Abstract
Retinoic acid (RA) induces rapid differentiation of embryonic stem cells (ESCs), partly by activating expression of the transcription factor Hoxa1, which regulates downstream target genes that promote ESCs differentiation. However, mechanisms of RA-induced Hoxa1 expression and ESCs early differentiation remain largely unknown. Here, we identify a distal enhancer interacting with the Hoxa1 locus through a long-range chromatin loop. Enhancer deletion significantly inhibited expression of RA-induced Hoxa1 and endoderm master control genes such as Gata4 and Gata6. Transcriptome analysis revealed that RA-induced early ESCs differentiation was blocked in Hoxa1 enhancer knockout cells, suggesting a requirement for the enhancer. Restoration of Hoxa1 expression partly rescued expression levels of ∼40% of genes whose expression changed following enhancer deletion, and ∼18% of promoters of those rescued genes were directly bound by Hoxa1. Our data show that a distal enhancer maintains Hoxa1 expression through long-range chromatin loop and that Hoxa1 directly regulates downstream target genes expression and then orchestrates RA-induced early differentiation of ESCs. This discovery reveals mechanisms of a novel enhancer regulating RA-induced Hoxa genes expression and early ESCs differentiation.
Highlights
Embryonic stem cells (ESCs) have the potential for both self-renewal and differentiation
We identify a distal enhancer that maintains Hoxa1 expression through a long-range chromatin loop, thereby regulating targets that function in Retinoic acid (RA)-induced early differentiation of ESCs
In WT cells, a distal enhancer interacts with the Hoxa1 locus through a chromatin loop to maintain Hoxa1 expression
Summary
Embryonic stem cells (ESCs) have the potential for both self-renewal and differentiation. Master control genes, which encode transcription factors that directly bind target gene promoters, must be expressed at appropriate stages. Among these are Oct, Nanog and Sox, which are essential for the maintenance of pluripotency [1,2,3], and Gata and Gata, which regulate endoderm development [4,5,6]. Recent studies show that expression of master regulatory genes is controlled by functional elements through long-range chromatin interactions Functional elements such as enhancers play a key role in maintaining their expression: for instance, Klf mediates changes in chromatin structure at the Oct locus to maintain ESCs pluripotency, an interaction that enhances reprogramming efficiency [7]. Knockout of multiple Gli enhancers promotes abnormal limb development in mouse [10]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
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.
