Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development

Abstract

The Tet family of enzymes (Tet1/2/3) converts 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Mouse embryonic stem cells (mESCs) highly express Tet1 and have an elevated level of 5hmC. Tet1 has been implicated in ESC maintenance and lineage specification in vitro but its precise function in development is not well defined. To establish the role of Tet1 in pluripotency and development, we have generated Tet1 mutant mESCs and mice. Tet1(-/-) ESCs have reduced levels of 5hmC and subtle changes in global gene expression, and are pluripotent and support development of live-born mice in tetraploid complementation assay, but display skewed differentiation toward trophectoderm in vitro. Tet1 mutant mice are viable, fertile, and grossly normal, though some mutant mice have a slightly smaller body size at birth. Our data suggest that Tet1 loss leading to a partial reduction in 5hmC levels does not affect pluripotency in ESCs and is compatible with embryonic and postnatal development.

Figure 1. Generation of Tet1 knockout mouse embryonic stem cells

(A) Schematic of gene targeting strategy applied to generate Tet1 knockout mouse embryonic stem cells (mESCs). H stands for the properly targeted 2-lox conditional/hypomorphic allele. (B–F) Southern blot confirmation of properly targeted Tet1 mESCs clones. Analysis of Tet1^+/H clones (B&C) and Tet1^−/H clones (E). Excision of exon 4 by transient Cre recombinase expression to generate Tet1^+/− mESCs (D) or Tet1^−/− cells (F). Note that the clones shown in these blots are representative clones and do not correspond numerically with each other. (G) Relative Tet1 mRNA levels measured by quantitative RT-PCR in Tet1 mESCs of indicated genotypes using primers in different exons, including the deleted exon 4. Data are normalized to GAPDH. Note that Tet1^−/− cells are completely depleted of mRNA containing exon 4. (H) Tet1 protein levels measured by western blot in lysates generated from mESCs of indicated genotypes using anti-Tet1 antibody. Actin is used as a loading control. Note that deletion of exon 4 in Tet1^−/− mESCs leads to complete depletion of Tet1 protein. Asterisk indicates nonspecific band.

Figure 2. Loss of Tet1 leads to partial reduction in 5hmC and subtle changes in global DNA methylation and gene expression profile

(A) Analysis of 5hmC levels in DNA isolated from Tet1 mESCs of indicated genotypes by dot blot assay using anti-5hmC antibody. Methylene blue staining is used to control for proper transfer. (B) Quantification of intensity of 5hmC signal for each genotype is plotted. Error bars represent SEM. (C&D) Locus specific quantification of 5hmC and 5mC in promoter CpG island regions of indicated genes in Tet1 knockout and wild type mESCs by glucosylation of genomic 5hmC followed by methylation sensitive qPCR (glucMS-qPCR). CpG Chr5 refers to a CpG island in chromosome 5:99466154-99466819. Error bars represent SEM. (E) Global quantification of 5mC in mESCs of indicated genotypes by liquid chromatography/mass spectrometry (LC/MS). Error bars represent SEM. (F) Gene ontology analysis for commonly deregulated genes in two Tet1^−/− mESCs compared to wild-type mESCs as determined by microarray gene expression profile analysis. Venn diagram shows in the intersection the number of genes commonly differentially expressed in the knockout cells (versus wild-type cells). Total number of genes differentially regulated between each knockout cell line versus wild-type cell line is also indicated. See also Figure S1 and S2.

Figure 3. Tet1 knockout ES cells are pluripotent and support post-implantation embryonic development in tetraploid complementation assay

(A) Alkaline phosphatase staining and morphological appearance of Tet1 mESCs of indicated genotypes on feeders. (B) Immunostaining for pluripotency markers Oct4 and Nanog. (C) Relative expression of core pluripotency network genes Oct4, Sox2 and Nanog measured by quantitative RT-PCR. Data are normalized to GAPDH. Error bars represent SEM. (D–G) Tetraploid (4n) complementation assay for Tet1 knockout mESCs. Gross appearance of pups delivered by c-section at day E21 is shown in D. Confirmation of genotypes of pups from tail DNA by Southern blot is shown in E. Tet1 targeted mESC DNA of indicated genotypes is used as controls for genotyping. Complete data from tetraploid complementation experiments are summarized in E. Histological analysis of various tissues and organs of fixed E21 pups from 4n assay is presented in G. (H) H&E staining of sections of teratomas generated from Tet1 mESCs of indicated genotypes. (I) Gross appearance of teratomas (top) and H&E histological analysis of Tet1 knockout teratomas (bottom). Note the presence of trophoblasts (arrow heads) and blood in knockout teratomas. (J) GFP-labeled Tet1 knockout or wild-type ES cells injected into wild-type 8-cell-stage embryos are traced until the blastocyst stage in a developing embryo. Note that the GFP signal is not seen in the outer layer of the blastocyst, which constitutes the trophectoderm (n=20 for each genotype). (G) Gross and fluorescence images of E10.5 chimeric embryos that were injected at blastocyst stage with GFP-labeled Tet1 knockout or wild-type ES cells. Note that GFP positive cells of both genotypes exclusively contribute to the embryo proper (left) and not the placenta (right). Number of embryos examined in this experiment is presented in the table. See also Figure S3.

Figure 4. Tet1 knockout mice are viable but vary in body size

(A) Schematic of crosses to generate Tet1 knockout mice. (B) Gross appearance of mice of indicated genotypes at various ages. Note that Tet1^−/− mice vary in size. (C) Genotype confirmation of mice from Tet1^+/− × Tet1^+/− cross by southern blot. (D) Table summarizing the litter size and Mendelian ratio of Tet1^−/− mice. (E) Mouse body weights at the indicated ages. Error bars represent SD. Asterisks indicate statistically significant than wild type (t-test p-value <0.05). (F) Gross images of E12.5 embryos from Tet1^+/− × Tet1^+/− cross. Arrowheads point to knockout embryos. Genotype and number of tail somite pairs of embryos is tabulated to the left. (G) Longitudinal sections of E13.5 gonads of indicated genotypes stained with antibody against the germ cell marker Mvh. Note that gonads were harvested from embryos of similar developmental stage and size. (H) Gross images of progeny of Tet1 knockout parents at birth. (J) PCR genotyping confirmation of offspring of Tet1 knockout mice. (K) Table summarizing average litter size from various crosses of 6- to 8-week-old Tet1 knockout mice. See also Figure S4.