RESEARCH

Current Research Projects

Project1: Mechanisms of Zygotic Genome Activation - A Major Nuclear Reprogramming Event

How does the naive genome in the early embryo progressively undergo a series of modifications to control gene expression in “time and space” such that proper cellular differentiation programs are correctly implemented? We investigate the mechanisms of the earliest genome activation to understand how the control of cell fates is transferred from maternal genes to zygotic genes during this period, and when transcription factors specify cell fates and establish epigenetic marks on the embryonic genome. We investigate how the chromatin dynamics are influenced by the coordinated action of maternal and zygotic transcription factors.

During embryonic endoderm formation, Foxh1 transcription factor selectively binds the genome, premarking developmental genes for activation beginning with the onset of zygotic gene activation. A cohort of maternal transcription factors interacts with Foxh1 around the CRMs harboring OVF (Otx/Tbox/Fox) triple binding motifs, prior to the deposition of enhancer marks. The OVF motifs cluster around endoderm specific genes, forming super enhancers, which is the docking sites for other zygotically active mesendodermal transcription factors. Our data support the view that the coordinated binding of maternal transcription factors drives early lineage specification to select CRM clusters frequently associated with super-enhancers to initiate specific developmental gene regulatory programs.

Paraiso KD, Blitz IL. Cho KWY. (2021) Maternal and zygotic factors sequentially shape the tissue regionalization of chromatin landscapes in early vertebrate embryos. 2021. BioRxiv. doi: https://doi.org/10.1101/2021.04.14.439777

Paraiso, K,, I L Blitz, Coley M, Cheung, Sudoh N., Taira, M., and Cho K.W.Y. (2019).Endodermal maternal transcription factors establish super enhancers during zygotic genome activation. Cell Reports 27:2962-2977. PMID: 31167141

Paraiso, K,, Blitz, IL., Zhou, J., and Cho K.W.Y. (2019). Morpholinos do not elicit an innate immune response during early Xenopus embryogenesis. Developmental Cell 49:643-650. PMID: 31112700

Charney, R.M., Forouzmand, E., Cho, J.S., Cheung, J., Paraiso, K.D., Yasuoka, Y., Takahashi, S., Taira, M., Blitz, I.L., Xie, X. and. Cho K.W.Y. (2017). Foxh1 occupies cis-regulatory modules prior to dynamic transcription factor interactions controlling the mesendoderm gene program. Developmental Cell 40:1-13. PMID:28325473.

Project 2: Transcriptomics and Epigenomics Controlling Embryo Development:

Gene regulatory networks consist of interactions between transcription factors and enhancers, and are responsible for the control of gene expression throughout the genome, in every biological process. We view that understanding the logic and function of GRNs is fundamental to biology, and have two major projects in this area. First, we perform and collect hundreds of bulk RNA-seq and ChIP-seq, ATAC-seq and DNase-seq datasets, and apply the state of the art Self-Organizing Map analysis to create interactome graph linking transcription factor inputs and target gene expression outputs, generating thousands of genomic links to understand the network structures that control endoderm development. Second, due to recent technological advances to analyze the complexities of biological systems at the single-cell level, we examine how different cell states arise to create various endodermal organ buds during embryonic endoderm development by applying single cell RNA-seq and ATAC-seq in both Xenopus and ES cells.

Jansen C, Paraiso KD, Zhou JJ, Blitz IL, Fish MB, Charney RM, Cho JS, Yasuoka Y, Sudou N, Bright AR, Wlizla M, Veenstra GJC, Taira M, Zorn AM, Mortazavi A, Cho KWY. (2022) Uncovering the mesendoderm gene regulatory network through multi-omic data integration. Cell Reports. 38(7):110364.

Charney RM, Paraiso KD, Blitz IL, Cho KWY. (2017). A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs. Seminars in Cell Dev Biol.66:12-24. PMID: 28341363

Owens, N.D.L. 1, Blitz, I.L.1, Lane, M.A., Overton, J.D., Gilchrist, M.J#, Cho, K.W.Y#.,Khokha, M.K.#(2016). Embryogenesis kinetics measured by high-resolution absolute quantitation of transcripts. 1: co-first authros, contributed equally. # co-senior authors. Cell Reports 14, 632-647.PMID: 26774488

Yasuoka, Y., Suzuki, Y., Takahashi, S., Sudou, N., Haramoto, Y., Cho, KW., Asashima, M., Sugano, S., and Taira, M. (2014). Otx2 and TLE/Groucho occupancy marks tissue-specific cis-regulatory modules for head specification. Nature Communications, 9:4322.

Project 3: Spatiotemporal mapping of enhancer activity in whole embryo: Newly Started Project

Typical mammalian genomes contain hundreds of thousands of CRMs distributed across large genomic distances that act collectively and collaboratively to produce differential gene expression patterns of extreme complexity. At present, our understanding of the biological roles of most of these CRMs remains limited. For instance, how are specific CRMs selected to regulate a given gene's expression? How do different CRMs coordinate and activate various target genes in a spatially and temporally regulated manner? Our lack of understanding is in large part due to current limitations in delivering simultaneous experimental measurements of the activities of large numbers of CRMs during animal development. We will use Xenopus tropicalis gastrula-stage embryos as the model system for generating a system-level understanding of CRM activities in single cells because of the key phylogenetic position amphibians occupy in the vertebrate evolutionary lineage. The approach proposed here would be much more difficult to perform in mammals, because their embryos are not easily accessed for certain necessary experimental manipulations, and because mammalian embryo availability is rate limiting for some genomic work.

Project 4: Mammalian Pre and Peri-implantation Development:

The standard non-invasive method to assess embryo quality and viability relies on the visual inspection of embryo morphology according to predefined criteria. Development of more quantitative and objective means for assessing embryo quality that are simpler, safer, and faster could provide significant advantages in assisted reproduction. We apply the non-invasive and label-free phasor-FLIM (Fluorescence Lifetime Imaging Microscopy) approach to preimplantation mouse embryos. FLIM produces an image based on the differences in the exponential decay rate of the fluorescence from a sample. We identify endogenous fluorescent biomarkers (metabolic signatures) of preimplantation embryos for embryo quality assessment. Our goals are to determine the best parameters in phasor-FLIM for predicting preimplantation embryo quality.

Cang Z, Wang Y, Cho KWY, Holmes W, Nie Q., (2020). A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development
PLoS Comp Biol. https://doi.org/10.1371/journal.pcbi.1008571 PMID: 33684098.

Ning Ma, Nabora Reyes de Mochel, Paula Pham Tae Yoo, Ken Cho#, Michelle Digman#.(2019). Label-free assessment of pre-implantation embryo quality by the Fluorescence Lifetime Imaging Microscopy (FLIM)-phasor approach. (# shared senior authors). Scientific Reports, 9:13206

Holmes,W.R., Mochel, S., Wang, Q., Du, H., Cinquin, O., Cho, K.W*., Nie, Q*. *contributed equally, co-senior authors. (2017). Intracellular noise aids construction of early embryonic structures..PLoS Comput Biol. 13(1):e1005320.PMID: 28114387

Reyes de Mochel, NS., Luong, M., Chiang, M., Javier, A.L., Luu, E., Cinquin, O., and Cho, KWY. (2015). BMP signaling regulates both cell proliferation and ICM lineage commitment in preimplantation-stage mouse embryos. Dev Biol. 397: 45-55.