GSE168168
CTCF and transcription orchestrate chromatin structure re-configuration after mitosis [ChIP-seq]
During mitosis, transcription is globally attenuated and chromatin architecture is dramatically reconfigured. Here we exploited the M-phase to G1-phase progression to interrogate the contributions of the architectural factor CTCF and the process of transcription to re-sculpting the genome in newborn nuclei. While CTCF appears to be dispensable for large scale post-mitotic compartmentalization, depletion of CTCF specifically during the M-phase to G1-phase transition alters the re-establishment of local short-range compartmentalization after mitosis. Without CTCF, structural loops fail to reform, leading to illegitimate contacts between cis-regulatory elements (CREs) and altered gene expression in G1-phase. Transient CRE contacts that are normally resolved after telophase persist deeply into G1-phase in CTCF depleted cells. Boundary reformation is largely disrupted upon CTCF loss. Yet, a subset (~27%) of boundaries emerges normally in the absence of CTCF and is characterized by transitions in chromatin states. Reformation of gene domains can occur prior to the full onset of transcription and can be linked to tri-methylation at lysine 36 of histone 3 (H3K36me3), a mark stable throughout mitosis. The focus on the de novo formation of nuclear architecture during G1 entry yielded novel insights into how CTCF and the process of transcription contribute to the dynamic re-configuration of chromatin architecture during the mitosis to G1 phase progression. Overall design: Uninduced G1E-ER4 (-GATA1) cells were synchronized to pro-metaphase with nocodazole treatment and treated with or without auxin to remove CTCF. Cells from both CTCF depleted and replated groups were released from nocodazole for a variety of durations. For PolII ChIP-seq: Cells were harvested at 0min (prometa), 60min (early-G1), 120min (mid-G1) or 240min (late-G1) after nocodazole release to assess post-mitotic PolII binding with or without CTCF. 2-3 biological replicates per time point were collected