Abstract
BackgroundDNA 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.ResultsWe 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0763-5) contains supplementary material, which is available to authorized users.
Highlights
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
DNA methylation is widely viewed as an epigenetic mark for gene silencing, we recently discovered that methylation at non-promoter CpG island (CGI), at the 3′ end of genes, promotes human gene activation through a CTCF-dependent enhancerblocking mechanism [13], underscoring the need for unbiased methods to study epigenetic regulation by DNA methylation during development
Since colonic intestinal stem cell (ISC) are continually undergoing differentiation to replace the short-lived population of differentiated epithelial cells, we analyzed the DNA methylomes of sorted epithelial cell adhesion molecule (EpCAM)-positive and Lgr5-enhanced green fluorescent protein (EGFP)-negative population [34,35,36] to identify DNA methylation changes that correlate with differentiation
Summary
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. The role of epigenetics in intestinal development has gained more attention recently [6,7,8,9,10], we still know little about the fundamental epigenetic mechanisms that control the origin, identity, and behavior of ISCs during development. DNA methylation of cytosine in CpG dinucleotides is a well-established epigenetic mechanism critical for mammalian development. DNA methylation is widely viewed as an epigenetic mark for gene silencing, we recently discovered that methylation at non-promoter CGIs, at the 3′ end of genes, promotes human gene activation through a CTCF-dependent enhancerblocking mechanism [13], underscoring the need for unbiased methods to study epigenetic regulation by DNA methylation during development
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