DNA methylation-mediated down-regulation of DNA methyltransferase-1 (DNMT1) is coincident with, but not essential for, global hypomethylation in human placenta.
The genome of extraembryonic tissue, such as the placenta, is hypomethylated relative to that in somatic tissues. However, the origin and role of this hypomethylation remains unclear. The DNA methyltransferases DNMT1, -3A, and -3B are the primary mediators of the establishment and maintenance of DNA methylation in mammals. In this study, we investigated promoter methylation-mediated epigenetic down-regulation of DNMT genes as a potential regulator of global methylation levels in placental tissue. Although DNMT3A and -3B promoters lack methylation in all somatic and extraembryonic tissues tested, we found specific hypermethylation of the maintenance DNA methyltransferase (DNMT1) gene and found hypomethylation of the DNMT3L gene in full term and first trimester placental tissues. Bisulfite DNA sequencing revealed monoallelic methylation of DNMT1, with no evidence of imprinting (parent of origin effect). In vitro reporter experiments confirmed that DNMT1 promoter methylation attenuates transcriptional activity in trophoblast cells. However, global hypomethylation in the absence of DNMT1 down-regulation is apparent in non-primate placentas and in vitro derived human cytotrophoblast stem cells, suggesting that DNMT1 down-regulation is not an absolute requirement for genomic hypomethylation in all instances. These data represent the first demonstration of methylation-mediated regulation of the DNMT1 gene in any system and demonstrate that the unique epigenome of the human placenta includes down-regulation of DNMT1 with concomitant hypomethylation of the DNMT3L gene. This strongly implicates epigenetic regulation of the DNMT gene family in the establishment of the unique epigenetic profile of extraembryonic tissue in humans.
Novakovic
Boris
B
Developmental Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia.
Wong
Nick C
NC
Developmental Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia.
Sibson
Mandy
M
Developmental Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia.
Ng
Hong-Kiat
HK
Developmental Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia.
Morley
Ruth
R
Developmental Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia.
Manuelpillai
Ursula
U
Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia.
Down
Thomas
T
Wellcome Trust Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom.
Rakyan
Vardhman K
VK
Institute of Cell and Molecular Science, Barts and the London, London E1 2AT, United Kingdom.
Beck
Stephan
S
University College London Cancer Institute, University College London, London WC1E 6BT, United Kingdom.
Hiendleder
Stefan
S
JS Davies Epigenetics and Genetics Group, Animal Science, Adelaide, South Australia 5005, Australia.
Roberts
Claire T
CT
School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia 5005, Australia.
Craig
Jeffrey M
JM
Developmental Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia.
Saffery
Richard
R
Developmental Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia. Electronic address: richard.saffery@mcri.edu.au.
D001483:Base Sequence; D002454:Cell Differentiation; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism*; D019175:DNA Methylation; D015536:Down-Regulation; D044127:Epigenesis, Genetic; D005260:Female; D015971:Gene Expression Regulation, Enzymologic; D006801:Humans; D008969:Molecular Sequence Data; D010920:Placenta / Q000201:enzymology* / Q000378:metabolism; D011247:Pregnancy; D017422:Sequence Analysis, DNA; D013234:Stem Cells / Q000166:cytology; D014327:Trophoblasts / Q000378:metabolism
D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases; C000619380:DNMT1 protein, human