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Developmental and Cell Biology
Center for Complex Biological Systems
​University of California, Irvine

      Systems Biology of Vertebrate Embryogenesis
 
Genomics approaches have contributed substantially to the study of early embryogenesis and development – from the level of transcriptional regulation to cellular differentiation and patterning. We now know that embryonic development is network-based and involves dynamic interactions between transcription factors and epigenetic states of chromatin. Our goals are to address the following major issues in developmental biology. 
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  1. Uncover the mechanism of zygotic genome activation, the first transcriptional event occurring after fertilization. 
  2. Apply systems approaches to embryogenesis to construct in silico biological models of the developing embryos at the organismal level.
  3. Apply cutting-edge genomic and imaging approaches to uncover the spatio-temporal dynamic (4D) events of embryonic development at single cell resolution. 



​Research Area: Keywords
  • ​Systems Biology of Development
  • Gene Regulatory Networks
  • Epigenomics and Transcriptomics
  • Preimplantion Mammalian Development
  • Growth Factor Signaling
  • Vertebrate Embryology
  • Xenopus Tropicalis







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News

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Jansen et al.,  published in Cell Reports, 2022: 
We developed a method of integrating large genomic data sets (over 150) derived from different data types and  report on building a highly-accurate mechanistic GRN.
"Uncovering the mesendoderm gene regulatory network through multi-omic data integration"
​Cell Rep. 38(7):110364.


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​Zhou et al., uploaded to BioRxiv (2022).
Histone acetylation is critical in regulating the transcriptional activities of the embryonic genome.  We  report how developing embryos regulate the spatiotemporal dynamic states of histone acetylation during embryogenesis .
"Histone deacetylase 1 maintains lineage integrity through histone acetylome refinement during early embryogenesis"
https://doi.org/10.1101/2022.05.05.490762

Han  et al.,. (2022). Nat Cell Biol. 
Collaborative work led to the discovery of a new role of Hippo pathway in heavy metal response.
"The Hippo pathway kinases LATS1 and LATS2 attenuate cellular responses to heavy metals through phosphorylating MTF1. "
doi: 10.1038/s41556-021-00813-8

Cho KWY, Blitz IL. (2022), (Review)
Basic concepts on gene regulatory network and its impacts on biomedical sciences
"Gene regulatory networks controlling Xenopus embryogenesis" Chapter 13 in Xenopus, from basic biology to disease models in the genomic era, Ed: Moody, S. and Faisod.

Paraiso KD, Blitz IL. Cho KWY. BioRxiv 2021, 
We report the importance of maternal transcription factors for forming tissue type specific super-enhancers.
"Maternal and zygotic factors sequentially shape the tissue regionalization of chromatin landscapes in early vertebrate embryos." doi: https://doi.org/10.1101/2021.04.14.439777

Blitz and Cho, 2021, Curr Top Dev Biol. (Review)
Comprehensive review on zygotic genome activation in Xenopus. 
Control of zygotic genome activation in Xenopus,   145:167-204.​
Links:
PubMed, Google Scholar, Xenbase, National Xenopus Resource, Gene Expression Charting Tools