CTCF and transcription influence chromatin structure re-configuration after mitosis

Abstract

During mitosis, transcription is globally attenuated and chromatin architecture is dramatically reconfigured. Here we exploited the M- 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. Depletion of CTCF specifically during the M- to G1-phase transition altered the re-establishment of local short-range compartmentalization after mitosis. Chromatin domain boundary reformation was impaired upon CTCF loss, but a subset (~27%) of boundaries, characterized by transitions in chromatin states, was established normally. Without CTCF, structural loops failed to form, leading to illegitimate contacts between cis-regulatory elements (CREs). Transient CRE contacts that are normally resolved after telophase persisted deeply into G1-phase in CTCF depleted cells. CTCF loss-associated gains in transcription were often linked to increased, normally illegitimate enhancer-promoter contacts. In contrast, at genes whose expression declined upon CTCF loss, CTCF seems to function as a conventional transcription activator, independent of its architectural role. CTCF-anchored structural loops facilitated formation CRE loops nested within them, especially those involving weak CREs. Transcription inhibition did not elicit global architectural changes and left transcription start site-associated boundaries intact. However, ongoing transcription contributed considerably to the formation of gene domains, regions of enriched contacts spanning the length of gene bodies. Notably, gene domains formed rapidly in ana/telophase prior to the completion of the first round of transcription, suggesting that epigenetic features in gene bodies contribute to genome reconfiguration prior to transcription. The focus on the de novo formation of nuclear architecture during G1 entry yielded novel insights into how CTCF and transcription contribute to the dynamic re-configuration of chromatin architecture during the mitosis to G1 phase progression.

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

“…Principal Component Analysis (PCA) revealed similar trajectories of the +/-IAA transcriptomes ( Fig.4B ), leading to nearly identical median gene reactivation dynamics ( Fig.4C ). These results indicate that the post-mitotic burst in ES cells is robust and largely insensitive to CTCF depletion, as recently shown in other biological contexts 12,23 . Nevertheless, careful examination of the PCA ( Fig.4B ) suggests that small differences exist along PC1 between + and -IAA treatments, 20 and 40min after mitosis.…”

“…Hence, at these genes, the reacquisition of CTCF binding after mitosis is accompanied by their sustained activation, indicating that even in the absence of mitotic binding, CTCF may contribute to gene activity before the onset of replication. This interpretation is supported by the fast rebinding of CTCF to DNA following mitosis 12,25 . Strikingly, genes responding rapidly after mitosis to the loss of CTCF displayed a strong statistical association to CTCF binding sites, with a very prominent enrichment of genes activated by CTCF (early-down) within 10kb of CTCF Book sites ( Fig.5B ).…”

“…Hence, perhaps transiently and randomly established contacts during the transition from a Condensin-mediated mode of 3D organisation in metaphase, to one driven by Cohesin in telophase 31 , could fuel the burst of transcription observed in G1. However, a main driver of TADs formation, CTCF 14 , does not influence the global dynamics of reactivation, neither in ES cells nor in somatic cells 12 . Additional properties, such as a sudden decondensation of the chromatin, should be envisioned as potential drivers.…”

“…Second, the post-mitotic hyper-active transcriptional state could be the indirect consequence of other properties of post-mitotic cells. For instance, the re-folding of the genome into topologically associating domains (TADs), which largely confine enhancer function, has been shown to take place, in average, after gene reactivation 12,25,30 . Importantly, before TADs are reestablished, intra and inter-TAD enhancer-promoter contacts drive inappropriate gene activation 25 .…”

Inferring functions of coding and non-coding genes using epigenomic patterns and deciphering the effect of combinatorics of transcription factors binding at promoters

“…Some of the top predictive transcription factors and cofactors shared among the functions of cluster-47 are CTCF, XRN2, BRD4, SMARCA4, and PARP1 (Figure 3B). The role of CTCF, MYC, PARP-1, and SMARCA4 in cell cycle regulation has been reported by previous studies (Hyle et al 2019;Haoyue Zhang et al 2021;L. Yang et al 2013;Hendricks, Shanahan, and Lees 2004).…”