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

TY - JOUR

T1 - Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation

AU - Kim, Rinho

AU - Sheaffer, Karyn L

AU - Choi, Inchan

AU - Won, Kyoung-Jae

AU - Kaestner, Klaus H

N1 - © 2016 Kim et al.; Published by Cold Spring Harbor Laboratory Press.

PY - 2016/11/1

Y1 - 2016/11/1

N2 - 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 organoid-forming 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.

AB - 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 organoid-forming 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.

KW - Animals

KW - Cell Differentiation/genetics

KW - Cells, Cultured

KW - DNA Methylation

KW - DNA-Binding Proteins/genetics

KW - Epigenesis, Genetic

KW - Gene Expression Regulation, Developmental/genetics

KW - Intestines/cytology

KW - Mice

KW - Mice, Inbred C57BL

KW - Proto-Oncogene Proteins/genetics

KW - Receptors, G-Protein-Coupled/genetics

KW - Sequence Deletion

KW - Stem Cells/cytology

KW - Wnt Signaling Pathway/genetics

U2 - 10.1101/gad.288035.116

DO - 10.1101/gad.288035.116

M3 - Journal article

C2 - 27856615

SN - 0890-9369

VL - 30

SP - 2433

EP - 2442

JO - Genes & Development

JF - Genes & Development

IS - 21

ER -