title: Simultaneous mapping of active DNA demethylation and sister chromatid exchange in single cells.
abstract: To understand mammalian active DNA demethylation, various methods have been developed to map the genomic distribution of the demethylation intermediates 5-formylcysotine (5fC) and 5-carboxylcytosine (5caC). However, the majority of these methods requires a large number of cells to begin with. In this study, we describe low-input methylase-assisted bisulfite sequencing (liMAB-seq ) and single-cell MAB-seq (scMAB-seq), capable of profiling 5fC and 5caC at genome scale using ∼100 cells and single cells, respectively. liMAB-seq analysis of preimplantation embryos reveals the oxidation of 5mC to 5fC/5caC and the positive correlation between chromatin accessibility and processivity of ten-eleven translocation (TET) enzymes. scMAB-seq captures the cell-to-cell heterogeneity of 5fC and 5caC and reveals the strand-biased distribution of 5fC and 5caC. scMAB-seq also allows the simultaneous high-resolution mapping of sister chromatid exchange (SCE), facilitating the study of this type of genomic rearrangement. Therefore, our study not only establishes new methods for the genomic mapping of active DNA demethylation using limited numbers of cells or single cells but also demonstrates the utilities of the methods in different biological contexts.
authors.affiliation: Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.|Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.|Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA.|Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.|PhD Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Xiaoji
authors.initials: X
authors.lastname: Wu
authors.affiliation: Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.|Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.|Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA.|Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Azusa
authors.initials: A
authors.lastname: Inoue
authors.affiliation: Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.|Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.|Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA.|Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Tsukasa
authors.initials: T
authors.lastname: Suzuki
authors.affiliation: Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.|Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.|Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA.|Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001757:Blastomeres / Q000378:metabolism; D002874:Chromosome Mapping / Q000379:methods*; D019175:DNA Methylation; D004261:DNA Replication; D004622:Embryo, Mammalian; D023281:Genomics / Q000379:methods*; D051379:Mice; D059010:Single-Cell Analysis / Q000379:methods*; D012854:Sister Chromatid Exchange
keywords: 5-carboxylcytosine; 5-formylcytosine; low input; methylase-assisted bisulfite sequencing; single cell; sister chromatid exchange