The intestinal epithelium is one of the most rapidly renewing tissues in the body, and thus the ideal tissue to study somatic stem and progenitor cell biology. The small intestinal epithelium is composed of a single layer of cells that contains four major differentiated cell types as well as intestinal stem cells (ISCs) and progenitor r transit amplifying cells that replenish differentiated cells throughout life. While the past twent years have seen great progress in our understanding of the signaling pathways and transcriptional regulators that control intestinal proliferation and differentiation, our understanding of the epigenetic factors that control these important processes is rather limited. To address this knowledge gap, I propose the following three interrelated yet independent Specific Aims:
In specific Aim 1, we will determine the genome-wide atlas of epigenetic modifications of Lgr5-positive stem cells, transit amplifying or progenitor cells, and mature epithelial cells. We will perform integrative data analyses to identify the gene sets that are regulated by epigenetic modifications as the cells progress from stem to differentiated epithelial cell.
In Aim 2, we will delineate the role of maintenance DNA methylation in intestinal stem cell renewal and epithelial differentiation, through conditional gene ablation of the maintenance DNA methylase Dnmt1.
In Aim 3, we will test the hypothesis that the repressive H3K27me3 mark must be removed by the histone demethylase Jmjd3 in order to allow differentiation of intestinal epithelial cells, using inducible gene deletion.

Public Health Relevance

Gastrointestinal cancer is a significant health problem, ranking fourth in incidence and second in death among cancers in the United States. Abnormal differentiation and increased proliferation of the intestinal epithelium are hallmarks of carcinogenesis. The molecular mechanisms that regulate cellular proliferation and differentiation in gastrointestinal development are far from being understood completely. Therefore, we will analyze the epigenomic regulation of intestinal stem cells, progenitor cells, and differentiated cells on the genome-wide level, and test the contribution of DNA methylation and histone demethylation to intestinal health.

Agency
National Institute of Health (NIH)
Institute
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Type
Method to Extend Research in Time (MERIT) Award (R37)
Project #
5R37DK053839-17
Application #
8719972
Study Section
Clinical, Integrative and Molecular Gastroenterology Study Section (CIMG)
Program Officer
Carrington, Jill L
Project Start
1998-06-01
Project End
2017-07-31
Budget Start
2014-08-01
Budget End
2015-07-31
Support Year
17
Fiscal Year
2014
Total Cost
$366,675
Indirect Cost
$130,652
Name
University of Pennsylvania
Department
Genetics
Type
Schools of Medicine
DUNS #
042250712
City
Philadelphia
State
PA
Country
United States
Zip Code
19104
Sheaffer, Karyn L; Elliott, Ellen N; Kaestner, Klaus H (2016) DNA Hypomethylation Contributes to Genomic Instability and Intestinal Cancer Initiation. Cancer Prev Res (Phila) 9:534-46
Kim, Rinho; Sheaffer, Karyn L; Choi, Inchan et al. (2016) Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation. Genes Dev 30:2433-2442
Aoki, Reina; Shoshkes-Carmel, Michal; Gao, Nan et al. (2016) Foxl1-expressing mesenchymal cells constitute the intestinal stem cell niche. Cell Mol Gastroenterol Hepatol 2:175-188
Elliott, Ellen N; Sheaffer, Karyn L; Schug, Jonathan et al. (2015) Dnmt1 is essential to maintain progenitors in the perinatal intestinal epithelium. Development 142:2163-72
Terry, Natalie A; Lee, Randall A; Walp, Erik R et al. (2015) Dysgenesis of enteroendocrine cells in Aristaless-Related Homeobox polyalanine expansion mutations. J Pediatr Gastroenterol Nutr 60:192-9
Elliott, Ellen N; Kaestner, Klaus H (2015) Epigenetic regulation of the intestinal epithelium. Cell Mol Life Sci 72:4139-56
Jiao, Yang; Ye, Diana Z; Li, Zhaoyu et al. (2015) Protein tyrosine phosphatase of liver regeneration-1 is required for normal timing of cell cycle progression during liver regeneration. Am J Physiol Gastrointest Liver Physiol 308:G85-91
Terry, Natalie A; Walp, Erik R; Lee, Randall A et al. (2014) Impaired enteroendocrine development in intestinal-specific Islet1 mouse mutants causes impaired glucose homeostasis. Am J Physiol Gastrointest Liver Physiol 307:G979-91
Sheaffer, Karyn L; Kim, Rinho; Aoki, Reina et al. (2014) DNA methylation is required for the control of stem cell differentiation in the small intestine. Genes Dev 28:652-64
Choi, Inchan; Kim, Rinho; Lim, Hee-Woong et al. (2014) 5-hydroxymethylcytosine represses the activity of enhancers in embryonic stem cells: a new epigenetic signature for gene regulation. BMC Genomics 15:670

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