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

Abstract

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. ll

Genetic control of pluripotency epigenome determines differentiation bias in mouse embryonic stem cells

“…This approach showed that chromatin accessibility at pluripotent TF motifs are higher in B6 compared to D2, indicating other trans acting chromatin regulation may determine pluripotent spectrum. We identified 6 QTL hotspots that alter binding of naïve 57 , as well as association with differences in priming sites of meiotic recombination 49 and stabilization of ground state pluripotency 14 . Notably, a single KZFP contained within our Chr 13 hotspot QTL interval was shown to be causal in the progression of a lupus phenotype 57 .…”

“…For each biological replicate ESC ChIP-seq library, 10 million cells were harvested and fixed as previously described 14 . Cell lysis, chromatin fragmentation, dialysis, and immunoprecipitation was performed as described 67 .…”

“…Further, success in derivation and differentiation of human induced PSCs (hiPSCs) and ESCs (hESCs) are influenced by genetic background [8][9][10][11][12][13] . While we 14 and others 15 have recently investigated how genetic variation impacts pluripotency, less is understood about how genetic backgrounds influence cell state transitions.…”

“…Transit through formative pluripotency is required for multi-lineage competency [21][22][23] , and this state can be modeled in vitro by EpiLCs 21 . While culture conditions can provide external signaling cues that positions a cell along the pluripotency spectrum 22 , variability in acquisition of desired pluripotent states is, in part, dependent on the ESC's strain of origin 6,14,15,[24][25][26][27] . Importantly, differentiation propensity to specific germ layers has been linked to the origin of ESCs within this pluripotency spectrum 28 .…”

A Bayesian model selection approach to mediation analysis

“…Applications of mediation analysis to large scale genetic and molecular profiling data have used modified versions of the traditional tests described above. Approximations to CS have been used in the multi-parent Collaborative Cross (CC [12,6,13]) and Diversity Outbred mouse populations (DO [14,5,15,16]). These studies identified QTL for gene expression (eQTL), protein abundance (pQTL), and chromatin accessibility (cQTL).…”