RESEARCH ARTICLE Embryonic Stem Cell Specific “Master” Replication Origins at the Heart of the Loss of

Epigenetic regulation of the replication program during mammalian cell differentiation re-mains poorly understood. We performed an integrative analysis of eleven genome-wide epigenetic profiles at 100 kb resolution of Mean Replication Timing (MRT) data in six human cell lines. Compared to the organization in four chromatin states shared by the five somatic cell lines, embryonic stem cell (ESC) line H1 displays (i) a gene-poor but highly dynamic chromatin state (EC4) associated to histone variant H2AZ rather than a HP1-associated heterochromatin state (C4) and (ii) a mid-S accessible chromatin state with bi-valent gene marks instead of a polycomb-repressed heterochromatin state. Plastic MRT regions ( ≲ 20 % of the genome) are predominantly localized at the borders of U-shaped timing domains. Whereas somatic-specific U-domain borders are gene-dense GC-rich re-gions, 31.6 % of H1-specific U-domain borders are early EC4 regions enriched in pluripo-tency transcription factors NANOG and OCT4 despite being GC poor and gene deserts. Silencing of these ESC-specific “master ” replication initiation zones during differentiation corresponds to a loss of H2AZ and an enrichment in H3K9me3 mark characteristic of lat