Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes.
DNA methylation patterns are reprogrammed in primordial germ cells and in preimplantation embryos by demethylation and subsequent de novo methylation. It has been suggested that epigenetic reprogramming may be necessary for the embryonic genome to return to a pluripotent state. We have carried out a genome-wide promoter analysis of DNA methylation in mouse embryonic stem (ES) cells, embryonic germ (EG) cells, sperm, trophoblast stem (TS) cells, and primary embryonic fibroblasts (pMEFs). Global clustering analysis shows that methylation patterns of ES cells, EG cells, and sperm are surprisingly similar, suggesting that while the sperm is a highly specialized cell type, its promoter epigenome is already largely reprogrammed and resembles a pluripotent state. Comparisons between pluripotent tissues and pMEFs reveal that a number of pluripotency related genes, including Nanog, Lefty1 and Tdgf1, as well as the nucleosome remodeller Smarcd1, are hypomethylated in stem cells and hypermethylated in differentiated cells. Differences in promoter methylation are associated with significant differences in transcription levels in more than 60% of genes analysed. Our comparative approach to promoter methylation thus identifies gene candidates for the regulation of pluripotency and epigenetic reprogramming. While the sperm genome is, overall, similarly methylated to that of ES and EG cells, there are some key exceptions, including Nanog and Lefty1, that are highly methylated in sperm. Nanog promoter methylation is erased by active and passive demethylation after fertilisation before expression commences in the morula. In ES cells the normally active Nanog promoter is silenced when targeted by de novo methylation. Our study suggests that reprogramming of promoter methylation is one of the key determinants of the epigenetic regulation of pluripotency genes. Epigenetic reprogramming in the germline prior to fertilisation and the reprogramming of key pluripotency genes in the early embryo is thus crucial for transmission of pluripotency.
Farthing
Cassandra R
CR
Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge, United Kingdom.
Ficz
Gabriella
G
Ng
Ray Kit
RK
Chan
Chun-Fung
CF
Andrews
Simon
S
Dean
Wendy
W
Hemberger
Myriam
M
Reik
Wolf
W
D000818:Animals; D002478:Cells, Cultured; D065150:Cellular Reprogramming; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D004815:Epidermal Growth Factor / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic; D005260:Female; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D018398:Homeodomain Proteins / Q000235:genetics* / Q000378:metabolism; D055458:Left-Right Determination Factors; D008297:Male; D008562:Membrane Glycoproteins / Q000235:genetics / Q000378:metabolism; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D051379:Mice; D008815:Mice, Inbred Strains; D046228:Microarray Analysis; D000071317:Nanog Homeobox Protein; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism; D039904:Pluripotent Stem Cells / Q000502:physiology; D011401:Promoter Regions, Genetic; D013094:Spermatozoa / Q000502:physiology; D013234:Stem Cells / Q000502:physiology*; D016212:Transforming Growth Factor beta / Q000235:genetics / Q000378:metabolism
D002868:Chromosomal Proteins, Non-Histone; D018398:Homeodomain Proteins; D055458:Left-Right Determination Factors; C111386:Lefty1 protein, mouse; D008562:Membrane Glycoproteins; D008565:Membrane Proteins; D000071317:Nanog Homeobox Protein; C475540:Nanog protein, mouse; D009363:Neoplasm Proteins; C529549:Smarcd1 protein, mouse; C489450:Tdgf1 protein, mouse; D016212:Transforming Growth Factor beta; D004815:Epidermal Growth Factor