title: Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome.
abstract: BACKGROUND
  DNA methylation is an epigenetic mechanism central to development and maintenance of complex mammalian tissues, but our understanding of its role in intestinal development is limited.
  
  
  RESULTS
  We use whole genome bisulfite sequencing, and find that differentiation of mouse colonic intestinal stem cells to intestinal epithelium is not associated with major changes in DNA methylation. However, we 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 find 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 show that postnatal 3' CGI methylation and associated gene activation in intestinal epithelial cells are significantly altered by germ-free conditions.
  
  
  CONCLUSIONS
  Our results demonstrate that the suckling period is critical for epigenetic development of intestinal stem cells, with potential important implications for lifelong gut health, and that the gut microbiome guides and/or facilitates these postnatal epigenetic processes.
authors.affiliation: Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Ste. 8020, Houston, TX, 77030, USA. dy1@bcm.edu.
authors.forename: Da-Hai
authors.initials: DH
authors.lastname: Yu
authors.affiliation: Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Ste. 8020, Houston, TX, 77030, USA. mansi_511@yahoo.com.
authors.forename: Manasi
authors.initials: M
authors.lastname: Gadkari
authors.affiliation: Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Ste. 8020, Houston, TX, 77030, USA. Quan.Zhou2@bcm.edu.
authors.forename: Quan
authors.initials: Q
authors.lastname: Zhou
authors.affiliation: Department of Biological Sciences, Rutgers University, Newark, NJ, 07102, USA. shiyan.yu@gmail.com.
authors.forename: Shiyan
authors.initials: S
authors.lastname: Yu
authors.affiliation: Department of Biological Sciences, Rutgers University, Newark, NJ, 07102, USA. ngao@andromeda.rutgers.edu.
authors.forename: Nan
authors.initials: N
authors.lastname: Gao
authors.affiliation: Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Ste. 8020, Houston, TX, 77030, USA. yongtaog@bcm.edu.|Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. yongtaog@bcm.edu.
authors.forename: Yongtao
authors.initials: Y
authors.lastname: Guan
authors.affiliation: Department of Pathology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA. daschady@texaschildrens.org.
authors.forename: Deborah
authors.initials: D
authors.lastname: Schady
authors.affiliation: Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Ste. 8020, Houston, TX, 77030, USA. Tony.Roshan@bcm.edu.
authors.forename: Tony N
authors.initials: TN
authors.lastname: Roshan
authors.affiliation: Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Ste. 8020, Houston, TX, 77030, USA. miaohsuc@bcm.edu.
authors.forename: Miao-Hsueh
authors.initials: MH
authors.lastname: Chen
authors.affiliation: Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Ste. 8020, Houston, TX, 77030, USA. laritsky@bcm.edu.
authors.forename: Eleonora
authors.initials: E
authors.lastname: Laritsky
authors.affiliation: Department of Molecular and Human Genetics, Human Genome Center, Baylor College of Medicine, Houston, TX, 77030, USA. Zhongqi.Ge@bcm.edu.
authors.forename: Zhongqi
authors.initials: Z
authors.lastname: Ge
authors.affiliation: Department of Molecular and Human Genetics, Human Genome Center, Baylor College of Medicine, Houston, TX, 77030, USA. hw11@bcm.edu.
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Molecular and Human Genetics, Human Genome Center, Baylor College of Medicine, Houston, TX, 77030, USA. ruichen@bcm.edu.
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
authors.affiliation: Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA. westwatc@musc.edu.
authors.forename: Caroline
authors.initials: C
authors.lastname: Westwater
authors.affiliation: Center for Clinical and Translational Metagenomics, Brigham & Women's Hospital Harvard Digestive Diseases Center, Boston, MA, 02115, USA. LBRY@PARTNERS.ORG.
authors.forename: Lynn
authors.initials: L
authors.lastname: Bry
authors.affiliation: Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Ste. 8020, Houston, TX, 77030, USA. waterland@bcm.edu.|Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. waterland@bcm.edu.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Waterland
authors.affiliation: Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Ste. 8020, Houston, TX, 77030, USA. Chelsea.Moriarty@bcm.edu.
authors.forename: Chelsea
authors.initials: C
authors.lastname: Moriarty
authors.affiliation: Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Ste. 8020, Houston, TX, 77030, USA. Cindy.Hwang@bcm.edu.
authors.forename: Cindy
authors.initials: C
authors.lastname: Hwang
authors.affiliation: Center for Comparative Medicine and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA. Alton.Swennes@bcm.edu.
authors.forename: Alton G
authors.initials: AG
authors.lastname: Swennes
authors.affiliation: Gastroenterology, Hepatology, & Nutrition, Center for Global Child Health, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. Sean.Moore@cchmc.org.
authors.forename: Sean R
authors.initials: SR
authors.lastname: Moore
authors.affiliation: Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Ste. 8020, Houston, TX, 77030, USA. Lanlan.Shen@bcm.edu.
authors.forename: Lanlan
authors.initials: L
authors.lastname: Shen
mesh_terms: D000818:Animals; D000833:Animals, Suckling / Q000235:genetics; D002454:Cell Differentiation / Q000235:genetics*; D018899:CpG Islands / Q000235:genetics; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D000090205:DNA Methyltransferase 3A; D044127:Epigenesis, Genetic; D007413:Intestinal Mucosa / Q000378:metabolism; D007422:Intestines / Q000382:microbiology*; D051379:Mice; D064307:Microbiota / Q000235:genetics; D013234:Stem Cells / Q000166:cytology / Q000378:metabolism*
chemical_list: C000717967:DNMT3A protein, human; C000715535:Dnmt3a protein, mouse; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases; D000090205:DNA Methyltransferase 3A; C000619381:Dnmt1 protein, mouse