Professional Education

  • Bachelor of Science, Simon Fraser University (2011)
  • Doctor of Philosophy, University of California San Francisco (2017)

All Publications

  • GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency CELL STEM CELL Chen, A. F., Liu, A. J., Krishnakumar, R., Freimer, J. W., DeVeale, B., Blelloch, R. 2018; 23 (2): 226-+


    The enhancer landscape of pluripotent stem cells undergoes extensive reorganization during early mammalian development. The functions and mechanisms behind such reorganization, however, are unclear. Here, we show that the transcription factor GRHL2 is necessary and sufficient to activate an epithelial subset of enhancers as naive embryonic stem cells (ESCs) transition into formative epiblast-like cells (EpiLCs). Surprisingly, many GRHL2 target genes do not change in expression during the ESC-EpiLC transition. Instead, enhancers regulating these genes in ESCs diminish in activity in EpiLCs while GRHL2-dependent alternative enhancers become activated to maintain transcription. GRHL2 therefore assumes control over a subset of the naive network via enhancer switching to maintain expression of epithelial genes upon exit from naive pluripotency. These data evoke a model where the naive pluripotency network becomes partitioned into smaller, independent networks regulated by EpiLC-specific transcription factors, thereby priming cells for lineage specification.

    View details for DOI 10.1016/j.stem.2018.06.005

    View details for Web of Science ID 000440583900013

    View details for PubMedID 30017589

  • The impact of microRNAs on transcriptional heterogeneity and gene co-expression across single embryonic stem cells. Nature communications Gambardella, G., Carissimo, A., Chen, A., Cutillo, L., Nowakowski, T. J., di Bernardo, D., Blelloch, R. 2017; 8: 14126


    MicroRNAs act posttranscriptionally to suppress multiple target genes within a cell population. To what extent this multi-target suppression occurs in individual cells and how it impacts transcriptional heterogeneity and gene co-expression remains unknown. Here we used single-cell sequencing combined with introduction of individual microRNAs. miR-294 and let-7c were introduced into otherwise microRNA-deficient Dgcr8 knockout mouse embryonic stem cells. Both microRNAs induce suppression and correlated expression of their respective gene targets. The two microRNAs had opposing effects on transcriptional heterogeneity within the cell population, with let-7c increasing and miR-294 decreasing the heterogeneity between cells. Furthermore, let-7c promotes, whereas miR-294 suppresses, the phasing of cell cycle genes. These results show at the individual cell level how a microRNA simultaneously has impacts on its many targets and how that in turn can influence a population of cells. The findings have important implications in the understanding of how microRNAs influence the co-expression of genes and pathways, and thus ultimately cell fate.

    View details for DOI 10.1038/ncomms14126

    View details for PubMedID 28102192

    View details for PubMedCentralID PMC5253645

  • FOXD3 Regulates Pluripotent Stem Cell Potential by Simultaneously Initiating and Repressing Enhancer Activity CELL STEM CELL Krishnakumar, R., Chen, A. F., Pantovich, M. G., Danial, M., Parchem, R. J., Labosky, P. A., Blelloch, R. 2016; 18 (1): 104–17


    Early development is governed by the ability of pluripotent cells to retain the full range of developmental potential and respond accurately to developmental cues. This property is achieved in large part by the temporal and contextual regulation of gene expression by enhancers. Here, we evaluated regulation of enhancer activity during differentiation of embryonic stem to epiblast cells and uncovered the forkhead transcription factor FOXD3 as a major regulator of the developmental potential of both pluripotent states. FOXD3 bound to distinct sites in the two cell types priming enhancers through a dual-functional mechanism. It recruited the SWI/SNF chromatin remodeling complex ATPase BRG1 to promote nucleosome removal while concurrently inhibiting maximal activation of the same enhancers by recruiting histone deacetylases1/2. Thus, FOXD3 prepares cognate genes for future maximal expression by establishing and simultaneously repressing enhancer activity. Through switching of target sites, FOXD3 modulates the developmental potential of pluripotent cells as they differentiate.

    View details for DOI 10.1016/j.stem.2015.10.003

    View details for Web of Science ID 000372321300016

    View details for PubMedID 26748757

    View details for PubMedCentralID PMC4775235