Multi-modal single-cell sequencing of differentiating mESCs using Smart-seq3 and scATAC-seq

ABSTRACT: We report dynamics of X-chromosome upregulation (XCU) along X-chromosome inactivation (XCI) in mESCs as they differentiate into EpiSCs. F1 hybrid C57BL6/J × CAST/EiJ male and female mESCs were grown in serum/LIF conditions were differentiated using Fgf2 and Activin A for 1, 2, 4 and 7 days to induce random XCI in female cells. Multi-modal single-cell sequencing was performed using scATAC on nuclei and Smart-seq3 to assay chromatin accessibility and poly-A+ RNA expression, respectively. Allelic resolution is achieved using strain-specific SNPs in the data. We reveal dynamic balancing of X alleles as cells undergo XCI to compensate dosage imbalances between sexes as well as between X and autosomes. Furthermore, we reveal that female naïve mESCs with two active X chromosomes lack XCU on both alleles which has major implications for reprogramming studies. Finally, we estimate allelic transcriptional burst kinetics from the data and find that progressively increased burst frequencies underlies the XCU process.

INSTRUMENT(S): Eppendorf EpMotion 5073m pipetting robot, NextSeq 550, Sony SH800

ORGANISM(S): Mus musculus

SUBMITTER: Antonio Lentini 

PROVIDER: E-MTAB-10714 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress