UMMS Affiliation

Program in Molecular Medicine; Diabetes Center of Excellence; Graduate School of Biomedical Sciences, Interdisciplinary Graduate Program

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Document Type



Amino Acids, Peptides, and Proteins | Cell Biology | Cells | Developmental Biology | Embryonic Structures | Genetic Phenomena | Nucleic Acids, Nucleotides, and Nucleosides


Studies in vertebrates have outlined conserved molecular control of definitive endoderm (END) development. However, recent work also shows that key molecular aspects of human END regulation differ even from rodents. Differentiation of human embryonic stem cells (ESCs) to END offers a tractable system to study the molecular basis of normal and defective human-specific END development. Here, we interrogated dynamics in chromatin accessibility during differentiation of ESCs to END, predicting DNA-binding proteins that may drive this cell fate transition. We then combined single-cell RNA-seq with parallel CRISPR perturbations to comprehensively define the loss-of-function phenotype of those factors in END development. Following a few candidates, we revealed distinct impairments in the differentiation trajectories for mediators of TGFbeta signaling and expose a role for the FOXA2 transcription factor in priming human END competence for human foregut and hepatic END specification. Together, this single-cell functional genomics study provides high-resolution insight on human END development.


CRISPRi, chromatin accessibility, dCas9-KRAB, endoderm, hepatic endoderm, human development, perturbation screen, pluripotent stem cells, single-cell RNA-seq, stem cell differentiation

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© 2019 The Author(s). This is an open access article under the CC BY-NC-ND license (

DOI of Published Version



Cell Rep. 2019 Apr 16;27(3):708-718.e10. doi: 10.1016/j.celrep.2019.03.076. Link to article on publisher's site

Journal/Book/Conference Title

Cell reports

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Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.