title: Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation.
abstract: Pluripotency, differentiation, and X Chromosome inactivation (XCI) are key aspects of embryonic development. However, the underlying relationship and mechanisms among these processes remain unclear. Here, we systematically dissected these features along developmental progression using mouse embryonic stem cells (mESCs) and single-cell RNA sequencing with allelic resolution. We found that mESCs grown in a ground state 2i condition displayed transcriptomic profiles diffused from preimplantation mouse embryonic cells, whereas EpiStem cells closely resembled the post-implantation epiblast. Sex-related gene expression varied greatly across distinct developmental states. We also identified novel markers that were highly enriched in each developmental state. Moreover, we revealed that several novel pathways, including PluriNetWork and Focal Adhesion, were responsible for the delayed progression of female EpiStem cells. Importantly, we "digitalized" XCI progression using allelic expression of active and inactive X Chromosomes and surprisingly found that XCI states exhibited profound variability in each developmental state, including the 2i condition. XCI progression was not tightly synchronized with loss of pluripotency and increase of differentiation at the single-cell level, although these processes were globally correlated. In addition, highly expressed genes, including core pluripotency factors, were in general biallelically expressed. Taken together, our study sheds light on the dynamics of XCI progression and the asynchronicity between pluripotency, differentiation, and XCI.
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; School of Pharmacy, Fudan University, 201203 Shanghai, China.
authors.forename: Geng
authors.initials: G
authors.lastname: Chen
authors.affiliation: Department of Clinical Science, Intervention and Technology and Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, 14186 Stockholm, Sweden.
authors.forename: John Paul
authors.initials: JP
authors.lastname: Schell
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden.
authors.forename: Julio Aguila
authors.initials: JA
authors.lastname: Benitez
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Clinical Science, Intervention and Technology and Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, 14186 Stockholm, Sweden.
authors.forename: Sophie
authors.initials: S
authors.lastname: Petropoulos
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
authors.forename: Marlene
authors.initials: M
authors.lastname: Yilmaz
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
authors.forename: Björn
authors.initials: B
authors.lastname: Reinius
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
authors.forename: Zhanna
authors.initials: Z
authors.lastname: Alekseenko
authors.affiliation: School of Pharmacy, Fudan University, 201203 Shanghai, China.
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
authors.affiliation: Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden.
authors.forename: Eva
authors.initials: E
authors.lastname: Hedlund
authors.affiliation: Department of Clinical Science, Intervention and Technology and Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, 14186 Stockholm, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Lanner
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden.
authors.forename: Rickard
authors.initials: R
authors.lastname: Sandberg
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
authors.forename: Qiaolin
authors.initials: Q
authors.lastname: Deng
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D002478:Cells, Cultured; D053595:Embryonic Stem Cells / Q000166:cytology* / Q000378:metabolism; D005260:Female; D018507:Gene Expression Regulation, Developmental; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D039904:Pluripotent Stem Cells / Q000166:cytology* / Q000378:metabolism; D059010:Single-Cell Analysis; D059467:Transcriptome; D049951:X Chromosome Inactivation