PLX105854

GSE154304: Runx-meRunx-mediated gene regulation during thymic T cell development and stage specific genomic interactions of Runx3

• Organsim mouse
• Type RNASEQ
• Target gene
• Project ARCHS4

Runx transcription factors play pivotal roles in the development of hematopoietic cells, including T cells. However, the Runx-target genes in early stages of thymic T cell development have been only partially elucidated. Moreover, the relationships of different Runx paralogs, whether they compete or collaborate with each other, are unknown.; We have performed CRISPR-Cas9 mediated acute deletion of Runx1 and Runx3, alone and in combination, to define the functions of Runx factors and their target genes. We focused on two distinct stages of early T cell development; before lineage commitment (Phase1) and after commitment (Phase2). Our data suggest that Runx1 and Runx3 are functionally redundant in Phase1, hence the absence of one factor was compensated by the other factor. In Phase2, Runx1 becomes a major contributor, while low levels of Runx3 still strengthened the Runx1-mediated target gene regulation and showed an additive effect.; Of importance, we found that Runx1 and Runx3 upregulate T cell programs and inhibit alternative lineage genes. In order to capture the developmental status of Runx-perturbed cells, we performed supervised principal component analysis (PCA) using a fixed frame of PC loadings from single cell RNA-seq analysis of normal in vivo-derived thymocytes. Unlike the reference in vitro and in vivo pro-T cell population or sgControl introduced cells, Runx knockout cells either failed to progress fully (Phase1) or deflected from the normal developmental trajectory (Phase2), suggesting essential roles of Runx factors in early stages of T development.; In addition, we analyzed the correlation between stage-specific genomic occupancy of Runx1 and Runx3 (using previously published data for Runx1, GSE103953) and Runx-mediated gene regulation responses at each stage. Interestingly, genes with dynamic, stage-sensitive expression showed a very significant association with phase-specific genomic interactions of Runx factors, and an especially strong correlation with Runx activated target genes.; In summary, our data suggest a pivotal role for Runx transcription factors in thymic T cell development by imposing T lineage specification in Phase1 and instructing the lineage-committed progenitor cells to progress through a normal T developmental trajectory. SOURCE: Boyoung Shin (boyoung@caltech.edu) - Californial Institute of Technology