Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation

Abstract

During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division.

Dynamic 3D Chromatin Reorganization during Establishment and Maintenance of Pluripotency

“…Here we focus on those that measured nascent transcriptional activity rather than steady-state RNA levels, by assays such as PRO-seq (precision nuclear run on sequencing) ( Core et al., 2008 ; Kwak et al., 2013 ) and EU-RNA-seq (ethyl uridine-labeled RNA sequencing) ( Palozola et al., 2017 ). These studies consistently showed that transcription of genes and enhancers is dramatically downregulated during mitosis but rapidly recovered during G1 entry ( Hsiung et al., 2016 ; Kang et al., 2020 ; Palozola et al., 2017 ; Pelham-Webb et al, 2020 ; Teves et al, 2018 ). Studies in somatic cells also saw a global, transient spike in transcription during mitotic exit, although groups of genes showed distinct kinetics ( Hsiung et al., 2016 ; Palozola et al., 2017 ).…”

“…Several recent studies have begun characterizing the dynamic resetting of chromatin architecture upon mitotic exit in different cell types ( Abramo et al., 2019 ; Kang et al., 2020 ; Naumova et al., 2013 ; Zhang et al., 2019 ), including mouse naive PSCs ( Nagano et al., 2017 ; Pelham-Webb et al, 2020 ). Nagano et al.…”

“…More recent studies have shed light on these remaining questions in various mouse and human cell lines ( Abramo et al., 2019 ; Kang et al., 2020 ; Zhang et al., 2019 ), including mouse PSCs ( Pelham-Webb et al, 2020 ), by performing bulk Hi-C in various time points after mitotic arrest and release. Despite the technical differences, these reports also observed a rapid but heterogeneous resetting of genome architecture, with many similarities to the single-cell Hi-C study ( Nagano et al., 2017 ).…”

“…A similar hypertranscriptional spike during G1 was independently detected in mouse PSCs ( Pelham-Webb et al, 2020 ), indicating that this is a general feature of transcriptional resetting. However, the relative timing of gene reactivation differed among cell types, with cell identity genes being slowly reactivated in somatic cells, such as hepatocytes ( Kang et al., 2020 ; Palozola et al., 2017 ), while PSC-associated genes and enhancers were among the first reactivated in stem cells ( Pelham-Webb et al, 2020 ), indicating different requirements for propagation/resetting of the PSC program. Interestingly, these studies also described a significant correlation in the reactivation kinetics between enhancers and their target genes (assigned by linear proximity or looping) ( Hsiung et al., 2016 ; Palozola et al., 2017 ; Pelham-Webb et al, 2020 ), suggesting that transcriptional reactivation is coordinated locally and/or through looping.…”

Interactions With Histone H3 & Tools to Study Them

“…For example, ChIP-seq in mitotically arrested mESCs demonstrated that H3K27ac was retained at housekeeping gene promoters and stem-cell associated enhancers during mitosis, suggesting that the mark primes transcriptional activation in G 0 /G 1 . Recent data demonstrated H3K4me3 remained associated with most promoters, while H3K27ac was maintained at only a subset of enhancers and promoters, but quickly reestablished at the anaphase/telophase transition (Kang et al, 2020). This was determined using a combinatorial approach with ChIP-seq and EU-RNA-seq, a technique where cells are treated with ethynyl uridine to label newly synthesized RNA, which can then be isolated and sequenced to generate a transcriptome of newly synthesized transcripts.…”