Erasure of DNA methylation, genomic imprints, and epimutations in a primordial germ-cell model derived from mouse pluripotent stem cells

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 113; no. 34; pp. 9545 - 9550
• Main Authors: Miyoshi, Norikatsu, Stel, Jente M., Shioda, Keiko, Qu, Na, Odajima, Junko, Mitsunaga, Shino, Zhang, Xiangfan, Nagano, Makoto, Hochedlinger, Konrad, Isselbacher, Kurt J., Shioda, Toshi
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 23.08.2016
• Subjects: 5-Methylcytosine - analogs & derivatives; 5-Methylcytosine - metabolism; Animals; Biological Sciences; DNA Demethylation; DNA Methylation; Embryo, Mammalian; Enzymes; Epigenesis, Genetic; Female; Gene expression; Genome; Genomic Imprinting; Genomics; Germ Cells - cytology; Germ Cells - metabolism; High-Throughput Nucleotide Sequencing; Intercellular Signaling Peptides and Proteins - genetics; Intercellular Signaling Peptides and Proteins - metabolism; Iodide Peroxidase - genetics; Iodide Peroxidase - metabolism; Male; Mice; Mutation; Pluripotent Stem Cells - cytology; Pluripotent Stem Cells - metabolism; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; Stem cells; epimutation; epigenetic reprogramming; genetic imprinting; PGCLC
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1610259113

The genome-wide depletion of 5-methylcytosines (5meCs) caused by passive dilution through DNA synthesis without daughter strand methylation and active enzymatic processes resulting in replacement of 5meCs with unmethylated cytosines is a hallmark of primordial germ cells (PGCs). Although recent studies have shown that in vitro differentiation of pluripotent stem cells (PSCs) to PGC-like cells (PGCLCs) mimics the in vivo differentiation of epiblast cells to PGCs, how DNA methylation status of PGCLCs resembles the dynamics of 5meC erasure in embryonic PGCs remains controversial. Here, by differential detection of genome-wide 5meC and 5-hydroxymethylcytosine (5hmeC) distributions by deep sequencing, we show that PGCLCs derived from mouse PSCs recapitulated the process of genome-wide DNA demethylation in embryonic PGCs, including significant demethylation of imprint control regions (ICRs) associated with increased mRNA expression of the corresponding imprinted genes. Although 5hmeCs were also significantly diminished in PGCLCs, they retained greater amounts of 5hmeCs than intragonadal PGCs. The genomes of both PGCLCs and PGCs selectively retained both 5meCs and 5hmeCs at a small number of repeat sequences such as GSAT_MM, of which the significant retention of bisulfite-resistant cytosines was corroborated by reanalysis of previously published whole-genome bisulfite sequencing data for intragonadal PGCs. PSCs harboring abnormal hypermethylation at ICRs of the Dlk1-Gtl2-Dio3 imprinting cluster diminished these 5meCs upon differentiation to PGCLCs, resulting in transcriptional reactivation of the Gtl2 gene. These observations support the usefulness of PGCLCs in studying the germline epigenetic erasure including imprinted genes, epimutations, and erasure-resistant loci, which may be involved in transgenerational epigenetic inheritance.