Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [scRepli-seq]

In mammals, chromosomes are partitioned into megabase-sized topologically associating domains (TADs). TADs can be in either A (active) or B (inactive) subnuclear compartments, which correspond to early (E) and late (L) replicating timing (RT) domains, respectively. Here, we show that RT changes are tightly correlated with A/B compartment changes during mouse embryonic stem cell (mESC) differentiation. A/B compartments changed mostly by a “boundary shift,” frequently causing compartment switching of single TADs, which coincided with or preceded RT changes. Upon differentiation, mESCs acquired an A/B compartment organization that closely resembled EpiSCs (epiblast-derived stem cells), suggesting that accumulation of compartment boundary repositioning eventually led to naïve-to-primed pluripotency transition in A/B compartment organization. We propose that large-scale reorganization of A/B compartments, which is reflected in RT domain reorganization, represents major cell fate changes. Collectively, our data provides valuable insights into the regulatory principles of 3-dimensional (3D) genome organization during early embryonic stages. Overall design: scRepli-seq: Single-cell Repli-seq experiments in G1 and S-phase cells (total 884 cells) of 7-day differentiation (d0~d7) of female mouse embryonic stem cells (CBMS1 mESCs) and epiblast stem cells (EpiSCs) incorporating our previous scRepli-seq data (under GSE108556). We also selected the sample sets from our previous scRepli-seq data (under GSE108556) to obtain additional sequence reads for analyzing the resolution at 40kb (28 Mid-S single cells for mESCs, and 15 Mid-S single cells for 7-day differentiated mESCs). Please note that, as most (49 out of 51 [GSM3142337 to GSM3142387]) of the re-analyzed GSE108556 samples/data include additional raw data, duplicated sample records (e.g. GSM3142338 for GSM2904979 in GSE108556) were created to link all associated raw data and re-analyzed processed data, as described in the corresponding sample description field.