The evolution and functional plasticity of vertebrate class V POU proteins in pluripotency

Oct4, a transcription factor belonging to the fifth class of POU proteins (POUV), plays essential roles in the maintenance of pluripotency, differentiation and the generation of induced pluripotent stem cells (iPSCs). Oct4 regulates two levels of pluripotency, which are distinguished by their gene expression profiles and epigenetic status, namely the naïve and primed state of pluripotency. Embryonic stem cells (ESCs) and embryonic germ cells (EGCs), which are isolated from inner cell mass and primordial germ cells in the embryo, respectively, are in vitro models in which the naïve state is propagated through self-renewal. Epiblast stem cells (EpiSCs) and traditional human ESCs have gene expression profiles that are closest to the post-implantation epiblast, which is closer to embryonic differentiation, and exhibit a primed state of pluripotency. As Oct4 is important for pluripotency in all these cell types, where it regulates different targets, it appears to have two distinct sets of functions, namely germ cell/naïve ESC-like activity and epiblast/primed pluripotency-like activity. Based on protein sequences and syntenic gene analysis, Oct4/POUV homologs of jawed vertebrates can be classified into two subfamilies: POU5F1 and POU5F3, which are thought to originate from a genome duplication event that occurred in a common ancestor. Most extant vertebrates have lost one of these paralogs, while a small fraction, including coelacanths, axolotls, turtles, and marsupials, retains both POUV forms. In my thesis, I investigated the gene duplication event that underlies divergence of POU5F1 and POU5F3 in both expression pattern and specialised function. In particular, I focused on species that have retained both genes and asked whether POUV functional divergence correlates with ancestral origin. To test the function of POU5F1 and POU5F3, I substituted endogenous mouse Oct4/Pou5f1 with different POUV proteins using a cell line in which endogenous Oct4 expression can be silenced with tetracycline (ZHBTc4). Results showed that POU5F1 proteins had a greater capacity to support naïve ESC pluripotency and self-renewal than POU5F3 proteins. Global transcriptome analysis of the POUV-rescued ESC lines revealed that coelacanth POU5F1 protein regulates gene expression in a similar manner to mouse Oct4, in that genes involved in stem cell maintenance, reproduction and development are upregulated in ESCs rescued by POU5F1, but not POU5F3. Coelacanth POU5F3 rescued lines, however, expressed genes involved in various cell differentiation programs, including cell adhesion (e.g. E-cadherin and N-cadherin). This suggests that POU5F3 plays a role in primed pluripotency, while POU5F1 regulates naïve pluripotency. However, there is one POU5F3 factor that rescues ESCs like Oct4, the Xenopus gene Xlpou91 (Pou5f3.1). In Xenopus, a further duplication of POU5F3 gene enabled specialization, and Xlpou91 is expressed specifically in the primordial germ cells. Xlpou25 (Pou5f3.2) exhibits epiblast-specific activities and lacks the capacity to maintain naïve ESC pluripotency, similar to other POU5F3 proteins. This functional distinction between the different Xenopus POUV paralogs enabled us to address how specific Oct4 functions (germ cell-like versus epiblast-like activity) are related to the induction of pluripotency. To address this question, mouse Oct4 was replaced by either Xlpou91 or Xlpou25 in murine cellular reprogramming using a Nanog-GFP reporter line to monitor iPSC generation. Results showed that Xlpou91 and mouse Oct4 were required at similar levels to reprogram somatic cells toward iPSCs and reprogrammed cells emerged with similar kinetics. Conversely, Xlpou25 was required at higher expression levels and the resulting iPSCs appeared at a later timepoint, while the pluripotent population in these cultures appeared to be less stable and more prone to differentiate. I found that this phenotype of enhanced differentiation in Xlpou25 reprogrammed cultures may be a product of a different set of immediate early genes induced at the first stages of differentiation. Global transcriptome analysis of the naïve ESC-like pluripotent subpopulation of these iPSC lines confirmed the capacity of all Xenopus POUVs to drive reprogramming towards the pluripotent state. However, the gene sets induced by both Xlpou91 and mouse Oct4, but not Xlpou25, were somewhat enriched for genes involved in reproduction, emphasizing the segregated role of Xlpou91 as a germ cell specific POUV protein. Lastly, I explored the evolutionary origin of these two POUV paralogs and attempted to identify a POUV-related gene in jawless vertebrate (cyclostomes). Based on in silico analysis of genomic and transcriptome databases, my collaborators and I were able to identify a single POUV gene in the Japanese/arctic lamprey, thus providing the first insight into the origin of gnathosome POUV genes.