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Published OnlineFirst July 12, 2018; DOI: 10.1158/1541-7786.MCR-18-0415 Review Molecular Cancer Research Mitotic Gene Bookmarking: An Epigenetic Program to Maintain Normal and Cancer Phenotypes Sayyed K. Zaidi1, Jeffrey A. Nickerson2, Anthony N. Imbalzano3, Jane B. Lian1, Janet L. Stein1, and Gary S. Stein1 Abstract Reconfiguration of nuclear structure and function during chromosomes is essential to sustain lineage commitment; (ii) mitosis presents a significant challenge to resume the next cell Select chromatin modifiers and posttranslational histone cycle in the progeny cells without compromising structural modifications/variants retain competency of mitotic chroma- and functional identity of the cells. Equally important is the tin for gene reactivation as cells exit mitosis; and (iii) Func- requirement for cancer cells to retain the transformed pheno- tional components of RNAP I and II transcription complexes type, that is, unrestricted proliferative potential, suppression (e.g., UBF and TBP, respectively) are retained on genes of cell phenotype, and activation of oncogenic pathways. poised for reactivation immediately following mitosis. Impor- Mitotic gene bookmarking retention of key regulatory proteins tantly, recent findings have identified oncogenes that are that include sequence-specific transcription factors, chroma- associated with target genes on mitotic chromosomes in cancer tin-modifying factors, and components of RNA Pol (RNAP) cells. The current review proposes that mitotic gene book- I and II regulatory machineries at gene loci on mitotic chro- marking is an extensively utilized epigenetic mechanism for mosomes plays key roles in coordinate control of cell pheno- stringent control of proliferation and identity in normal type, growth, and proliferation postmitotically. There is grow- cells and hypothesizes that bookmarking plays a pivotal role ing recognition that three distinct protein types, mechanisti- in maintenance of tumor phenotypes, that is, unrestricted cally, play obligatory roles in mitotic gene bookmarking: (i) proliferation and compromised control of differentiation. Retention of phenotypic transcription factors on mitotic Mol Cancer Res; 16(11); 1617–24. Ó2018 AACR. Introduction by our group, and others, have shown that mitotic gene book- marking is mediated by key regulatory proteins that include Functional compartmentalization of regulatory proteins and components of RNAP I and II machineries, chromatin-modifying nucleic acids in the interphase nuclear microenvironments is factors and sequence-specific transcription factors and coregula- essential for physiologic control of gene expression (1–6). This tory proteins as well as variants and selective modifications of organization is disrupted in cancer, leading to deregulated nucleosomal histones (15–37). The functional outcome of mitot- transcriptional programming during the onset and progression ic gene bookmarking is the sustained normal cell phenotype of tumorigenesis (6–11). Mitosis is an essential cellular process across successive cell divisions. Evidence is accruing for role(s) that requires structural and functional remodeling of regulatory of mitotic gene bookmarking in regulating stem cell plasticity machinery in the nucleus (12–14). Disruption of this physiologic and in the onset, progression and maintenance of the tumor process poses a serious challenge to cell phenotype and identity phenotype. In this review, we present evolution of the concept and every cell cycle. Over the past two decades, mitotic gene book- discuss recent findings that indicate mitotic gene bookmarking is a marking—retention of regulatory proteins and selective histone specific and broadly relevant epigenetic program for coordinate variants and modifications at gene loci that are poised for imme- control of cell growth and identity through regulation of RNAP I diate reactivation postmitotically—has emerged as a key epige- and Pol II-mediated gene transcription and is obligatory to netic mechanism that plays a pivotal role in maintaining cell maintain normal and cancer phenotypes. phenotype and identity through successive cell divisions. Studies Mitotic Gene Bookmarking: Evolution of the 1Department of Biochemistry and University of Vermont Cancer Centre, Concept and Evidence for Specificity University of Vermont, Burlington Vermont. 2Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts. A conceptual framework for mitotic gene bookmarking was 3Graduate Program in Cell Biology and Department of Biochemistry initiated with the identification of a limited number of nuclease and Molecular Pharmacology, University of Massachusetts Medical School, accessible sites on the condensed mitotic chromatin that persist Worcester, Massachusetts. through the cell cycle. In the 1990s, Levens and colleagues showed Corresponding Author: Gary S. Stein, University of Vermont College of Medicine, that the chromatin is conformationally distorted at transcription 89 Beaumont Avenue, Burlington, VT 05405. Phone: 802-656-6613; Fax: 802-656- start sites (TSS) in genes poised for reactivation following mitosis 6613; E-mail: [email protected] and proposed that a subset of factors remains bound to mitotic doi: 10.1158/1541-7786.MCR-18-0415 chromosomes, providing a molecular bookmark to restore Ó2018 American Association for Cancer Research. chromatin conformation and gene expression postmitotically www.aacrjournals.org 1617 Downloaded from mcr.aacrjournals.org on September 28, 2021. © 2018 American Association for Cancer Research. Published OnlineFirst July 12, 2018; DOI: 10.1158/1541-7786.MCR-18-0415 Zaidi et al. (20, 38). Consistent with this model, Wu and colleagues showed Mitotic retention of key components of RNA polymerase that the hsp70i gene promoter contains nuclease accessible sites (RNAP) machineries support competency for a basal level of that persist through mitosis. However, Wu and colleague also transcription throughout mitosis found that several sequence-specific transcription factors were Mitosis is accompanied by striking biochemical changes, displaced from the condensed mitotic chromatin (39). In 2003, including a decline in nuclear RNA transcription (12, 14, 42). our group identified the osteogenic master regulator RUNX2 as Mitotic repression of transcription was first noted over 60 years the first sequence-specific and phenotypic bookmark that remains ago in studies analyzing incorporation of radiolabeled RNA associated with target genes on mitotic chromosomes (40). precursors during the cell cycle (47). Initial studies examining Subsequent studies identified mitotic retention of several mechanisms that repress transcription in mitotic cells reported tissue-restricted transcription factors, indicating that mitotic that most of the RNAP II elongation complexes were physically bookmarking is a key epigenetic mechanism for regulation of excluded from mitotic chromosomes, although some genes genes that coordinately control cell growth and lineage mainte- retained active RNAP II complexes (48). The authors suggested nance following mitosis (15, 18, 22, 25, 41). that limitations of pulse-labeling approaches may prevent detec- It was long thought that highly condensed mitotic chromo- tion of low levels of mitotic transcriptional activity. Recent somes interfere with accessibility of gene regulatory factors, a approaches designed to detect subtle transcriptional changes have concept that extended to accessibility of antibodies to detect identified waves of transcriptional activity throughout mitosis. endogenous proteins on mitotic chromosomes by immunofluo- Using cell-permeable 5-ethynyluridine to pulse-label nascent rescence microscopy (42, 43). However, advances in genome- transcripts, Zaret and colleagues showed that mitotic cells main- wide biochemical and cell biological approaches have supported tain a steady-state level of transcriptional activity, and that the unbiased examination of transcriptional and epigenetic states genes involved in fundamental cellular functions, for example, during mitosis. Recent studies by several groups demonstrate that cell growth and proliferation, are among the first to be transcribed, mitotic gene bookmarking and downstream transcriptional while lineage-specific genes are expressed to establish cell identity events are a rule, and not the exception. The Tjian group has as cells exit mitosis (46). These findings are consistent with reports reported that the observation of sequence-specific regulatory from our group, and others, that components of RNAP I machin- protein displacement from mitotic chromosomes is an artifact ery that include upstream binding factor 1 (UBF1) remain asso- of formaldehyde fixation (44). Using live cell microscopy, the ciated with ribosomal RNA genes during mitosis (49, 50). A recent authors show that the kinetics of formaldehyde fixation prevents report from the Tjian group further shows that TBP, a key com- detection of sequence-specific transcription factors that are ponent of the RNAP II machinery, is also stably retained on retained on mitotic chromosomes, further strengthening the mitotic chromosomes and facilitates recruitment of RNAP II to role of mitotic gene bookmarking as a physiologically relevant genes for transcription as cells progress through and exit mitosis epigenetic mechanism. Studies from the Blobel group have estab- (51). These studies support a mechanism for transcriptional lished that nuclease accessibility of mitotic chromatin is a wide- memory through successive cell