TY - JOUR
T1 - Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development
AU - Sen, Maya
AU - Mooijman, Dylan
AU - Chialastri, Alex
AU - Boisset, Jean-Charles
AU - Popovic, Mina
AU - Heindryckx, Björn
AU - Chuva de Sousa Lopes, Susana M
AU - Dey, Siddharth S
AU - van Oudenaarden, Alexander
PY - 2021/2/24
Y1 - 2021/2/24
N2 - DNA methylation (5mC) is central to cellular identity. The global erasure of 5mC from the parental genomes during preimplantation mammalian development is critical to reset the methylome of gametes to the cells in the blastocyst. While active and passive modes of demethylation have both been suggested to play a role in this process, the relative contribution of these two mechanisms to 5mC erasure remains unclear. Here, we report a single-cell method (scMspJI-seq) that enables strand-specific quantification of 5mC, allowing us to systematically probe the dynamics of global demethylation. When applied to mouse embryonic stem cells, we identified substantial cell-to-cell strand-specific 5mC heterogeneity, with a small group of cells displaying asymmetric levels of 5mCpG between the two DNA strands of a chromosome suggesting loss of maintenance methylation. Next, in preimplantation mouse embryos, we discovered that methylation maintenance is active till the 16-cell stage followed by passive demethylation in a fraction of cells within the early blastocyst at the 32-cell stage of development. Finally, human preimplantation embryos qualitatively show temporally delayed yet similar demethylation dynamics as mouse embryos. Collectively, these results demonstrate that scMspJI-seq is a sensitive and cost-effective method to map the strand-specific genome-wide patterns of 5mC in single cells.
AB - DNA methylation (5mC) is central to cellular identity. The global erasure of 5mC from the parental genomes during preimplantation mammalian development is critical to reset the methylome of gametes to the cells in the blastocyst. While active and passive modes of demethylation have both been suggested to play a role in this process, the relative contribution of these two mechanisms to 5mC erasure remains unclear. Here, we report a single-cell method (scMspJI-seq) that enables strand-specific quantification of 5mC, allowing us to systematically probe the dynamics of global demethylation. When applied to mouse embryonic stem cells, we identified substantial cell-to-cell strand-specific 5mC heterogeneity, with a small group of cells displaying asymmetric levels of 5mCpG between the two DNA strands of a chromosome suggesting loss of maintenance methylation. Next, in preimplantation mouse embryos, we discovered that methylation maintenance is active till the 16-cell stage followed by passive demethylation in a fraction of cells within the early blastocyst at the 32-cell stage of development. Finally, human preimplantation embryos qualitatively show temporally delayed yet similar demethylation dynamics as mouse embryos. Collectively, these results demonstrate that scMspJI-seq is a sensitive and cost-effective method to map the strand-specific genome-wide patterns of 5mC in single cells.
KW - Animals
KW - Blastocyst/metabolism
KW - DNA (Cytosine-5-)-Methyltransferase 1/deficiency
KW - DNA Demethylation
KW - DNA Methylation/genetics
KW - Embryonic Development/genetics
KW - Embryonic Stem Cells/cytology
KW - Female
KW - Humans
KW - Mice
KW - Mice, Knockout
KW - Pregnancy
U2 - 10.1038/s41467-021-21532-6
DO - 10.1038/s41467-021-21532-6
M3 - Article
C2 - 33627650
SN - 2041-1723
VL - 12
SP - 1286
JO - Nature Communications
JF - Nature Communications
IS - 1
ER -