Dynamics and Memory of Heterochromatin in Living Cells

Howard Hughes Medical Institute, Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Cell (Impact Factor: 32.24). 06/2012; 149(7):1447-60. DOI: 10.1016/j.cell.2012.03.052
Source: PubMed


Posttranslational histone modifications are important for gene regulation, yet the mode of propagation and the contribution to heritable gene expression states remains controversial. To address these questions, we developed a chromatin in vivo assay (CiA) system employing chemically induced proximity to initiate and terminate chromatin modifications in living cells. We selectively recruited HP1α to induce H3K9me3-dependent gene silencing and describe the kinetics and extent of chromatin modifications at the Oct4 locus in fibroblasts and pluripotent cells. H3K9me3 propagated symmetrically and continuously at average rates of ~0.18 nucleosomes/hr to produce domains of up to 10 kb. After removal of the HP1α stimulus, heterochromatic domains were heritably transmitted, undiminished through multiple cell generations. Our data enabled quantitative modeling of reaction kinetics, which revealed that dynamic competition between histone marking and turnover, determines the boundaries and stability of H3K9me3 domains. This framework predicts the steady-state dynamics and spatial features of the majority of euchromatic H3K9me3 domains over the genome.

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Available from: Nathaniel A Hathaway,
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    • "For example, JAK2- mediated phosphorylation of H3Y41, a site located at the DNA entry/ exit point [55], was found to be refractory to HP1α chromatin association by perturbing an interaction between the HP1α chromoshadow domain and H3 in this region. While H3Y41 was shown to relieve HP1-mediated gene repression, it remains to be determined whether H3Y41 phosphorylation negates HP1α interaction in the context of H3K9me3 [56] [57]. Interestingly, neighboring H3R42 was recently identified as a substrate for CARM1 and PRMT6-mediated asymmetric dimethylation (H3R42me2a) [58]. "
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    ABSTRACT: A major mechanism regulating the accessibility and function of eukaryotic genomes are the covalent modifications to DNA and histone proteins that dependably package our genetic information inside the nucleus of every cell. Formally postulated over a decade ago, it is becoming increasingly clear that post-translational modifications (PTMs) on histones act singly and in combination to form a language or ‘code’ that is read by specialized proteins to facilitate downstream functions in chromatin. Underappreciated at the time was the level of complexity harbored both within histone PTMs and their combinations, as well as within the proteins that read and interpret the language. In addition to histone PTMs, newly-identified DNA modifications that can recruit specific effector proteins has raised further awareness that histone PTMs operate within a broader language of epigenetic modifications to orchestrate the dynamic functions associated with chromatin. Here, we highlight key recent advances in our understanding of the epigenetic language encompassing histone and DNA modifications and foreshadow challenges that lie ahead as we continue our quest to decipher the fundamental mechanisms of chromatin regulation. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
    Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 08/2014; 1839(8). DOI:10.1016/j.bbagrm.2014.03.001 · 6.33 Impact Factor
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    • "Theoretical models based on a combination of such feedback loops have suggested the existence of two discrete chromatin states that can stably co-exist ( " bistability " ) for a certain range of conditions (Schreiber & Bernstein, 2002; Dodd et al, 2007; Angel et al, 2011). Hathaway et al have proposed an alternative, " monostable " model of heterochromatin propagation through interactions between neighboring nucleosomes (Hathaway et al, 2012). However, direct evidence on how such epigenetic networks might operate in living cells is lacking. "
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    ABSTRACT: The cell establishes heritable patterns of active and silenced chromatin via interacting factors that set, remove, and read epigenetic marks. To understand how the underlying networks operate, we have dissected transcriptional silencing in pericentric heterochromatin (PCH) of mouse fibroblasts. We assembled a quantitative map for the abundance and interactions of 16 factors related to PCH in living cells and found that stably bound complexes of the histone methyltransferase SUV39H1/2 demarcate the PCH state. From the experimental data, we developed a predictive mathematical model that explains how chromatin-bound SUV39H1/2 complexes act as nucleation sites and propagate a spatially confined PCH domain with elevated histone H3 lysine 9 trimethylation levels via chromatin dynamics. This “nucleation and looping” mechanism is particularly robust toward transient perturbations and stably maintains the PCH state. These features make it an attractive model for establishing functional epigenetic domains throughout the genome based on the localized immobilization of chromatin-modifying enzymes.
    Molecular Systems Biology 08/2014; 10(8). DOI:10.15252/msb.20145377 · 10.87 Impact Factor
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    • "However, a recent study demonstrated that the maintenance of induced heterochromatin is not dependent on DNA methylation. Using a chromatin in vivo assay (CiA), which enables induction and termination of chromatin modifications in living cells, the authors selectively targeted HP1α to induce a H3K9me3 heterochromatic domain at the Oct4 locus (Hathaway et al., 2012). Interestingly, they found that after removal of HP1α these heterochromatic domains were heritably transmitted over multiple cell divisions independently of DNA methylation, suggesting that H3K9me3 is the epigenetic mark required for inheritance of heterochromatic state. "
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    ABSTRACT: During embryonic development a large number of widely differing and specialized cell types with identical genomes are generated from a single totipotent zygote. Tissue specific transcription factors cooperate with epigenetic modifiers to establish cellular identity in differentiated cells and epigenetic regulatory mechanisms contribute to the maintenance of distinct chromatin states and cell-type specific gene expression patterns, a phenomenon referred to as epigenetic memory. This is accomplished via the stable maintenance of various epigenetic marks through successive rounds of cell division. Preservation of DNA methylation patterns is a well-established mechanism of epigenetic memory, but more recently it has become clear that many other epigenetic modifications can also be maintained following DNA replication and cell division. In this review, we present an overview of the current knowledge regarding the role of histone lysine methylation in the establishment and maintenance of stable epigenetic states.
    Frontiers in Genetics 02/2014; 5:19. DOI:10.3389/fgene.2014.00019
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