Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation

Abstract

Methylated cytosines are associated with gene silencing. The ten-eleven translocation (TET) hydroxylases, which oxidize methylated cytosines to 5-hydroxymethylcytosine (5hmC), are essential for cytosine demethylation. Gene silencing and activation are critical for intestinal stem cell (ISC) maintenance and differentiation, but the potential role of TET hydroxylases in these processes has not yet been examined. Here, we generated genome-wide maps of the 5hmC mark in ISCs and their differentiated progeny. Genes with high levels of hydroxymethylation in ISCs are strongly associated with Wnt signaling and developmental processes. We found Tet1 to be the most abundantly expressed Tet gene in ISCs; therefore, we analyzed intestinal development in Tet1-deficient mice and determined that these mice are growth-retarded, exhibit partial postnatal lethality, and have significantly reduced numbers of proliferative cells in the intestinal epithelium. In addition, the Tet1-deficient intestine displays reduced organoidforming capacity. In the Tet1-deficient crypt, decreased expression of Wnt target genes such as Axin2 and Lgr5 correlates with lower 5hmC levels at their promoters. These data demonstrate that Tet1-mediated DNA hydroxymethylation plays a critical role in the epigenetic regulation of the Wnt pathway in intestinal stem and progenitor cells and consequently in the self-renewal of the intestinal epithelium.

5-Hydroxymethylcytosine (5hmC), or How to Identify Your Favorite Cell

“…In addition, stable accumulation of 5hmC has been described for enterocyte differentiation in well-known TF binding sites and targets involved in this process [75,76]. This contrasts with the pattern shown for blood cell subtypes, at least at earlier stages of blood cell differentiation (i.e., from HSCs) [19], in which there is a more general presence of 5hmC followed by a global drop that respects lineage-related loci, as described above.…”

Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells

“…We therefore analysed distribution of 5mC and 5-hydroxymethylcytosine (5hmC) (37) at H3K27Ac positive distal elements in intestinal epithelial cells. Here, we considered that at least one MBD/ MeDIP peak (150 bp) must overlap with H3K27Ac positive region.…”

Hydroxymethylation Influences on Intestinal Epithelial Cells in Health and Disease

“…These mice are smaller than their litermate controls and ultimately deletion of Tet1 is lethal. Furthermore, LGR5 + cells derived from these TET1-deicient mice are also unable to form organoids, which conirms the role of TET1 and hydroxymethylation as a critical step in epithelial cell diferentiation and maintenance [33,35].…”

“…These studies showed relatively similar levels of methylation in the crypts and in association with rapidly dividing (Ki67+) cells in the transition zone; whereas, there was an enrichment of hydroxymethylation at the tips of the villi and a decreased prevalence of hydroxymethylation in the crypts in Ki67-positive cells. These data suggest that hydroxymethylation is gained during diferentiation and preferentially expressed in non-dividing, terminally diferentiated cells [33].…”

“…Hydroxymethylation in LGR5 + cells localized to promoters of intestinal stem cell markers, such as LGR5, and gene ontology analysis revealed that the functions of the preferentially hydroxymethylated genes were involved in developmental processes, cell diferentiation and other stem cell functions. In contrast, in the LGR5 − colonocytes that were terminally diferentiated, hydroxymethylation was enhanced in the promoters and within genes that control metabolic processes, nutrient transport and other enterocyte functions, and genes with enriched hydroxymethylation also exhibited higher expression at the RNA level [33]. TET1, which actively can convert methylated cytosine to hydroxymethylated cytosine in epithelial cells, is critical for intestinal epithelial cell maintenance and diferentiation.…”