Large-scale dissection suggests that ultraconserved elements are dispensable for mouse embryonic stem cell survival and fitness

ABSTRACT

Ultraconserved elements (UCEs) are genomic regions that are highly conserved among vertebrates and are under extreme purifying selection. Despite this extreme conservation, the biological importance of UCEs has remained elusive thus far. Here, we investigate the relevance of 93 UCEs for survival and fitness of mouse embryonic stem cells (mESCs) utilizing CRISPR/Cas9 technology. Surprisingly, systematic analyses of deletion clones revealed no measurable effects on mESC viability, proliferation or morphology. Furthermore, growth of homozygous UCE knockout clones under stress conditions or growth in direct competition with wild-type mESC revealed no phenotypic difference. Likewise, no difference in differentiation potential and on the expression level of key marker genes of differentiation was observed upon embryonic body formation. While functional overlap (redundancy) between several UCEs has been proposed to account for the absence of effects in single UCE knockouts, we obtained phenotypically normal mESC clones carrying up to five homozygous UCEs deletions, challenging this model. Finally, integration of additional UCE copies into the genome of mESCs also revealed no adverse effects. In summary, under all tested experimental conditions, UCEs appear to be dispensable for fitness, viability and differentiation potential of mESCs, despite their strong conservation.