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Dev Cell. 2019 Jan 7;48(1):49-63.e7. doi: 10.1016/j.devcel.2018.11.048.

Neurog3-Independent Methylation Is the Earliest Detectable Mark Distinguishing Pancreatic Progenitor Identity.

Author information

1
Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
2
Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
3
Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN 37232, USA.
4
Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Biochemistry and the Vanderbilt Genetic Institute, Vanderbilt University, Nashville, TN 37232, USA.
5
Center for AIDS Health Disparities Research, Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville, TN 37208, USA.
6
Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA.
7
Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Stanford University School of Medicine, Palo Alto, CA 94304, USA.
8
Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN 37232, USA. Electronic address: ken.s.lau@vanderbilt.edu.
9
Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. Electronic address: guoqiang.gu@vanderbilt.edu.

Abstract

In the developing pancreas, transient Neurog3-expressing progenitors give rise to four major islet cell types: α, β, δ, and γ; when and how the Neurog3+ cells choose cell fate is unknown. Using single-cell RNA-seq, trajectory analysis, and combinatorial lineage tracing, we showed here that the Neurog3+ cells co-expressing Myt1 (i.e., Myt1+Neurog3+) were biased toward β cell fate, while those not simultaneously expressing Myt1 (Myt1-Neurog3+) favored α fate. Myt1 manipulation only marginally affected α versus β cell specification, suggesting Myt1 as a marker but not determinant for islet-cell-type specification. The Myt1+Neurog3+ cells displayed higher Dnmt1 expression and enhancer methylation at Arx, an α-fate-promoting gene. Inhibiting Dnmts in pancreatic progenitors promoted α cell specification, while Dnmt1 overexpression or Arx enhancer hypermethylation favored β cell production. Moreover, the pancreatic progenitors contained distinct Arx enhancer methylation states without transcriptionally definable sub-populations, a phenotype independent of Neurog3 activity. These data suggest that Neurog3-independent methylation on fate-determining gene enhancers specifies distinct endocrine-cell programs.

KEYWORDS:

Arx; DMR; DNA methylation; DNMT; HMR; Myt1; azacytidine; combinatorial lineage tracing; diabetes; epigenetics; glucagon; insulin; lineage priming; p-Creode; pseudotime; single-cell RNA-seq; specification; stochastic gene expression; trajectory; transcriptional noise; α cell; β cell

PMID:
30620902
PMCID:
PMC6327977
[Available on 2020-01-07]
DOI:
10.1016/j.devcel.2018.11.048

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