Mapping the Effects of Genetic Variation on Chromatin State and Gene Expression Reveals Loci That Control Ground State Pluripotency

• Published in: Cell stem cell 2020-09, Vol.27 (3), p.459-469.e8
• Main Authors: Skelly, Daniel A., Czechanski, Anne, Byers, Candice, Aydin, Selcan, Spruce, Catrina, Olivier, Chris, Choi, Kwangbom, Gatti, Daniel M., Raghupathy, Narayanan, Keele, Gregory R., Stanton, Alexander, Vincent, Matthew, Dion, Stephanie, Greenstein, Ian, Pankratz, Matthew, Porter, Devin K., Martin, Whitney, O’Connor, Callan, Qin, Wenning, Harrill, Alison H., Choi, Ted, Churchill, Gary A., Munger, Steven C., Baker, Christopher L., Reinholdt, Laura G.
• Format: Article
• Language: English
• Subjects: Animals; Cell Differentiation; Chromatin - genetics; chromatin accessibility; Diversity Outbred; Gene Expression; Genetic Variation; Glycogen Synthase Kinase 3; ground state pluripotency; Lifr; mESC; metastability; Mice; Pluripotent Stem Cells; quantitative trait locus
• ISSN: 1934-5909; 1875-9777
• DOI: 10.1016/j.stem.2020.07.005

Mouse embryonic stem cells (mESCs) cultured in the presence of LIF occupy a ground state with highly active pluripotency-associated transcriptional and epigenetic circuitry. However, ground state pluripotency in some inbred strain backgrounds is unstable in the absence of ERK1/2 and GSK3 inhibition. Using an unbiased genetic approach, we dissect the basis of this divergent response to extracellular cues by profiling gene expression and chromatin accessibility in 170 genetically heterogeneous mESCs. We map thousands of loci affecting chromatin accessibility and/or transcript abundance, including 10 QTL hotspots where genetic variation at a single locus coordinates the regulation of genes throughout the genome. For one hotspot, we identify a single enhancer variant ∼10 kb upstream of Lifr associated with chromatin accessibility and mediating a cascade of molecular events affecting pluripotency. We validate causation through reciprocal allele swaps, demonstrating the functional consequences of noncoding variation in gene regulatory networks that stabilize pluripotent states in vitro. [Display omitted] •Genetically diverse mouse ESCs have distinct molecular and functional properties•Genetic mapping reveals thousands of loci that affect chromatin accessibility•Ten QTL hotspots coordinate genome-wide chromatin and/or gene expression changes•A Chr15 QTL harbors an SNV that drives changes in Lifr transcript levels and function Mouse ESCs occupy a highly stable pluripotent ground state, which can be unstable in some genetic backgrounds. Skelly et al. used an unbiased genetic approach to reveal how genetic variation influences chromatin state and gene expression and validate a single enhancer variant upstream of Lifr that affects ground state stability.