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Genome Res. 2016 Oct;26(10):1342-1354. Epub 2016 Aug 2.

Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation.

Author information

1
Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; School of Pharmacy, Fudan University, 201203 Shanghai, China.
2
Department of Clinical Science, Intervention and Technology and Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, 14186 Stockholm, Sweden.
3
Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden.
4
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.
5
Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
6
School of Pharmacy, Fudan University, 201203 Shanghai, China.
7
Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden.
8
Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden.

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.

PMID:
27486082
PMCID:
PMC5052059
DOI:
10.1101/gr.201954.115
[Indexed for MEDLINE]
Free PMC Article

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