Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution

Abstract

Although mitotic chromosomes are highly compacted and transcriptionally inert, some active chromatin features are retained during mitosis to ensure the proper postmitotic reestablishment of maternal transcriptional programs, a phenomenon termed “mitotic bookmarking.” However, the dynamics and regulation of mitotic bookmarking have not been systemically surveyed. Using single-cell transposase-accessible chromatin sequencing (scATAC-seq), we examined 6538 mitotic L02 human liver cells of variable stages and found that chromatin accessibility remained changing throughout cell division, with a constant decrease until metaphase and a gradual increase as chromosomes segregated. In particular, a subset of chromatin regions were identified to remain open throughout mitosis, and genes associated with these bookmarked regions are primarily linked to rapid reactivation upon mitotic exit. We also demonstrated that nuclear transcription factor Y subunit α (NF-YA) preferentially occupied bookmarked regions and contributed to transcriptional reactivation after mitosis. Our study uncovers the dynamic and regulatory blueprint of mitotic bookmarking.

Maintaining transcriptional homeostasis during cell cycle

“…However, genes transcribed during mitosis primarily support fundamental cellular functions, and the transcripts that rapidly achieve high expression levels upon exiting mitosis also pertain to basic cellular functions [ 14 ]. In accordance with a recent study employing single-cell ATAC-sequencing to map accessible regions of mitotic chromatin discovered that these regions are marked by NF-YA, which maintains their accessibility and facilitates the rapid reactivation of housekeeping genes upon mitotic exit [ 7 ]. Other mechanisms involving GTF, TBP and TFIID, as well as Topoisomerase I, have been demonstrated to sustain promoter accessibility during the M phase and contribute to mitotic transcription or gene reactivation during early G1 (reviewed in [ 28 ]).…”

“…Currently, two non-exclusive mechanisms have been proposed. First, certain regulators such as TBP, NF-YA, or GAF associate persistently with mitotic chromatin in a sequence-specific manner, thereby potentially preserving the accessibility of chromatin for the transcriptional machinery upon mitotic exit [ 7 , 92–94 ]. Second, gene regulators like ESRRβ and FOXA1 coat chromosomes and dynamically survey mitotic chromatin through both sequence-specific and nonspecific interactions.…”

“…However, the application of formaldehyde crosslinking in ChIP or microscopy caused the translocation of transcription factors to the cytoplasm or failed to capture the swift turnover of transcription regulators on mitotic chromatin [ 20 ], which prevented the detection of mitotic gene regulators. In fact, recent studies have provided compelling evidence regarding the preservation of genome accessibility at specific enhancers and promoters during mitosis, despite the loss of long-range intrachromosomal interactions such as topologically associating domains (TADs), enhancer-promoter loops, and enhancer accessibility [ 7 , 13 , 21 , 22 ]. This preservation is supported by observations from live-cell imaging, which have demonstrated the co-localization of TFs with mitotic chromatin [ 23 , 24 ].…”

Repair of DNA double-strand breaks leaves heritable impairment to genome function

“…On the one hand, the extensive DNA compaction during mitosis and re-formation of the interphase nucleus in the subsequent G1 phase ( 39 ) could provide a window of opportunity for the cell to reset the chromatin state and reverse potential alterations in chromatin structure introduced during DSB repair. On the other hand, our findings raise the possibility that the de novo DSB-induced changes in 3-D chromatin makeup could be stabilized by mechanisms similar to mitotic bookmarking, which manifest in stabilized chromatin accessibility patterns to enforce physiological chromatin memory ( 83 , 84 ). Indeed, at least one key component of transcriptional mitotic bookmarking, the SWI/SNF chromatin remodeler SMARCE1 was recently shown to be among proteins that are recruited to DSB-flanking chromatin ( 85 ).…”

Compaction of Active Chromatin Domains and Promoters by H3S10 Phosphorylation during Mitosis Preserves Interphase-Specific Chromatin Structure and Function

“…Contrary to the complete loss of chromatin domains, some histone modifications, chromatin remodelers and transcription factors remain bound during mitosis, known as mitotic bookmarking (Martínez-Balbás et al, 1995;Valls, Sánchez-Molina and Martínez-Balbás, 2005;Muramoto et al, 2010;Zhao et al, 2011;Kadauke et al, 2012;Caravaca et al, 2013;Hsiung et al, 2015;Teves et al, 2016;Oomen et al, 2019;Kang et al, 2020;Pelham-Webb et al, 2021;Yu et al, 2023;Zhu et al, 2023). Mitotic persistence of these bookmarkers is critical for enhancer-promoter function and gene transcription in the next interphase.…”