In a functional genomics screen of mouse embryonic stem cells (ESCs) with nested hemizygous chromosomal deletions, we reveal that ribosomal protein (RP) genes are the most significant haploinsufficient determinants for embryoid body (EB) formation. Hemizygocity for three RP genes (Rps5, Rps14, or Rps28), distinguished by the proximity of their corresponding protein to the ribosome's mRNA exit site, is associated with the most profound phenotype. This EB phenotype was fully rescued by BAC or cDNA complementation but not by the reduction of p53 levels, although such reduction was effective with most other RP-deleted clones corresponding to non-mRNA exit-site proteins. RNAsequencing studies further revealed that undifferentiated ESCs hemizygous for Rps5 showed reduced expression levels of several mesoderm-specific genes as compared with wild-type counterparts. Together, these results reveal that RP gene dosage limits the differentiation, not the self-renewal, of mouse ESCs. They also highlight two separate mechanisms underlying this process, one of which is p53 independent.embryonic stem cells | differentiation | embryoid body | ribosomal proteins E mbryonic stem cell (ESC) fate is intricately controlled at the transcriptional level by factors such as Oct4 (Pou5f1), Sox2 and Nanog (1-3), Dax1, Rex1, and SalI (reviewed in ref. 4), and the Mediator complex (3, 5, 6). Although much progress has been made on the identification of the transcriptional circuitry that defines pluripotency, the regulation of mRNA translation and posttranslational protein modifications currently are considered in this context only as fine-tuning to balance protein production and activity (7).ESC self-renewal can be assessed readily by their ability to give rise to undifferentiated progeny in a clonal fashion. Similarly, in the absence of leukemia inhibitory factor (LIF) and bone morphogenetic protein signaling, ESC pluripotent potential can be investigated in vitro by initiating differentiation of the three germ layers using an embryoid body (EB) formation assay (8, 9).To identify novel regulators of ESC fate, we developed a retrovirus-based methodology that randomly generates hemizygous chromosomal deletions with increasing size (nested) (Fig. 1A and detailed in ref. 10). Using this method, we reported the generation of a library of 1,307 ESC clones covering more than 25% of the mouse genome (the DelES library) along with an improved methodology for BAC recombineering and complementation (11). Phenotypical characteristics and a genetic map of all clones in our DelES collection are available at www.bioinfo.iric.ca/deles.Here, we report the integrative analysis linking the physical mapping to phenotype for all 1,307 clones in our library, documenting that genes involved in ribosome biogenesis and function are key players in ESC fate. We tested this hypothesis extensively in functional studies and identified a p53-independent response to ribosomal stress for mRNA exit-site ribosomal proteins (RPs).
ResultsGene Ontology Term Analysis Identifies...