HomeFacultyKen Cho

Ken Cho


Ken Cho, Ph.D.
ProfessorKen Cho, PhD

4410 Nat Sci II
University of California Irvine
Irvine, CA 92697

Lab Tel: (949) 824-7950
Office Tel: (949) 824-4067
Email: kwcho, please place @uci.edu after kwcho
Website: http://897788976207812023.weebly.com

Member: Center for Complex Biological Systems, Institute for Genomics and Bioinformatics,  UCI Cancer Center

Research Keywords: 

Gene regulatory network, transcriptome, epigenetic, zygotic genome activation, super-enhancers, pioneer transcription factors, preimplantation mammalian development, fluorescent lifetime imaging analysis, germ layer specification, endoderm development.


Research Topics:

Building Gene Regulatory Networks Regulating Endoderm Development using ChIP-seq, RNA-seq and ATAC-seq

Metazoan development begins with a single totipotent cell that gives rise to numerous cell types, each expressing lineage-restricted sets of genes. The activation of gene transcription in the embryo relies on maternal transcription factors (TFs), which sit high in the regulatory hierarchy to coordinate the gene regulatory cascades that lead to stereotypical development of embryos. Since TFs drive lineage-specific transcription programs by binding CRMs dispersed throughout the genome, a major question that remains to be addressed is how maternal TFs bind a subset of sequence motifs in chromatin to endow the transcriptional responses that initiate germ layer specification. We address these fundamentally important biological questions by going back to the earliest stages of embryonic development when transcription from the embryonic genome has not yet begun, the number of different cell types is small, and the genome appears relatively naïve.  Our goal is to elucidate the mechanisms controlling endoderm formation by combining experimental (e.g., ChIPseq and RNAseq) and computational approaches. Production of a thorough endodermal gene regulatory network will provide a useful framework for prediction, that is applicable to early mouse and human embryogenesis, thereby offering valuable knowledge to the broader scientific community for reprogramming stem cells along endodermal cell lineages.




Preimplantation Mammalian Development and Live Imaging

Development of quantitative, safe and rapid techniques for assessing embryo quality provide significant advances during assisted reproduction. Instead of assessing the embryo quality by the standard morphologic evaluation, we adopted the the phasor-FLIM (Fluorescence Lifetime Imaging Microscopy) method, which is a non-invasive live imaging approach,to capture endogenous autofluorescent biomarkers of pre-implantation embryos as a readout of embryo quality. Using the parameters derived by the fluorescence lifetime histograms distributions, we have defined an Embryo Viability Index (EVI), which is a non-morphological index that distinguishes pre-implantation embryo quality.  The phasor-FLIM combined with the EVI provides a much needed alternative non-invasive qualitative technology for identifying healthy embryos from potential poorly developing embryos and thus may be useful in the future for assisted reproduction.

Using quantitative imaging techniques and analyses, we map and quantitate the dynamic activities of BMP signaling activities in preimplantation mouse embryos and demonstrate for the first time the biological function and mechanism of BMP signaling in the preimplantation mammalian embryos. We show that BMP signaling regulates cell division and is critical for the establishment of mouse blastocysts.Our work will shed light on an issue of early pregnancy loss: failure of the blastocyst to undergo normal development.

Mouse preimplatation



Genome engineering using the CRISPR/Cas9

The CRISPR/Cas9 system relies upon the formation of double-stranded hybrids between synthetic guide RNA and genomic DNA and confers mutations in the genome. With Xenopus, the ability to microinject hundreds of synchronous, in vitro-fertilized embryos represents a significant advantage over other systems for examining mutations in the F0 generation. We use Xenopus tropicalis and develop methods to eliminate a large genomic region and induce a homologous recombination at a desired locus within the genome.



Recent Publications


  • Paraiso, K.,, Blitz, I.L., Coley, M., Cheung, J., Sudou, N., Taira, M.,Cho, K.W. (2019) Endodermal maternal transcription factors establish super enhancers prior to zygotic genome activation. Cell Reports, In press.
  • Paraiso, K.,, Blitz, I.L., Zhou, J.J., Cho, KW.Y. (2019). Morpholino antisense oligonucleotides do not elicit induction of a general innate immune response in early Xenopus.  Developmental Cell, in press.


  • Ma, N., de Mochel, N.R., Pham, P., Yoon, Y.,  Cho, K.W.Y.,  Digman, M. (2018). Label-free assessment of pre-implantation embryo quality by the Fluorescence Lifetime Imaging Microscopy (FLIM)-phasor approach. bioRxiv 286682; doi: https://doi.org/10.1101/286682
  • Jin S Cho, Ira L. Blitz and Ken W.Y. Cho, (2018). DNase-seq to study chromatin accessibility in early Xenopus tropicalis. Chapter 14, Xenopus Laboratory Manual, Cold Spring Habor Press, Cold Spring Harb Protoc. doi: 10.1101/pdb.prot098335.
  • Charney RM, Paraiso KD, Blitz IL, Cho KWY. (2017). A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs. Semin Cell Dev Biol. 66:12-24.
  • Blitz, I.L., Paraiso, K.D., Patrushev, I., Chiu, W.T.Y., Cho, K.W.Y*., Gilchrist,M.J.* (2017). . *contributed equally, co-senior authors. A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo. Dev Biol, S0012-1606(16)30118-X. PMID: 27475627.


  • 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).
  • 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


  • Forouzmand, E., Owens, N.D.L., Blitz, I.L., Paraiso, K.D., Khokha, M.K., Gilchrist, M.J., Xie X., Cho, K.W.Y. (2016).  Developmentally regulated long non-coding RNAs in Xenopus tropicalis. Dev Biol. S0012-1606: 30120-8. PMID: 27418388
  • Blitz, I.L., Fish, M.B., and Cho, K.W.Y. (2016). Leapfrogging: Primordial Germ Cell Transplantation Permits Recovery of CRISPR/Cas9-Induced Mutations in Essential Genes. Development, 143:2868-75. PMID: 27385011
  • 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. Submitted. 1: co-first authros, contributed equally. Cell Reports.14, 632-647.


  • Chiang, M., Hallman, S., Cinquin, A., Reyes de Mochel, N., Paz, A., Kawauchi, S., Calof, A., Cho, KWY., Fowlkes, C.C., & Cinquin, O. (2015). Analysis of in vivo single cell behavior by high throughput, human-in-the-loop segmentation of three-dimensional images. BMC Bioinformatics. DOI 10.1186/s12859-015-0814-7
  • Wang, X., Hsi, H., Guerrero-Juarez, CF., Pham, K., Cho, K., Monuki, ES, Cho, KWY., Gay, DL., Plikus, (2015). Principles and mechanisms of regeneration in the mouse model for wound-induced hair follicle neogenesis. Regeneration. doi: 10.1002/reg2.38.
  • 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.


  • Yang, G., Yuan, G., Cho, K.W.Y., and Chen, Y. (2014). An atypical canonical BMP signaling pathway regulates Msx1 expression during odontogenesis. J Biol Chem. 289, 31492-31502.
  • Chiu, WT., Le, R., Beisinger, J., Blitz, IL., Xie, X., Cho, KWY. (2014). Comprehensive genomic view of Foxh1 and Smad2/3 interaction in mesendoderm development. Development, 141, 4537-4547.
  • Nakayama, T., Blitz I.L., Fish, M.B., Sumanth, A., Cho, K.W.Y., Grainger R. (2014). Cas9-based genome editing in Xenopus tropicalis. Methods in Enzymplogy, 546, 355-375.
  • 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 Communiations, 9:4322.
  • Blitz, IL., Luong, M., Chu, W. and Cho, K.W. (2014). Application of genomic approaches to developmental biology (book chapter for Principal of Developmental Genetics, 2nd edition. Edited by Sally Moody). 37-48.
  • Zheng, Z., Christley, S., Chiu, WT., Blitz, IL., Xie, X., Cho, KWY., Nie, Q. (2014) Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. BMS Systems Biology. BMC Syst Biol. 8:3