Abstract
Enhancer activity drives cell differentiation and cell fate determination, but it remains unclear how enhancers cooperate during these processes. Here we investigate enhancer cooperation during transdifferentiation of human leukemia B-cells to macrophages. Putative enhancers are established by binding of the pioneer factor C/EBPα followed by chromatin opening and enhancer RNA (eRNA) synthesis from H3K4-monomethylated regions. Using eRNA synthesis as a proxy for enhancer activity, we find that most putative enhancers cooperate in an additive way to regulate transcription of assigned target genes. However, transcription from 136 target genes depends exponentially on the summed activity of its putative paired enhancers, indicating that these enhancers cooperate synergistically. The target genes are cell type-specific, suggesting that enhancer synergy can contribute to cell fate determination. Enhancer synergy appears to depend on cell type-specific transcription factors, and such interacting enhancers are not predicted from occupancy or accessibility data that are used to detect superenhancers.
Highlights
Enhancers are cis-regulatory DNA elements that drive the transcription activity of target gene promoters (Beagrie and Pombo, 2016; Long et al, 2016; Spitz and Furlong, 2012)
To study the temporal order of gene regulatory events during transdifferentiation of human precursor leukemia B cells to macrophage-like cells, the master transcription factor (TF) C/EBPa fused to estrogen receptor were activated by addition of beta estradiol (Figure 1A)
As revealed by Fluorescence-activated cell sorting (FACS) analysis of the macrophage marker CD14 and the B cell marker CD19, as well as additional markers monitored by RTqPCR, transdifferentiation was efficient and occurred in a nearly synchronous manner (Figure 1—figure supplement 1A and B)
Summary
Enhancers are cis-regulatory DNA elements that drive the transcription activity of target gene promoters (Beagrie and Pombo, 2016; Long et al, 2016; Spitz and Furlong, 2012). It has been suggested that the individual constituent enhancers of such clusters cooperate in a synergistic manner to activate target genes (Hnisz et al, 2017; Shin et al, 2016). Evidence for enhancer–enhancer interactions was obtained in Drosophila (Lim et al, 2018) Despite these studies, the functional cooperation between enhancers over time has not yet been studied in a native genomic context and a genome-wide manner. At the end of the process, cells gain the characteristics of macrophages, including acquisition of adherence, phagocytic activity, and inflammatory response (Gaidt et al, 2016; Rapino et al, 2013) Due to these properties, the C/EBPa-induced transdifferentiation system enables quantitative data acquisition and analysis and is ideally suited for addressing mechanistic questions on enhancer function and cooperation in vivo. For about one-fifth of the enhancers tested (136 in total), the change in transcription activity of the target gene was larger than the change attributable to the sum of the enhancer activities, indicating that enhancers cooperate synergistically at these loci to drive target gene transcription
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
