Genomic Localization of RUNX Proteins in Neonatal Germ Cells.
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE292902 | GEO | 2026/02/26
REPOSITORIES: GEO
Similar Datasets
Project description:Although Runt-related transcription factor 1 (RUNX1) has been generally considered to be a tumor suppressor, a growing body of evidence strongly suggests its pro-oncogenic property in acute myeloid leukemia (AML), Here we demonstrate that anti-leukemic effect mediated by RUNX1 depletion is highly dependent on a functional p53-mediated cell death pathway. Based on our present findings, anti-tumor effect elicited by RUNX1 silencing was compensated by the other RUNX family members such as RUNX2 and RUNX3, and a simultaneous attenuation of whole RUNX family members as a cluster displayed a much stronger anti-tumor effect relative to their individual suppression. Notably, switching off RUNX cluster utilizing the novel alkylating agent-conjugated pyrrole-imidazole (PI) polyamides, which specifically bound to the consensus RUNX-binding sequences, was highly effective against leukemia as well as dismal-prognostic solid tumors arising from diverse origins in vivo without any significant adverse events. Together, this work identifies the crucial role of RUNX cluster in the maintenance and the progression of cancer cells, and the indicated gene switch technology-dependent its modulation would be a novel strategy to control malignancies.
2017-03-26 | GSE94835 | GEO
Project description:The RUNX genes encode for transcription factors involved in development and human disease. RUNX1 and RUNX3 are frequently associated with leukemias, yet the basis for their involvement in leukemogenesis is not fully understood. Here we show that Runx1;Runx3 double knockout (DKO) mice exhibited lethal phenotypes due to bone marrow failure and myeloproliferative disorder. These contradictory clinical manifestations are reminiscent of human inherited bone marrow failure syndromes like Fanconi anemia (FA), caused by defective DNA repair. Indeed, Runx1;Runx3 DKO cells showed mitomycin C hypersensitivity, due to impairment of monoubiquitinated-FANCD2 recruitment to DNA damage foci, although FANCD2 monoubiquitination in the FA pathway was unaffected. RUNX1 and RUNX3 interact with FANCD2 independent of CBFβ, suggesting non-transcriptional role for RUNX in DNA repair. These findings suggest that RUNX dysfunction causes DNA repair defect, besides transcriptional misregulation, and promotes development of leukemias and other cancers.
2014-08-26 | GSE51107 | GEO
Project description: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.
2020-07-14 | GSE154304 | GEO
Project description:Runx1 and Runx3 function redundantly in early T-development, and together drive T-lineage developmental progression by regulating distinct sets of genes in different stages. Context-specific Runx target genes are particularly enriched near Runx binding sites that dynamically shift from pre-T-commitment stages (Phase 1) to post-T-commitment stages (Phase 2). As total Runx activities (Runx1+Runx3) are maintained stably throughout early T-development stages, yet Runx factors physically interact with multiple collaborators, we hypothesized that different Runx-collaborating transcription factors compete to recruit a limited pool of Runx transcription factors. To test whether increasing Runx availability can alter Runx DNA-binding site choices, Runx1 overexpression vectors were introduced to two different systems. First, we increased Runx1 expression in a DN3-like cell line (representing a post-commitment, Phase 2 stage) in the presence or absence of exogenous Phase 1 co-factor, PU.1. Second, we increased Runx1 expression in Phase 1 primary cells which naturally express PU.1 and other Phase 1 collaborators. Then, Runx1 binding behaviors were measured using ChIP-seq or CUT&RUN (C&R). A modest increase of Runx1 levels (about 2-3 fold increase) substantially increased the number of Runx binding sites seen and the intensity of occupancy in both systems. When Runx expression was at physiological levels, PU.1 dominated Runx1 site choice before T commitment by recruiting Runx1 to PU.1 sites. The Phase 2 cell line system showed that it did this while depleting Runx1 from alternative high quality Runx motif sites. However, when Runx1 was overexpressed, Runx1 was still recruited to PU.1 sites, but this recruitment did not evacuate Runx1 occupancy from default preferred sites. Notably, Runx1 overexpression in primary Phase 1 cells caused precocious occupancy of post-commitment, Phase 2-specific sites. We found that these are often co-occupied with TCF1, E2A, and HEB, but have minimal co-binding with PU.1. In addition, Runx1 overexpression resulted in new binding sites that were not normally observed in pro-T cells, which are mostly sequestered by closed chromatin normally although they harbor more numerous Runx motifs. Thus, these data suggest that Runx DNA binding site choices are sensitive to Runx concentration and co-factors during early T-development.
2023-07-09 | GSE218147 | GEO
Project description:Ikaros family zinc finger protein 1 and 3 (IKZF1 and IKZF3) are transcription factors that promote multiple myeloma (MM) proliferation. The immunomodulatory imide drug (IMiD) lenalidomide promotes myeloma cell death via Cereblon (CRBN)-dependent ubiquitylation and proteasome-dependent degradation of IKZF1 and IKZF3. Although IMiDs have been used as first-line drugs for MM, the overall survival of refractory MM patients remains poor and demands the identification of novel agents to potentiate the therapeutic effect of IMiDs. Using an unbiased screen based on mass spectrometry, we identified the Runt-related transcription factor 1 and 3 (RUNX1 and RUNX3) as interactors of IKZF1 and IKZF3. Interaction with RUNX1 and RUNX3 inhibits CRBN-dependent binding, ubiquitylation and degradation of IKZF1 and IKZF3 upon lenalidomide treatment. Inhibition of RUNXs, via genetic ablation or a small molecule (AI-10-104), results in sensitization of myeloma cell lines and primary tumors to lenalidomide. Thus, RUNX inhibition represents a valuable therapeutic opportunity to potentiate IMiDs therapy for the treatment of multiple myeloma.
2020-04-13 | GSE123660 | GEO
Project description:To study the role of RUNX transcription factors in the epididymal epithelial cells we deleted Runt domains of Runx1 and Runx2 from mouse epididymal cell line mE-Cap18 using CRISPR-Cas9 technique.
2024-05-02 | GSE236104 | GEO
Project description:Runt-related transcription (RUNX) factors play a key role in T cell development. At the T-lineage commitment checkpoint, RUNX1 undergoes dynamic partner switching, resulting in its redeployment. Here, we investigated the functional differences in RUNX factors between the lymphoid progenitor (LP)- and Notch-stimulated earliest T progenitor stages (Phase 1). We identified CCCTC-binding factor (CTCF) as an LP-specific RUNX1-interacting partner, with LP-specific RUNX1 binding genomic sites significantly enriched for CTCF consensus motifs and co-occupied by CTCF. On Notch stimulation, Notch1 intracellular domain (Notch1-IC) directly interacts with RUNX1 and recruits the RUNX1/Mediator/p300 transcriptional activation complex to Notch-regulated T-signature gene loci. CRISPR/Cas9-mediated stage-specific deletion of RUNX factors and their binding partners revealed that the RUNX1/CTCF complex in LP negatively regulates T-signature gene expression, whereas the RUNX1/Mediator/p300 complex in Phase 1 promotes it. Our findings highlight the crucial role of Notch-mediated functional conversion of RUNX factors, including protein complex re-organization and genomic redeployment in initiating T-lineage program.
2025-05-07 | GSE296265 | GEO
Project description:Gene expression profiles of Cbfb-deficient and control Treg cells were compared. Abstract: Naturally arising regulatory T (Treg) cells express the transcription factor FoxP3, which critically controls the development and function of Treg cells. FoxP3 interacts with another transcription factor Runx1 (also known as AML1). Here we showed that Treg cell-specific deficiency of Cbfβ, a cofactor for all Runx proteins, or that of Runx1, but not Runx3, induced lymphoproliferation, autoimmune disease, and hyper-production of IgE. Cbfb-deleted Treg cells exhibited impaired suppressive function in vitro and in vivo, with altered gene expression profiles including attenuated expression of FoxP3 and high expression of interleukin-4. The Runx complex bound to more than 3000 gene loci in Treg cells, including the Foxp3 regulatory regions and the Il4 silencer. In addition, knockdown of RUNX1 showed that RUNX1 is required for the optimal regulation of FoxP3 expression in human T cells. Taken together, our results indicate that the Runx1-Cbfβ heterodimer is indispensable for in vivo Treg cell function, in particular, suppressive activity and optimal expression of FoxP3. Experiment Overall Design: CD4+CD25hi cells, most of which were Foxp3+ Treg cells, were isolated from Cbfb-flox/flox: Foxp3-ires-Cre (n = 3) and control Cbfb-flox/wt: Foxp3-ires-Cre (n = 3) mice. Total RNA was extracted from those purified Cbfb-deficient or control Treg cells.
2009-09-25 | E-GEOD-18148 | biostudies-arrayexpress
Project description:Runx transcription factors are essential for generating functional T cells starting from the earliest stages in thymic T-development. To evaluate how Runx factors instruct T cell development, we perturbed Runx activities using 1) CRISPR-Cas9, simultaneously deleting two predominant, redundant Runx factors, Runx1 and Runx3, and 2) Runx1-overepxression at a stage before pro-T cells commit to a T cell fate. Then single-cell transcriptome analysis was performed. Runx1/Runx3 knockout (KO) vs. Runx1 overexpression (OE) resulted in contrasting deviations from the normal developmental trajectory. The separation of both perturbation conditions from the controls implied that Runx factors regulate gene networks in individual cells to control separate pathways instead of changing distributions of cells among different stages along the control pathway. Notably, a common core set of genes responded to both KO and OE, in opposite directions. Runx activation target genes were selectively enriched for T-identity program and innate lymphoid cell program genes, whereas inhibition targets were significantly associated with stem/progenitor program and myeloid lineage pathways. Pseudotime inference analysis suggested that Runx perturbations also substantially regulate developmental speed, as Runx KO significantly slowed down developmental progression, whereas Runx1 OE resulted in pronounced acceleration. This interpretation was largely supported by Runx activities regulating key transcription factors involved in establishing distinct gene network modules during T cell development. Indeed, further analysis showed that Runx target genes get combinatorial inputs from these Runx-regulated transcription factors as well as from Runx factors themselves. Together, our data suggest that Runx transcription factors drive early T developmental progression by launching gene expression modules associated with T-identity and innate lymphoid cells through mediating other transcription factor cooperativities.
2023-07-09 | GSE218149 | GEO
Project description:In B cells infected by the cancer-associated Epstein-Barr virus (EBV), RUNX3 and RUNX1 transcription is manipulated to control cell growth. The EBV-encoded EBNA2 transcription factor (TF) activates RUNX3 transcription leading to RUNX3-mediated repression of the RUNX1 promoter and the relief of RUNX1-directed growth repression. We show that EBNA2 activates RUNX3 through a specific element within a -97 kb super-enhancer in a manner dependent on the expression of the Notch DNA-binding partner RBP-J. We also reveal that the EBV TFs EBNA3B and EBNA3C contribute to RUNX3 activation in EBV-infected cells by targeting the same element. Uncovering a counter-regulatory feed-forward step, we demonstrate EBNA2 activation of a RUNX1 super-enhancer (-139 to -250 kb) that results in low-level RUNX1 expression in cells refractory to RUNX1-mediated growth inhibition. EBNA2 activation of the RUNX1 super-enhancer is also dependent on RBP-J. Consistent with the context-dependent roles of EBNA3B and EBNA3C as activators or repressors, we find that these proteins negatively regulate the RUNX1 super-enhancer, curbing EBNA2 activation. Taken together our results reveal cell-type specific exploitation of RUNX gene super-enhancers by multiple EBV TFs via the Notch pathway to fine tune RUNX3 and RUNX1 expression and manipulate B-cell growth.
2016-03-03 | GSE76869 | GEO