title: Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos.
abstract: The mammalian post-implantation embryo has been extensively investigated at the tissue level. However, to unravel the molecular basis for the cell-fate plasticity and determination, it is essential to study the characteristics of individual cells. In particular, the individual definitive endoderm (DE) cells have not been characterizedin vivoHere, we report gene expression patterns in single cells freshly isolated from mouse embryos on days 5.5 and 6.5. Initial transcriptome data from 124 single cells yielded signature genes for the epiblast, visceral endoderm, and extra-embryonic ectoderm and revealed a unique distribution pattern of fibroblast growth factor (FGF) ligands and receptors. Further analysis indicated that early-stage epiblast cells do not segregate into lineages of the major germ layers. Instead, some cells began to diverge from epiblast cells, displaying molecular features of the premesendoderm by expressing higher levels of mesendoderm markers and lower levels ofSox3transcripts. Analysis of single-cell high-throughput quantitative RT-PCR data from 441 cells identified a late stage of the day 6.5 embryo in which mesoderm and DE cells emerge, with many of them coexpressingOct4andGata6Analysis of single-cell RNA-sequence data from 112 cells of the late-stage day 6.5 embryos revealed differentially expressed signaling genes and networks of transcription factors that might underlie the segregation of the mesoderm and DE lineages. Moreover, we discovered a subpopulation of mesoderm cells that possess molecular features of the extraembryonic mesoderm. This study provides fundamental insight into the molecular basis for lineage segregation in post-implantation mouse embryos.
authors.affiliation: From the Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, Shanghai 200031.
authors.forename: Jing
authors.initials: J
authors.lastname: Wen
authors.affiliation: the Department of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, and.
authors.forename: Yanwu
authors.initials: Y
authors.lastname: Zeng
authors.affiliation: From the Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, Shanghai 200031.
authors.forename: Zhuoqing
authors.initials: Z
authors.lastname: Fang
authors.affiliation: the Department of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, and.
authors.forename: Junjie
authors.initials: J
authors.lastname: Gu
authors.affiliation: the Department of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, and.
authors.forename: Laixiang
authors.initials: L
authors.lastname: Ge
authors.affiliation: the Department of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, and.
authors.forename: Fan
authors.initials: F
authors.lastname: Tang
authors.affiliation: the Department of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, and.
authors.forename: Zepeng
authors.initials: Z
authors.lastname: Qu
authors.affiliation: the Department of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, and.
authors.forename: Jing
authors.initials: J
authors.lastname: Hu
authors.affiliation: the Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, China.
authors.forename: Yaru
authors.initials: Y
authors.lastname: Cui
authors.affiliation: the Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, China.
authors.forename: Kushan
authors.initials: K
authors.lastname: Zhang
authors.affiliation: the Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, China.
authors.forename: Junbang
authors.initials: J
authors.lastname: Wang
authors.affiliation: the Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, China.
authors.forename: Siguang
authors.initials: S
authors.lastname: Li
authors.affiliation: the Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Sun
authors.affiliation: From the Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, Shanghai 200031, yjin@sibs.ac.cn.|the Department of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, and.
authors.forename: Ying
authors.initials: Y
authors.lastname: Jin
mesh_terms: D000818:Animals; D000943:Antigens, Differentiation / Q000096:biosynthesis*; D019070:Cell Lineage / Q000502:physiology*; D004622:Embryo, Mammalian / Q000166:cytology / Q000378:metabolism; D047108:Embryonic Development / Q000502:physiology*; D050993:GATA6 Transcription Factor / Q000096:biosynthesis; D018507:Gene Expression Regulation, Developmental / Q000502:physiology*; D051379:Mice; D050814:Octamer Transcription Factor-3 / Q000096:biosynthesis; D055748:SOXB1 Transcription Factors / Q000096:biosynthesis; D059467:Transcriptome / Q000502:physiology*
chemical_list: D000943:Antigens, Differentiation; D050993:GATA6 Transcription Factor; C494760:Gata6 protein, mouse; D050814:Octamer Transcription Factor-3; C494174:Pou5f1 protein, mouse; D055748:SOXB1 Transcription Factors; C527786:Sox3 protein, mouse
keywords: definitive endoderm; development; differentiation; embryo; extraembryonic mesoderm; gastrulation; gene regulation; mesoderm; single-cell RNA-Seq; transcriptomics