Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis

Abstract

Differentiation of mouse embryonic stem cells (mESCs) is accompanied by changes in replication timing. To explore the relationship between replication timing and cell fate transitions, we constructed genome-wide replication-timing profiles of 22 independent mouse cell lines representing 10 stages of early mouse development, and transcription profiles for seven of these stages. Replication profiles were cell-type specific, with 45% of the genome exhibiting significant changes at some point during development that were generally coordinated with changes in transcription. Comparison of early and late epiblast cell culture models revealed a set of early-to-late replication switches completed at a stage equivalent to the postimplantation epiblast, prior to germ layer specification and down-regulation of key pluripotency transcription factors [POU5F1 (also known as OCT4)/NANOG/SOX2] and coinciding with the emergence of compact chromatin near the nuclear periphery. These changes were maintained in all subsequent lineages (lineage-independent) and involved a group of irreversibly down-regulated genes, at least some of which were repositioned closer to the nuclear periphery. Importantly, many genomic regions of partially reprogrammed induced pluripotent stem cells (piPSCs) failed to re-establish ESC-specific replication-timing and transcription programs. These regions were enriched for lineage-independent earlyto-late changes, which in female cells included the inactive X chromosome. Together, these results constitute a comprehensive ''fate map'' of replication-timing changes during early mouse development. Moreover, they support a model in which a distinct set of replication domains undergoes a form of ''autosomal Lyonization'' in the epiblast that is difficult to reprogram and coincides with an epigenetic commitment to differentiation prior to germ layer specification.

p53 and p16INK4A independent induction of senescence by chromatin-dependent alteration of S-phase progression

“…3g). A correlation between replication time, chromatin structure and transcriptional activity has long been observed, but recent genome-wide studies revealed that a large fraction of the genome is subjected to dynamic changes during development, allowing the establishment of cell-type specific replication timing profiles [35][36][37] . Replication timing is therefore thought to represent a mitotically stable cell-type specific feature of chromosomes.…”

Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape

“…Importantly, reprogramming is still not very efficient from EpiSCs to the ES cell state, and it is not understood why [114]. As we will discuss later, a possible reason for this observation is that EpiSCs and ES cells differ in their global nuclear organization [116].…”

“…Interestingly, pre-iPS cells appear to be intermediates between ES cells and fibroblasts, also in their cell cycle profile. A pre-iPS cell culture seems to have about equal percent of cells in G1 and S phase, and interestingly, this cell cycle profile is rather similar to EpiSCs, whereas the vast majority of fibroblast and ES cells are in G1 or S phase, respectively [116]. What is different in pre-iPSCs/ EpiSCs as opposed to ES/iPS cells in terms of cell cycle regulation and how is that related to pluripotency?…”

“…Detailed genome-wide DNA replication studies of ES cells, their differentiation and EpiSCs, revealed that differentiation is associated with global nuclear reorganization events and replication timing changes that occur in a sequential manner [116]. First, shortly after induction of differentiation of ES cells, replication timing switches occur mainly from early to late in S phase, concomitant with the downregulation of only very few pluripotency genes such as Dppa2 and Zfp42, and a switch of the Xi in female cells from early-to-late replication [116].…”

“…First, shortly after induction of differentiation of ES cells, replication timing switches occur mainly from early to late in S phase, concomitant with the downregulation of only very few pluripotency genes such as Dppa2 and Zfp42, and a switch of the Xi in female cells from early-to-late replication [116]. Thus, during in vitro differentiation, before the EpiSClike stage is reached, a global epigenetic reorganization has occurred, prior to the silencing of most pluripotency genes, including Oct4 and Nanog [116]. The G1 cell cycle length also increases at this time, suggesting that the two events are linked and that in the in vivo equivalent stage they might happen approximately in one day at around the implantation of the blastocyst [116].…”