RT Journal
A1 Chen, Geng
A1 Schell, John Paul
A1 Benitez, Julio Aguila
A1 Petropoulos, Sophie
A1 Yilmaz, Marlene
A1 Reinius, Björn
A1 Alekseenko, Zhanna
A1 Shi, Leming
A1 Hedlund, Eva
A1 Lanner, Fredrik
A1 Sandberg, Rickard
A1 Deng, Qiaolin
T1 Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation
JF Genome Research 
JO Genome Research 
YR 2016 
FD October 01 
VO 26 
IS 10 
SP 1342 
OP 1354 
DO 10.1101/gr.201954.115 
UL http://genome.cshlp.org/content/26/10/1342.abstract 
AB 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.