We are interested in understanding how the epigenome is established during human development and stem cell differentiation, and how epigenetic information changes over the life course of an individual.
We propose that there are two main phases of epigenome remodelling during the early stages of development. The acquisition phase occurs during the transition of epiblast cells between pre-implantation and post-implantation stages (largely recapitulated by naïve to primed pluripotent state transitions) and is associated with a dramatic and global change in the epigenome. For example, DNA methylation levels increase from ~30% to ~70%, gene promoters acquire specific histone modifications such as H3K27me3, and higher-order chromatin becomes more structured. This remodelling occurs rapidly (within ~24 hours in mouse development) and coincides with major metabolic and signalling changes. The purpose of these changes is probably to help reconfigure the genome to be responsive to inductive signals in preparation for cell differentiation. The maturation phase occurs during the transition from undifferentiated postimplantation epiblast to differentiated cells of the three germ layers (recapitulated by primed pluripotent cells as they undergo lineage specification) and involves the relocation of epigenetic marks and the rewiring of DNA interaction loops. This phase of epigenetic remodelling probably helps to stabilise the genome in response to lineage-specific cues, and supports robust cell differentiation.
Epigenetic changes during the acquisition phase - a tale of two states
We are currently developing new strategies to study how the human epigenome is remodeled. One approach is based on the identification of cell-surface markers that enable the isolation and characterisation of specific cell types during the transition between naïve and primed pluripotent states (Collier, Panula et al., Cell Stem Cell 2017) (see figure below). This will allow us to look much more precisely at the events that occur during epigenome remodeling and we hope to better understand the mechanisms that drive these events.
Naïve and primed pluripotent stem cells provide very useful models to investigate epigenetic events in human development. For example, together with the Reik lab, we have recently profiled DNA methylation changes that occur during naïve cell to primitive germ cell differentiation (von Meyenn et al., Developmental Cell 2016). And with colleagues in Paris, we have discovered a human-specific, X-chromosome pre-inactivation state, which is defined by the co-expression of two opposing long, non-coding, RNAs XIST and XACT, and this pattern is tightly linked to pluripotent state in human embryos and stem cell lines (Vallot et al., Cell Stem Cell 2017) (see image below). As XACT exists in humans but not in mice, this works exemplifies that mechanisms of epigenetic regulation can vary substantially between species.
Epigenetic changes during the maturation phase - controlling gene activity in human development
Focusing on the regulation of early lineage-decisions, we have recently characterised the first EZH2-deficient human pluripotent stem cells and found there is a broad conservation of Polycomb-group protein function in controlling cell-fate decisions and transcriptional programs during early human development (Collinson et al., Cell Reports 2016) (see figure below). We also uncovered unexpected human-specific differences that result in a more severe self-renewal and proliferation phenotype than that of PRC2-deficient mouse ESCs.
Defining new connections between pluripotency and genome organisation
One topic of interest is to better understand what triggers the epigenome to be remodeled at specific stages of development. On these lines, we have recently found that pluripotency transcription factors provide a direct connection between cell-state and chromatin organisation through modulation of heterochromatin regions in embryonic stem cells (Novo et al., Genes & Development 2016) (see figure below). We are now investigating how changes in heterochromatin organisation might affect centromere function and chromosome stability in pluripotent cells and during cell reprogramming. We are also interested in how pluripotency factors might shape DNA looping interactions within the 3D nuclear space.
Epigenetic changes associated with the decline of stem cell function upon ageing
We are also interested in understanding how epigenetic information changes over the life course of an individual. For example, adult neural stem progenitor cell (NSPC) function declines with ageing but the underlying molecular causes are largely unknown. We are examining the intrinsic changes that occur upon NSPC ageing through genome-wide transcriptional, histone methylation and DNA methylation analyses of NSPCs derived from the subventricular zone of adult (3 months old) and aged (18 months old) mice. We found that the genome-wide profiles were largely unchanged upon ageing, however, within this large data set, we also identified significant transcriptional and epigenetic differences at several hundred loci. We are now following up on these results to see if we can uncover new regulators of age-associated neurogenic decline and neural stem cell function.