FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation

Kihyun Lee; Hyunwoo Cho; Robert W. Rickert; Qing V. Li; Julian Pulecio; Christina S. Leslie; Danwei Huangfu

doi:10.1016/j.celrep.2019.06.034

FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation

Kihyun Lee, Hyunwoo Cho, Robert W. Rickert, Qing V. Li, Julian Pulecio, Christina S. Leslie, Danwei Huangfu

Pharmaceutical Sciences

Research output: Contribution to journal › Article › peer-review

77 Scopus citations

Abstract

Transcriptional regulatory mechanisms of lineage priming in embryonic development are largely uncharacterized because of the difficulty of isolating transient progenitor populations. Directed differentiation of human pluripotent stem cells (hPSCs) combined with gene editing provides a powerful system to define precise temporal gene requirements for progressive chromatin changes during cell fate transitions. Here, we map the dynamic chromatin landscape associated with sequential stages of pancreatic differentiation from hPSCs. Our analysis of chromatin accessibility dynamics led us to uncover a requirement for FOXA2, known as a pioneer factor, in human pancreas specification not previously shown from mouse knockout studies. FOXA2 knockout hPSCs formed reduced numbers of pancreatic progenitors accompanied by impaired recruitment of GATA6 to pancreatic enhancers. Furthermore, FOXA2 is required for proper chromatin remodeling and H3K4me1 deposition during enhancer priming. This work highlights the power of combining hPSC differentiation, genome editing, and computational genomics for discovering transcriptional mechanisms during development. Lee et al. use ATAC-seq to identify key transcriptional factors involved in human pancreatic differentiation. FOXA2 knockout human pluripotent stem cells showed impaired differentiation to pancreatic progenitors, a phenotype not observed in Foxa2 conditional knockout mice. Furthermore, FOXA2 is required for proper chromatin remodeling and H3K4me1 deposition during enhancer priming.

Original language	English
Pages (from-to)	382-393.e7
Journal	Cell Reports
Volume	28
Issue number	2
DOIs	https://doi.org/10.1016/j.celrep.2019.06.034
State	Published - 9 Jul 2019

Bibliographical note

Funding Information:
We thank Matthew D. Witkin for assistance with ATAC-seq and ChIP-seq experiments; E. Apostolou and T. Vierbuchen for critical comments on the manuscript; and T. Evans, L. Studer, and members of D.H.’s laboratory for insightful discussions. This study was supported in part by the NIH/NIDDK ( R01DK096239 ), the New York State Stem Cell Science (NYSTEM C029567 , C029156 , and C32593GG ), and the MSKCC Cancer Center Support Grant ( P30CA008748 ). K.L. was supported by the Korean Government Scholarship Program for Study Overseas and the Mogam Science Scholarship Foundation . The monoclonal antibody NKX6-1 (DSHB F55A12-c) developed by Hagedorn Research Institute was obtained from the Developmental Studies Hybridoma Bank, created by the NICHD of the NIH, and maintained at the University of Iowa, Department of Biology, Iowa City, IA 52242, USA.

Funding Information:
We thank Matthew D. Witkin for assistance with ATAC-seq and ChIP-seq experiments; E. Apostolou and T. Vierbuchen for critical comments on the manuscript; and T. Evans, L. Studer, and members of D.H.’s laboratory for insightful discussions. This study was supported in part by the NIH/NIDDK (R01DK096239), the New York State Stem Cell Science (NYSTEM C029567, C029156, and C32593GG), and the MSKCC Cancer Center Support Grant (P30CA008748). K.L. was supported by the Korean Government Scholarship Program for Study Overseas and the Mogam Science Scholarship Foundation. The monoclonal antibody NKX6-1 (DSHB F55A12-c) developed by Hagedorn Research Institute was obtained from the Developmental Studies Hybridoma Bank, created by the NICHD of the NIH, and maintained at the University of Iowa, Department of Biology, Iowa City, IA 52242, USA. K.L. conceived the initial ideas and performed most experiments. K.L. and D.H. wrote the manuscript. H.C. carried out the bioinformatic analyses of ATAC-seq, RNA-seq, and ChIP-seq data. R.W.R. J.P. and Q.V.L. performed other necessary experiments. D.H. and C.S.L. supervised the work. All authors provided intellectual input and approved the final manuscript. The authors declare no competing interests.

Publisher Copyright:
© 2019 The Author(s)

Keywords

ATAC-seq and chromatin accessibility
FOXA1
FOXA2
GATA6
PDX1
enhancer priming and activation
hESCs
hPSCs
human embryonic stem cells
human pluripotent stem cells
nucleosome remodeling
pancreatic progenitors

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10.1016/j.celrep.2019.06.034

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title = "FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation",

abstract = "Transcriptional regulatory mechanisms of lineage priming in embryonic development are largely uncharacterized because of the difficulty of isolating transient progenitor populations. Directed differentiation of human pluripotent stem cells (hPSCs) combined with gene editing provides a powerful system to define precise temporal gene requirements for progressive chromatin changes during cell fate transitions. Here, we map the dynamic chromatin landscape associated with sequential stages of pancreatic differentiation from hPSCs. Our analysis of chromatin accessibility dynamics led us to uncover a requirement for FOXA2, known as a pioneer factor, in human pancreas specification not previously shown from mouse knockout studies. FOXA2 knockout hPSCs formed reduced numbers of pancreatic progenitors accompanied by impaired recruitment of GATA6 to pancreatic enhancers. Furthermore, FOXA2 is required for proper chromatin remodeling and H3K4me1 deposition during enhancer priming. This work highlights the power of combining hPSC differentiation, genome editing, and computational genomics for discovering transcriptional mechanisms during development. Lee et al. use ATAC-seq to identify key transcriptional factors involved in human pancreatic differentiation. FOXA2 knockout human pluripotent stem cells showed impaired differentiation to pancreatic progenitors, a phenotype not observed in Foxa2 conditional knockout mice. Furthermore, FOXA2 is required for proper chromatin remodeling and H3K4me1 deposition during enhancer priming.",

keywords = "ATAC-seq and chromatin accessibility, FOXA1, FOXA2, GATA6, PDX1, enhancer priming and activation, hESCs, hPSCs, human embryonic stem cells, human pluripotent stem cells, nucleosome remodeling, pancreatic progenitors",

author = "Kihyun Lee and Hyunwoo Cho and Rickert, {Robert W.} and Li, {Qing V.} and Julian Pulecio and Leslie, {Christina S.} and Danwei Huangfu",

note = "Funding Information: We thank Matthew D. Witkin for assistance with ATAC-seq and ChIP-seq experiments; E. Apostolou and T. Vierbuchen for critical comments on the manuscript; and T. Evans, L. Studer, and members of D.H.{\textquoteright}s laboratory for insightful discussions. This study was supported in part by the NIH/NIDDK ( R01DK096239 ), the New York State Stem Cell Science (NYSTEM C029567 , C029156 , and C32593GG ), and the MSKCC Cancer Center Support Grant ( P30CA008748 ). K.L. was supported by the Korean Government Scholarship Program for Study Overseas and the Mogam Science Scholarship Foundation . The monoclonal antibody NKX6-1 (DSHB F55A12-c) developed by Hagedorn Research Institute was obtained from the Developmental Studies Hybridoma Bank, created by the NICHD of the NIH, and maintained at the University of Iowa, Department of Biology, Iowa City, IA 52242, USA. Funding Information: We thank Matthew D. Witkin for assistance with ATAC-seq and ChIP-seq experiments; E. Apostolou and T. Vierbuchen for critical comments on the manuscript; and T. Evans, L. Studer, and members of D.H.{\textquoteright}s laboratory for insightful discussions. This study was supported in part by the NIH/NIDDK (R01DK096239), the New York State Stem Cell Science (NYSTEM C029567, C029156, and C32593GG), and the MSKCC Cancer Center Support Grant (P30CA008748). K.L. was supported by the Korean Government Scholarship Program for Study Overseas and the Mogam Science Scholarship Foundation. The monoclonal antibody NKX6-1 (DSHB F55A12-c) developed by Hagedorn Research Institute was obtained from the Developmental Studies Hybridoma Bank, created by the NICHD of the NIH, and maintained at the University of Iowa, Department of Biology, Iowa City, IA 52242, USA. K.L. conceived the initial ideas and performed most experiments. K.L. and D.H. wrote the manuscript. H.C. carried out the bioinformatic analyses of ATAC-seq, RNA-seq, and ChIP-seq data. R.W.R. J.P. and Q.V.L. performed other necessary experiments. D.H. and C.S.L. supervised the work. All authors provided intellectual input and approved the final manuscript. The authors declare no competing interests. Publisher Copyright: {\textcopyright} 2019 The Author(s)",

year = "2019",

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doi = "10.1016/j.celrep.2019.06.034",

language = "English",

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AU - Lee, Kihyun

AU - Cho, Hyunwoo

AU - Rickert, Robert W.

AU - Li, Qing V.

AU - Pulecio, Julian

AU - Leslie, Christina S.

AU - Huangfu, Danwei

N1 - Funding Information: We thank Matthew D. Witkin for assistance with ATAC-seq and ChIP-seq experiments; E. Apostolou and T. Vierbuchen for critical comments on the manuscript; and T. Evans, L. Studer, and members of D.H.’s laboratory for insightful discussions. This study was supported in part by the NIH/NIDDK ( R01DK096239 ), the New York State Stem Cell Science (NYSTEM C029567 , C029156 , and C32593GG ), and the MSKCC Cancer Center Support Grant ( P30CA008748 ). K.L. was supported by the Korean Government Scholarship Program for Study Overseas and the Mogam Science Scholarship Foundation . The monoclonal antibody NKX6-1 (DSHB F55A12-c) developed by Hagedorn Research Institute was obtained from the Developmental Studies Hybridoma Bank, created by the NICHD of the NIH, and maintained at the University of Iowa, Department of Biology, Iowa City, IA 52242, USA. Funding Information: We thank Matthew D. Witkin for assistance with ATAC-seq and ChIP-seq experiments; E. Apostolou and T. Vierbuchen for critical comments on the manuscript; and T. Evans, L. Studer, and members of D.H.’s laboratory for insightful discussions. This study was supported in part by the NIH/NIDDK (R01DK096239), the New York State Stem Cell Science (NYSTEM C029567, C029156, and C32593GG), and the MSKCC Cancer Center Support Grant (P30CA008748). K.L. was supported by the Korean Government Scholarship Program for Study Overseas and the Mogam Science Scholarship Foundation. The monoclonal antibody NKX6-1 (DSHB F55A12-c) developed by Hagedorn Research Institute was obtained from the Developmental Studies Hybridoma Bank, created by the NICHD of the NIH, and maintained at the University of Iowa, Department of Biology, Iowa City, IA 52242, USA. K.L. conceived the initial ideas and performed most experiments. K.L. and D.H. wrote the manuscript. H.C. carried out the bioinformatic analyses of ATAC-seq, RNA-seq, and ChIP-seq data. R.W.R. J.P. and Q.V.L. performed other necessary experiments. D.H. and C.S.L. supervised the work. All authors provided intellectual input and approved the final manuscript. The authors declare no competing interests. Publisher Copyright: © 2019 The Author(s)

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N2 - Transcriptional regulatory mechanisms of lineage priming in embryonic development are largely uncharacterized because of the difficulty of isolating transient progenitor populations. Directed differentiation of human pluripotent stem cells (hPSCs) combined with gene editing provides a powerful system to define precise temporal gene requirements for progressive chromatin changes during cell fate transitions. Here, we map the dynamic chromatin landscape associated with sequential stages of pancreatic differentiation from hPSCs. Our analysis of chromatin accessibility dynamics led us to uncover a requirement for FOXA2, known as a pioneer factor, in human pancreas specification not previously shown from mouse knockout studies. FOXA2 knockout hPSCs formed reduced numbers of pancreatic progenitors accompanied by impaired recruitment of GATA6 to pancreatic enhancers. Furthermore, FOXA2 is required for proper chromatin remodeling and H3K4me1 deposition during enhancer priming. This work highlights the power of combining hPSC differentiation, genome editing, and computational genomics for discovering transcriptional mechanisms during development. Lee et al. use ATAC-seq to identify key transcriptional factors involved in human pancreatic differentiation. FOXA2 knockout human pluripotent stem cells showed impaired differentiation to pancreatic progenitors, a phenotype not observed in Foxa2 conditional knockout mice. Furthermore, FOXA2 is required for proper chromatin remodeling and H3K4me1 deposition during enhancer priming.

AB - Transcriptional regulatory mechanisms of lineage priming in embryonic development are largely uncharacterized because of the difficulty of isolating transient progenitor populations. Directed differentiation of human pluripotent stem cells (hPSCs) combined with gene editing provides a powerful system to define precise temporal gene requirements for progressive chromatin changes during cell fate transitions. Here, we map the dynamic chromatin landscape associated with sequential stages of pancreatic differentiation from hPSCs. Our analysis of chromatin accessibility dynamics led us to uncover a requirement for FOXA2, known as a pioneer factor, in human pancreas specification not previously shown from mouse knockout studies. FOXA2 knockout hPSCs formed reduced numbers of pancreatic progenitors accompanied by impaired recruitment of GATA6 to pancreatic enhancers. Furthermore, FOXA2 is required for proper chromatin remodeling and H3K4me1 deposition during enhancer priming. This work highlights the power of combining hPSC differentiation, genome editing, and computational genomics for discovering transcriptional mechanisms during development. Lee et al. use ATAC-seq to identify key transcriptional factors involved in human pancreatic differentiation. FOXA2 knockout human pluripotent stem cells showed impaired differentiation to pancreatic progenitors, a phenotype not observed in Foxa2 conditional knockout mice. Furthermore, FOXA2 is required for proper chromatin remodeling and H3K4me1 deposition during enhancer priming.

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KW - GATA6

KW - PDX1

KW - enhancer priming and activation

KW - hESCs

KW - hPSCs

KW - human embryonic stem cells

KW - human pluripotent stem cells

KW - nucleosome remodeling

KW - pancreatic progenitors

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DO - 10.1016/j.celrep.2019.06.034

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SP - 382-393.e7

JO - Cell Reports

JF - Cell Reports

IS - 2

ER -

FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation

Abstract

Bibliographical note

Keywords

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