ArticleNature communications2021
Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 29 citations in OpenAlex.
- Photolabile oligonucleotides with topological light gradients enable spatially resolved single-cell transcriptomics and epigenomics.Nature biotechnology · 2026Article
- Unraveling the interplay of DNA methylation and chromosome organization.Biochemical Society transactions · 2025Review
- Macrophages in Hematopoiesis and Related Blood Diseases.Genomics, proteomics & bioinformatics · 2025Review
- Biology of host-dependent restriction-modification in prokaryotes.EcoSal Plus · 2025Review
- Homeostasis of DNA Hemi-Methylation in Arabidopsis through Methylation Maintenance, DNA Replication, and Nucleosome Positioning Mechanisms.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq.Nature biotechnology · 2025Article
- Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity.Nature structural & molecular biology · 2024Article
- Semiconservative transmission of DNAGenome research · 2024Article
- Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects.Nature biotechnology · 2024Article
- Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing.Nucleic acids research · 2024Article
- Single-cell bisulfite-free 5mC and 5hmC sequencing with high sensitivity and scalability.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Cost-effective DNA methylation profiling by FML-seq.Life science alliance · 2023Article
- scNanoCOOL-seq: a long-read single-cell sequencing method for multi-omics profiling within individual cells.Cell research · 2023Article
- Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development.Genomics, proteomics & bioinformatics · 2023Review
- Cost-effective DNA methylation profiling by FML-seq.bioRxiv : the preprint server for biology · 2023Article
- Technologies and applications of single-cell DNA methylation sequencing.Theranostics · 2023Review
- Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers.Development (Cambridge, England) · 2022Review
- A probabilistic framework for cellular lineage reconstruction using integrated single-cell 5-hydroxymethylcytosine and genomic DNA sequencing.Cell reports methods · 2021Article
- Introduction to Single-Cell DNA Methylation Profiling Methods.Biomolecules · 2021Review
- Simultaneous quantification of protein-DNA interactions and transcriptomes in single cells with scDam&T-seq.Nature protocols · 2020Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 4 countries.
Funding
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.