Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development

Abstract

The transcription factor RUNX1 is a critical regulator of developmental hematopoiesis and is frequently disrupted in leukemia. Runx1 is a large, complex gene that is expressed from two alternative promoters under the spatiotemporal control of multiple hematopoietic enhancers. To dissect the dynamic regulation of Runx1 in hematopoietic development, we analyzed its three-dimensional chromatin conformation in mouse embryonic stem cell (ESC) differentiation cultures. Runx1 resides in a 1.1 Mb topologically associating domain (TAD) demarcated by convergent CTCF motifs. As ESCs differentiate to mesoderm, chromatin accessibility, Runx1 enhancer-promoter (E-P) interactions, and CTCF-CTCF interactions increase in the TAD, along with initiation of Runx1 expression from the P2 promoter. Differentiation to hematopoietic progenitor cells is associated with the formation of tissue-specific sub-TADs over Runx1, a shift in E-P interactions, P1 promoter demethylation, and robust expression from both Runx1 promoters. Deletion of promoter-proximal CTCF sites at the sub-TAD boundaries has no obvious effects on E-P interactions but leads to partial loss of domain structure, mildly affects gene expression, and delays hematopoietic development. Together, our analysis of gene regulation at a large multi-promoter developmental gene reveals that dynamic sub-TAD chromatin boundaries play a role in establishing TAD structure and coordinated gene expression.

A lncRNA identifies Irf8 enhancer element in negative feedback control of dendritic cell differentiation

“…Interestingly, most of the Irf8 flanking enhancers ( Durai et al, 2019 ; Grajales-Reyes et al, 2015 ; Murakami et al, 2021 ; Schönheit et al, 2013 ) are located within convergent CTCF binding sites upstream and downstream of the Irf8 gene ( Figure 1B and Figure 1—figure supplement 1 ). There are also multiple interactions within this region without convergent CTCF binding sites, suggesting interactions with Irf8 promoter in a CTCF independent manner, such as by TF binding, active histone modifications and gene transcription ( Figure 1B and Figure 1—figure supplement 1 ; Owens et al, 2022 ).…”

A lncRNA identifiesIRF8enhancer element in negative feedback control of dendritic cell differentiation

“…Interestingly, most of the IRF8 flanking enhancers (Durai et al, 2019; Grajales-Reyes et al, 2015; Murakami et al, 2021; Schönheit et al, 2013) are located within convergent CTCF binding sites upstream and downstream of the IRF8 gene (Figure 1B and Figure S1). There are also multiple interactions within this region without convergent CTCF binding sites, suggesting interactions with IRF8 promoter in a CTCF independent manner, such as by TF binding, active histone modifications and gene transcription (Figure 1B and Figure S1) (Owens et al, 2022).…”

TIMP3 Gene Polymorphisms of -1296 T > C and -915 A > G Increase the Susceptibility to Arsenic-Induced Skin Cancer: A Cohort Study and In Silico Analysis of Mutation Impacts

“…E2F8 is a transcription repressor that antagonizes E2F1 in regulating the cell cycle, apoptosis, and tumor promotion [ 29 ]. RUNX1 was initially described as a critical regulator of developmental hematopoiesis [ 30 ]. Recently, RUNX1 was also associated with solid tumor development in the skin, lungs, intestines, and breast [ 42 ].…”

“…( b ) TF-binding site scores were obtained using the JASPAR scan tool for the wild-type and mutant forms of each studied single-nucleotide polymorphism (SNP). For references of gene function: BACH2 [ 25 ], MEIS2 [ 26 ], NFE2L2 [ 27 ], PBX2 [ 28 ], E2F8 [ 29 ], RUNX1 [ 30 ]. N.A., not available.…”