Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, 02129, USA. Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles and Department of Biological Chemistry, David Geffen School of Medicine, Los Angeles, CA 90095, USA.
Molecular biology of the cell (Impact Factor: 5.98). 08/2013; DOI: 10.1091/mbc.E12-07-0529
Source: PubMed

ABSTRACT The transition between proliferation and quiescence is frequently associated with changes in gene expression, in the extent of chromatin compaction and in histone modifications, but whether changes in chromatin state actually regulate cell cycle exit with quiescence is unclear. We discovered that primary human fibroblasts induced into quiescence exhibited tighter chromatin compaction. Mass spectrometry analysis of histone modifications revealed that H4K20me2 and -me3 are increased in quiescence and that other histone modifications are present at similar levels in proliferating and quiescent cells. Analysis of cells in S, G2/M, and G1 phases shows that H4K20me1 increases after S phase and is converted to -me2 and -me3 in quiescence. Knockdown of the enzymes that create H4K20me2 and -me3 resulted in an increased fraction of cells in S phase, a defect in exiting the cell cycle, and decreased chromatin compaction. Overexpression of Suv4-20h1, the enzyme that creates H4K20me2 from H4K20me1, resulted in G2 arrest, consistent with a role for H4K20me1 in mitosis. The results suggest that the same lysine on H4K20 may, in its different methylation states, facilitate mitotic functions in M phase and promote chromatin compaction and cell cycle exit in quiescent cells.

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    ABSTRACT: A complex network of regulatory pathways links transcription to cell growth and proliferation. Here we show that cellular quiescence alters chromatin structure by promoting trimethylation of histone H4 at lysine 20 (H4K20me3). In contrast to pericentric or telomeric regions, recruitment of the H4K20 methyltransferase Suv4-20h2 to rRNA genes and IAP elements requires neither trimethylation of H3K9 nor interaction with HP1 proteins but depends on long noncoding RNAs (lncRNAs) that interact with Suv4-20h2. Growth factor deprivation and terminal differentiation lead to upregulation of these lncRNAs, increase in H4K20me3, and chromatin compaction. The results uncover a lncRNA-mediated mechanism that guides Suv4-20h2 to specific genomic loci to establish a more compact chromatin structure in growth-arrested cells.
    Molecular cell 04/2014; DOI:10.1016/j.molcel.2014.03.032 · 14.46 Impact Factor
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    ABSTRACT: Interphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales, from sub-genic regions associated with DNA-binding proteins at the order of tens or hundreds of bases, through larger regions with active or repressed chromatin states, up to multi-megabase-scale domains associated with nuclear positioning, replication timing and other qualities. However, we have lacked detailed, quantitative models to understand the interactions between these different strata. Here we collate large collections of matched locus-level chromatin features and Hi-C interaction data, representing higher-order organization, across three human cell types. We use quantitative modeling approaches to assess whether locus-level features are sufficient to explain higher-order structure, and identify the most influential underlying features. We identify structurally variable domains between cell types and examine the underlying features to discover a general association with cell-type-specific enhancer activity. We also identify the most prominent features marking the boundaries of two types of higher-order domains at different scales: topologically associating domains and nuclear compartments. We find parallel enrichments of particular chromatin features for both types, including features associated with active promoters and the architectural proteins CTCF and YY1. We show that integrative modeling of large chromatin dataset collections using random forests can generate useful insights into chromosome structure. The models produced recapitulate known biological features of the cell types involved, allow exploration of the antecedents of higher-order structures and generate testable hypotheses for further experimental studies.
    Genome Biology 05/2015; 16(1). DOI:10.1186/s13059-015-0661-x · 10.47 Impact Factor
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    ABSTRACT: Cells in many organs exist in both proliferating and quiescent states. Proliferating cells are more radio-sensitive, DNA damage pathways including p53 pathway are activated to undergo either G1/S or G2/M arrest to avoid entering S and M phase with DNA damage. On the other hand, quiescent cells are already arrested in G0, therefore there may be fundamental difference of irradiation response between proliferating and quiescent cells, and this difference may affect their radiosensitivity. To understand these differences, proliferating and quiescent human normal lung fibroblasts were exposed to 0.10 -1Gy of γ-radiation. The response of key proteins involved in the cell cycle, cell death, and metabolism as well as histone H2AX phosphorylation were examined. Interestingly, p53 and p53 phosphorylation (Ser-15), as well as the cyclin-dependent kinase inhibitors p21 and p27, were induced similarly in both proliferating and quiescent cells after irradiation. Furthermore, the p53 protein half-life, and expression of cyclin A, cyclin E, proliferating cell nuclear antigen (PCNA), Bax, or cytochrome c expression as well as histone H2AX phosphorylation were comparable after irradiation in both phases of cells. The effect of radioprotection by a glycogen synthase kinase 3β inhibitor on p53 pathway was also similar between proliferating and quiescent cells. Our results showed that quiescence does not affect irradiation response of key proteins involved in stress and DNA damage at least in normal fibroblasts, providing a better understanding of the radiation response in quiescent cells, which is crucial for tissue repair and regeneration. Copyright © 2015. Published by Elsevier Inc.
    Biochemical and Biophysical Research Communications 01/2015; 458(1). DOI:10.1016/j.bbrc.2015.01.076 · 2.28 Impact Factor


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