Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome

Authors: YU, DA-HAI - Children'S Nutrition Research Center (CNRC); GADKARI, MANASI - Children'S Nutrition Research Center (CNRC); ZHOU, QUAN - Children'S Nutrition Research Center (CNRC); YU, SHIYAN - Rutgers University; GAO, NAN - Rutgers University; GUAN, YONGTAO - Children'S Nutrition Research Center (CNRC); SCHADY, DEBORAH - Baylor College Of Medicine; ROSHAN, TONY - Children'S Nutrition Research Center (CNRC); CHEN, MIAO-HSUEH - Children'S Nutrition Research Center (CNRC); LARITSKY, ELEONORA - Children'S Nutrition Research Center (CNRC); GE, ZHONGQI - Baylor College Of Medicine; WANG, HUI - Baylor College Of Medicine; CHEN, RUI - Baylor College Of Medicine; WESTWATER, CAROLINE - Medical University Of South Carolina; BRY, LYN - Brigham & Women'S Hospital; WATERLAND, ROBERT - Children'S Nutrition Research Center (CNRC); MORIARTY, CHELSEA - Children'S Nutrition Research Center (CNRC); HWANG, CINDY - Children'S Nutrition Research Center (CNRC); SWENNES, ALTON - Baylor College Of Medicine; MOORE, SEAN - Cincinnati Children'S Research Hospital; SHEN, LANLAN - Children'S Nutrition Research Center (CNRC)

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/28/2015
Publication Date: 9/30/2015
Publication URL: https://handle.nal.usda.gov/10113/62077
Citation: Yu, D., Gadkari, M., Zhou, Q., Yu, S., Gao, N., Guan, Y., Schady, D., Roshan, T.N., Chen, M., Laritsky, E., Ge, Z., Wang, H., Chen, R., Westwater, C., Bry, L., Waterland, R.A., Moriarty, C., Hwang, C., Swennes, A.G., Moore, S.R., Shen, L. 2015. Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome. Genome Biology. 16:211.

Interpretive Summary: Nutrition and microbial colonization in early life induce persistent structural and functional alterations in the intestine, and can modulate the risk of chronic intestinal diseases throughout the life-span. Such 'developmental programming' of intestinal structure and function likely involves DNA methylation (the addition of a methyl molecule) and other epigenetic mechanisms to control gene expression. Remarkably, however, despite its obvious relevance to human health, the epigenetic regulation of normal intestinal development is rather understudied. Cells are continually being replaced in the intestinal epithelium: they only last around four days and then new cells are formed by intestinal stem cells (ISCs). ISCs are the 'control center' that regulates lifelong intestinal health and disease. Using mouse models, we were able to isolate the pure ISC population and though analysis we found that DNA methylation plays a regulatory role during the suckling period and that DNA methylation turns on important genes involved in the intestinal development and functional maturation. While many recent studies demonstrate that the gut microbiome has a significant and long-term impact on gastrointestinal health, our work provides a clue about how this works. Our future direction is to see if we can translate these findings to humans. Our work opens the possibility for epigenetically targeted probiotic therapies to provide lifelong protection against intestinal disease.

Technical Abstract: DNA methylation is an epigenetic mechanism central to the development and maintenance of complex mammalian tissues, but our understanding of its role in intestinal development is limited. We used whole genome bisulfite sequencing, and found that differentiation of mouse colonic intestinal stem cells to intestinal epithelium is not associated with major changes in DNA methylation. However, we did detect extensive dynamic epigenetic changes in intestinal stem cells and their progeny during the suckling period, suggesting postnatal epigenetic development in this stem cell population. We also learned that postnatal DNA methylation increases at 3' CpG islands (CGIs) correlate with transcriptional activation of glycosylation genes responsible for intestinal maturation. To directly test whether 3' CGI methylation regulates transcription, we conditionally disrupted two major DNA methyltransferases, Dnmt1 or Dnmt3a, in fetal and adult intestine. Deficiency of Dnmt1 causes severe intestinal abnormalities in neonates and disrupts crypt homeostasis in adults, whereas Dnmt3a loss was compatible with intestinal development. These studies reveal that 3' CGI methylation is functionally involved in the regulation of transcriptional activation in vivo, and that Dnmt1 is a critical regulator of postnatal epigenetic changes in intestinal stem cells. Finally, we showed that postnatal 3' CGI methylation and associated gene activation in intestinal epithelial cells are significantly altered by germ-free conditions.