIX1 and FOXN1 itself, as key factors inducing Foxn1 expression in embryonic and neonatal TECs. Together, our data provide important mechanistic insights into the transcriptional regulation of the Foxn1 gene in TEC vs. HFC and highlight the role of FOXN1 in its autoregulation Overall design: mRNA profiles of sorted thymic epithelial populations at different developmental time points as well as sorted HFC from Foxn1 EGFP mice, were generated by MARSeq Method. GSE192871 pubmed 36026441 parent_bioproject PRJNA793576