Mitotic bookmarking by CTCF controls selected genes during the fast post-mitotic genome reactivation of ES cells

Abstract

Mitosis leads to a global downregulation of transcription that then needs to be efficiently restored. In somatic cells, this is mediated by a transient hyper-active state that first leads to the reactivation of genes necessary to rebuild the interphasic cell and then of those executing specific cell functions. Here, we hypothesized that cells displaying rapid cell cycles may display accelerated gene reactivation dynamics. To test this, we focused on mouse Embryonic Stem (ES) cells, which have a short cell cycle and spend a minor time in G1. Compared to previous studies, we observed a uniquely fast global reactivation, which displays little specificity towards housekeeping versus cell identity genes. Such lack of specificity may enable the restoration of the entirety of regulatory functions before the onset of DNA replication. Genes displaying the fastest reactivation dynamics are associated with binding of CTCF, a transcription factor that largely maintains binding to its targets on DNA during mitosis. Nevertheless, we show that the post-mitotic global burst is robust and largely insensitive to CTCF depletion. There are, however, around 350 genes that respond to CTCF depletion rapidly after mitotic exit. Remarkably, these are characterised by promoter-proximal mitotic bookmarking by CTCF. We propose that the structure of the cell cycle imposes distinct constrains to post-mitotic gene reactivation dynamics in different cell types, via mechanisms that are yet to be identified but that can be modulated by mitotic bookmarking factors.

Function and regulation of transcription factors during mitosis-to-G1 transition

“…housekeeping) [ 9 ]. By contrast, the timing of transcriptional reactivation of house-keeping and pluripotency genes does not differ significantly in ES cells, which are characterized by an overall faster kinetics of gene reactivation [ 12 , 63 ]. This may result from constraints imposed by the cell-cycle in ES cells, namely their shorter G1 phase.…”

“…In HeLa cells, the majority of enhancer-promoter contacts were identified in telophase/cytokinesis, although also before structural loops are reformed [ 58 , 65 ]. Interestingly, mitotic-specific CTCF degradation has a marginal impact on gene reactivation during M-G1 in both ES and erythroblasts, in line with a preponderant role for enhancer-promoter contacts in driving gene expression prior to the establishment of structural loops [ 63 , 66 ].…”