Epigenetic Transcriptional Memory Research Articles

Nrf2 pre-recruitment at Enhancer 2 is a hallmark of H2 O2 -induced epigenetic transcriptional memory in the HMOX1 gene in human umbilical artery endothelial cells.

Maternal obesity (MO) is a significant cause of increased cardiometabolic risk in offspring, who present endothelial dysfunction at birth. Alterations in physiologic and cellular redox status are strongly associated with altered gene regulation in arterial endothelium. However, specific mechanisms by which the pro-oxidant fetal environment in MO could modulate the vascular gene expression and function during the offspring's postnatal life are elusive. We tested if oxidative stress could reprogram the antioxidant-coding gene's response to a pro-oxidant challenge through an epigenetic transcriptional memory (ETM) mechanism. A pro-oxidant double-hit protocol was applied to human umbilical artery endothelial cells (HUAECs) and EA.hy 926 endothelial cell lines. The ETM acquisition in the HMOX1 gene was analyzed by RT-qPCR. HMOX1 mRNA decay was evaluated by Actinomycin-D treatment and RT-qPCR. To assess the chromatin accessibility and the enrichment of NRF2, RNAP2, and phosphorylation at serin-5 of RNAP2, at HMOX1 gene regulatory regions, were used DNase HS-qPCR and ChIP-qPCR assays, respectively. The CpG methylation pattern at the HMOX1 core promoter was analyzed by DNA bisulfite conversion and Sanger sequencing. Data were analyzed using two-way ANOVA, and p < 0.05 was statistically significant. Using a pro-oxidant double-hit protocol, we found that the Heme Oxygenase gene (HMOX1) presents an ETM response associated with changes in the chromatin structure at the promoter and gene regulatory regions. The ETM response was characterized by a paused-RNA Polymerase 2 and NRF2 enrichment at the transcription start site and Enhancer 2 of the HMOX1 gene, respectively. Changes in DNA methylation pattern at the HMOX1 promoter were not a hallmark of this oxidative stress-induced ETM. These data suggest that a pro-oxidant milieu could trigger an ETM at the vascular level, indicating a potential epigenetic mechanism involved in the increased cardiovascular risk in the offspring of women with obesity.

Inheritance of epigenetic transcriptional memory through read-write replication of a histone modification.

Epigenetic transcriptional regulation frequently requires histone modifications. Some, but not all, of these modifications are able to template their own inheritance. Here, I discuss the molecular mechanisms by which histone modifications can be inherited and relate these ideas to new results about epigenetic transcriptional memory, a phenomenon that poises recently repressed genes for faster reactivation and has been observed in diverse organisms. Recently, we found that the histone H3 lysine 4 dimethylation that is associated with this phenomenon plays a critical role in sustaining memory and, when factors critical for the establishment of memory are inactivated, can be stably maintained through multiple mitoses. This chromatin-mediated inheritance mechanism may involve a physical interaction between an H3K4me2 reader, SET3C, and an H3K4me2 writer, Spp1- COMPASS. This is the first example of a chromatin-mediated inheritance of a mark that promotes transcription.

Establishment and inheritance of epigenetic transcriptional memory.

For certain inducible genes, the rate and molecular mechanism of transcriptional activation depends on the prior experiences of the cell. This phenomenon, called epigenetic transcriptional memory, accelerates reactivation and requires both changes in chromatin structure and recruitment of poised RNA Polymerase II (RNAPII) to the promoter. Forms of epigenetic transcriptional memory have been identified in S. cerevisiae, D. melanogaster, C. elegans, and mammals. A well-characterized model of memory is found in budding yeast where memory of inositol starvation involves a positive feedback loop between gene-and condition-specific transcription factors, which mediate an interaction with the nuclear pore complex and a characteristic histone modification: histone H3 lysine 4 dimethylation (H3K4me2). This histone modification permits recruitment of a memory-specific pre-initiation complex, poising RNAPII at the promoter. During memory, H3K4me2 is essential for recruitment of RNAPII and faster reactivation, but RNAPII is not required for H3K4me2. Unlike the RNAPII-dependent H3K4me2 associated with active transcription, RNAPII-independent H3K4me2 requires Nup100, SET3C, the Leo1 subunit of the Paf1 complex and can be inherited through multiple cell cycles upon disrupting the interaction with the Nuclear Pore Complex. The H3K4 methyltransferase (COMPASS) physically interacts with the potential reader (SET3C), suggesting a molecular mechanism for the spreading and re-incorporation of H3K4me2 following DNA replication. Thus, epigenetic transcriptional memory is a conserved adaptation that utilizes a heritable chromatin state, allowing cells and organisms to alter their gene expression programs in response to recent experiences over intermediate time scales.

Mitotically heritable, RNA polymerase II-independent H3K4 dimethylation stimulates INO1 transcriptional memory.

For some inducible genes, the rate and molecular mechanism of transcriptional activation depend on the prior experiences of the cell. This phenomenon, called epigenetic transcriptional memory, accelerates reactivation, and requires both changes in chromatin structure and recruitment of poised RNA polymerase II (RNAPII) to the promoter. Memory of inositol starvation in budding yeast involves a positive feedback loop between transcription factor-dependent interaction with the nuclear pore complex and histone H3 lysine 4 dimethylation (H3K4me2). While H3K4me2 is essential for recruitment of RNAPII and faster reactivation, RNAPII is not required for H3K4me2. Unlike RNAPII-dependent H3K4me2 associated with transcription, RNAPII-independent H3K4me2 requires Nup100, SET3C, the Leo1 subunit of the Paf1 complex and, upon degradation of an essential transcription factor, is inherited through multiple cell cycles. The writer of this mark (COMPASS) physically interacts with the potential reader (SET3C), suggesting a molecular mechanism for the spreading and re-incorporation of H3K4me2 following DNA replication.

Epigenetic regulation and transcriptional memory in development; selection facilitating prudence.

The epigenetic mechanisms regulating developmental gene expression are examples of a strategy to generate unique expression profiles with global regulators controlling several genes. In a simplified view, a common set of tools, that include DNA motif recognizing proteins (recruiters), binding/interacting surfaces (ARPs- actin related proteins), epigenetic writers (histone methyltransferases, acetylases), readers (chromatin remodeling proteins, PRC1 members) and erasers (demethylases, deacetylases) form complexes which not only regulate transcription, but also retain the transcriptional memory through mitosis. There are two arms of epigenetic regulation: covalent modification of DNA and the post-translational modification of histones. In this review, we discuss both of these aspects briefly to illustrate functional diversity. We discuss our efforts at utilization of the genome sequence data for de novo identification of new players and their functional validation in this remarkable process.

Genetic and Epigenetic Strategies Potentiate Gal4 Activation to Enhance Fitness in Recently Diverged Yeast Species

Certain genes show more rapid reactivation for several generations following repression, a conserved phenomenon called epigenetic transcriptional memory. Following previous growth in galactose, GAL gene transcriptional memory confers a strong fitness benefit in Saccharomyces cerevisiae adapting to growth in galactose for up to 8 generations. A genetic screen for mutants defective for GAL gene memory revealed new insights into the molecular mechanism, adaptive consequences, and evolutionary history of memory. A point mutation in the Gal1 co-activator that disrupts the interaction with the Gal80 inhibitor specifically and completely disrupted memory. This mutation confirms that cytoplasmically inherited Gal1 produced during previous growth in galactose directly interferes with Gal80 repression to promote faster induction of GAL genes. This mitotically heritable mode of regulation is recently evolved; in a diverged Saccharomyces species, GAL genes show constitutively faster activation due to genetically encoded basal expression of Gal1. Thus, recently diverged species utilize either epigenetic or genetic strategies to regulate the same molecular mechanism. The screen also revealed that the central domain of the Gal4 transcription factor both regulates the stochasticity of GAL gene expression and potentiates stronger GAL gene activation in the presence of Gal1. The central domain is critical for GAL gene transcriptional memory; Gal4 lacking the central domain fails to potentiate GAL gene expression and is unresponsive to previous Gal1 expression.

Epigenetic Transcriptional Memory of GAL Genes Depends on Growth in Glucose and the Tup1 Transcription Factor in Saccharomyces cerevisiae.

Previously expressed inducible genes can remain poised for faster reactivation for multiple cell divisions, a conserved phenomenon called epigenetic transcriptional memory. The GAL genes in Saccharomyces cerevisiae show faster reactivation for up to seven generations after being repressed. During memory, previously produced Gal1 protein enhances the rate of reactivation of GAL1, GAL10, GAL2, and GAL7 These genes also interact with the nuclear pore complex (NPC) and localize to the nuclear periphery both when active and during memory. Peripheral localization of GAL1 during memory requires the Gal1 protein, a memory-specific cis-acting element in the promoter, and the NPC protein Nup100 However, unlike other examples of transcriptional memory, the interaction with NPC is not required for faster GAL gene reactivation. Rather, downstream of Gal1, the Tup1 transcription factor and growth in glucose promote GAL transcriptional memory. Cells only show signs of memory and only benefit from memory when growing in glucose. Tup1 promotes memory-specific chromatin changes at the GAL1 promoter: incorporation of histone variant H2A.Z and dimethylation of histone H3, lysine 4. Tup1 and H2A.Z function downstream of Gal1 to promote binding of a preinitiation form of RNA Polymerase II at the GAL1 promoter, poising the gene for faster reactivation. This mechanism allows cells to integrate a previous experience (growth in galactose, reflected by Gal1 levels) with current conditions (growth in glucose, potentially through Tup1 function) to overcome repression and to poise critical GAL genes for future reactivation.

Epigenetic transcriptional memory.

Organisms alter gene expression to adapt to changes in environmental conditions such as temperature, nutrients, inflammatory signals, and stress (Gialitakis et al. in Mol Cell Biol 30:2046-2056, 2010; Conrath in Trends Plant Sci 16:524-531, 2011; Avramova in Plant J 83:149-159, 2015; Solé et al. in Curr Genet 61:299-308, 2015; Ho and Gasch in Curr Genet 61:503-511, 2015; Bevington et al. in EMBO J 35:515-535, 2016; Hilker et al. in Biol Rev Camb Philos Soc 91:1118-1133, 2016). In some cases, organisms can "remember" a previous environmental condition and adapt to that condition more rapidly in the future (Gems and Partridge 2008). Epigenetic transcriptional memory in response to a previous stimulus can produce heritable changes in the response of an organism to the same stimulus, quantitatively or qualitatively altering changes in gene expression (Brickner et al. in PLoS Biol, 5:e81, 2007; Light et al. in Mol Cell 40:112-125, 2010; in PLoS Biol, 11:e1001524, 2013; D'Urso and Brickner in Trends Genet 30:230-236, 2014; Avramova in Plant J 83:149-159, 2015; D'Urso et al. in Elife. doi: 10.7554/eLife.16691 , 2016). The role of chromatin changes in controlling binding of poised RNAPII during memory is conserved from yeast to humans. Here, we discuss epigenetic transcriptional memory in different systems and our current understanding of its molecular basis. Our recent work with a well-characterized model for transcriptional memory demonstrated that memory is initiated by binding of a transcription factor, leading to essential changes in chromatin structure and allowing binding of a poised form of RNA polymerase II to promote the rate of future reactivation (D'Urso et al. in Elife. doi: 10.7554/eLife.16691 , 2016).

Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory.

In yeast and humans, previous experiences can lead to epigenetic transcriptional memory: repressed genes that exhibit mitotically heritable changes in chromatin structure and promoter recruitment of poised RNA polymerase II preinitiation complex (RNAPII PIC), which enhances future reactivation. Here, we show that INO1 memory in yeast is initiated by binding of the Sfl1 transcription factor to the cis-acting Memory Recruitment Sequence, targeting INO1 to the nuclear periphery. Memory requires a remodeled form of the Set1/COMPASS methyltransferase lacking Spp1, which dimethylates histone H3 lysine 4 (H3K4me2). H3K4me2 recruits the SET3C complex, which plays an essential role in maintaining this mark. Finally, while active INO1 is associated with Cdk8(-) Mediator, during memory, Cdk8(+) Mediator recruits poised RNAPII PIC lacking the Kin28 CTD kinase. Aspects of this mechanism are generalizable to yeast and conserved in human cells. Thus, COMPASS and Mediator are repurposed to promote epigenetic transcriptional poising by a highly conserved mechanism.

INO1 transcriptional memory leads to DNA zip code-dependent interchromosomal clustering.

Many genes localize at the nuclear periphery through physical interaction with the nuclear pore complex (NPC). We have found that the yeast INO1 gene is targeted to the NPC both upon activation and for several generations after repression, a phenomenon called epigenetic transcriptional memory. Targeting of INO1 to the NPC requires distinct cis-acting promoter DNA zip codes under activating conditions and under memory conditions. When at the nuclear periphery, active INO1 clusters with itself and with other genes that share the GRS I zip code. Here, we show that during memory, the two alleles of INO1 cluster in diploids and endogenous INO1 clusters with an ectopic INO1 in haploids. After repression, INO1 does not cluster with GRS I - containing genes. Furthermore, clustering during memory requires Nup100 and two sets of DNA zip codes, those that target INO1 to the periphery when active and those that target it to the periphery after repression. Therefore, the interchromosomal clustering of INO1 that occurs during transcriptional memory is dependent upon, but mechanistically distinct from, the clustering of active INO1. Finally, while localization to the nuclear periphery is not regulated through the cell cycle during memory, clustering of INO1 during memory is regulated through the cell cycle.

The role of nuclear pore proteins in epigenetic regulation and spatial organization of the genome (471.2)

In yeast and metazoa, active genes interact with nuclear pore proteins, which promotes stronger transcription. Targeting to the NPC in yeast is mediated by cis‐acting “DNA zip codes” that are necessary and sufficient to confer targeting to the nuclear periphery. Loci with the same zip codes cluster together. Some inducible genes remain associated with the NPC for several generations after being repressed, a phenomenon called epigenetic transcriptional memory. This interaction poises genes for future reactivation and requires the nuclear pore protein Nup100, a homologue of human Nup98. A similar phenomenon occurs in human cells; for at least four generations after treatment with interferon gamma (IFNg), many IFNg‐inducible genes are induced more rapidly and more strongly than in cells that have not previously been exposed to IFNg. In both yeast and human cells, the recently expressed promoters of genes with memory exhibit persistent dimethylation of histone H3 lysine 4 (H3K4me2) and physically interact with Nups and a poised form of RNA polymerase II. Transcriptional memory in yeast requires several chromatin modifications: H2B ubiquitination, H3K4 methylation and the SET3C histone deacetylase. In human cells transiently depleted of Nup98 or yeast cells lacking Nup100, transcriptional memory is lost; RNA polymerase II does not remain associated with promoters, H3K4me2 is lost, and the rate of transcriptional reactivation is reduced. Thus, Nup binding to active genes plays a conserved role in promoting stronger transcription and Nup binding to recently expressed promoters plays a conserved role in promoting epigenetic transcriptional memory.

A Conserved Role for Human Nup98 in Altering Chromatin Structure and Promoting Epigenetic Transcriptional Memory

Author SummaryCells respond to changes in nutrients or signaling molecules by altering the expression of genes. The rate at which genes are turned on is not uniform; some genes are induced rapidly and others are induced slowly. In brewer's yeast, previous experience can enhance the rate at which genes are turned on again, a phenomenon called “transcriptional memory.” After repression, such genes physically interact with the nuclear pore complex, leading to altered chromatin structure and binding of a poised RNA polymerase II. Human genes that are induced by interferon gamma show a similar behavior. In both cases, the phenomenon persists through several cell divisions, suggesting that it is epigenetically inherited. Here, we find that yeast and human cells utilize a similar molecular mechanism to prime genes for reactivation. In both species, the nuclear pore protein Nup100/Nup98 binds to the promoters of genes that exhibit transcriptional memory. This leads to an altered chromatin state in the promoter and binding of RNA polymerase II, poising genes for future expression. We conclude that both unicellular and multicellular organisms use nuclear pore proteins in a novel way to alter transcription based on previous experiences.

The HDAC interaction network

News & View11 June 2013Open Access The HDAC interaction network Ilana Livyatan Ilana Livyatan Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel Search for more papers by this author Eran Meshorer Corresponding Author Eran Meshorer Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel Search for more papers by this author Ilana Livyatan Ilana Livyatan Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel Search for more papers by this author Eran Meshorer Corresponding Author Eran Meshorer Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel Search for more papers by this author Author Information Ilana Livyatan1 and Eran Meshorer 1 1Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel *Corresponding author. Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israe1. Tel.:+972 2 6585161; Fax +972 2 6586073; E-mail: [email protected] Molecular Systems Biology (2013)9:671https://doi.org/10.1038/msb.2013.33 PDFDownload PDF of article text and main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info The new age of social networking has taught us that a lot can be inferred about you and me just based on our ‘friendship network’. Biochemists have been exploiting this approach for years when trying to discover the functional roles of proteins. Protein–protein interactions are the basis for the diverse cellular functionality that builds a living organism, manifested in multi-protein complexes, signal–transduction pathways and other protein effector pathways. As protein function heavily relies on these interactions, in many cases the function of a protein can be inferred from the list of its interacting partners. In a recent article published in Molecular Systems Biology, Joshi et al (2013) describe a novel systematic approach integrating advanced proteomic and computational methods for uncovering specific protein interactions. Applying this new methodology, they built a comprehensive network of functional protein interactions for 11 members of the histone deacetylase (HDAC) protein family, filling an important gap in our basic understanding of how HDACs affect cellular processes, are involved in disease, and can be targeted with drugs to alleviate disease phenotypes. HDACs are a family of enzymes responsible primarily for deacetylating lysine residues within histones, although they often act on non-histone proteins as well, and many are not confined to the cell nucleus. HDACs are divided into five groups based on their sequence similarity and function. Class I is comprised of HDAC1, 2, 3 and 8, all of which have the simplest structure; class IIa includes HDAC4, 5, 7 and 9, which have large N-terminal extensions; class IIb consists of HDAC6 and 10, with extended C-termini; class III comprises of the Sirtuins (SIRT1–7), and class IV includes a single member, HDAC11, which shares features with both class I and class II HDAC enzymes (Haberland et al, 2009). When they operate on histone proteins, which package nuclear DNA into chromatin, the DNA generally wraps more tightly around the histone proteins once the acetyl group is removed, making some DNA regions more accessible (‘euchromatin’ or ‘active chromatin’) and some less accessible (‘heterochromatin’ or ‘suppressive chromatin’) to other proteins and the transcriptional machinery. This simple chemical modification has considerable effects as DNA accessibility is a major regulator of all DNA-related mechanisms, particularly gene expression. Acetylated lysines are recognized by a set of proteins, containing either a bromodomain or a tandem PhD-finger domain, and which can recruit additional protein complexes that modify the expression pattern of the specific region. As the transcriptional program of the cell largely defines its identity, any changes in DNA expression patterns can result in something as remarkable as embryonic development or as devastating as out-of-control metastatic cancer. Therefore, it is not surprising that perturbations of HDAC functions have profound effects on a variety of cellular processes, including cell cycle regulation (Telles and Seto, 2012), stem cell differentiation (Hezroni et al, 2011), development (Reichert et al, 2012), and memory and brain function (Guan et al, 2009; Sailaja et al, 2012). Consequently, HDACs have turned into promising targets for the treatment of multiple diseases including, but not limited to, neurodegenerative diseases (e.g., Huntington's disease (McFarland et al, 2012) and other PolyQ diseases (Cohen-Carmon and Meshorer, 2012)) and cancer (Barneda-Zahonero and Parra, 2012), while small-molecule inhibitors of HDACs are being increasingly used in research of such diseases. Several HDAC inhibitors including SAHA (vorinostat) and valproic acid have even been FDA approved for advanced cutaneous T-cell lymphoma, and for neurological symptoms such as epilepsy, respectively. Despite the exponential growth in the number of publications related to HDACs, the question of whether their main role is to regulate gene expression remains open. How do these enzymes, especially the ones that are closely related in sequence and structure, achieve specificity? What controls their nuclear versus cytoplasmic localization? To start answering some of these questions Joshi et al (2013) used a novel proteomic approach to identify the protein interaction networks of HDACs in T cells. Specific protein interactions were determined by a label-free affinity purification followed by mass spectrometry-based proteomics approach followed by downstream computational analysis using a modeling algorithm. A complementary metabolic labeling strategy, based on the SILAC (stable isotope labeling by amino acids) technology, was used to ascertain the stability of the identified interactions. This integrative hybrid approach led to the identification of over 200 novel protein interactions with the HDAC family, thus linking HDACs to a variety of functional processes beyond chromatin and epigenetic gene regulation (Figure 1). These include RNA processing, protein ubiquitination, signal transduction and nuclear import, just to name a few. Independent analysis of the HDAC11 protein network revealed association with the SMN protein subnetwork that affects RNA splicing of minor introns, suggesting that, when misregulated, the HDAC11 network can contribute to the phenotype of spinal muscular atrophy patients. Downregulation of HDAC11 recapitulated splicing defects associated with the downregulation of the SMN1 member of the SMN complex, providing a new avenue of association between HDACs and disease. Figure 1.The newly identified interactome of the HDAC family links HDACs to a variety of functional processes beyond chromatin and epigenetic gene regulation. Download figure Download PowerPoint The HDAC network published in this study provides a sorely needed platform for research on HDAC functions outside of the DNA expression box. Going forward, research efforts can now investigate the specific roles of individual HDACs in a broad variety of cellular processes and uncover the respective underlying molecular mechanisms. Further work is required in order to distinguish the proteins that work in complex with HDACs from those that are substrate targets. Additionally, establishing the HDAC interaction network outside of T cells will facilitate the analysis of its function beyond T-cell biology. One of the most important future outcomes should be the ability to propose specific targets for inhibition of specific mechanisms, thus allowing safer and more targeted pharmaceutical approaches to diseases involving HDACs as well as facilitating advanced research of biological processes. References Barneda-Zahonero B, Parra M (2012) Histone deacetylases and cancer. Mol Oncol 6: 579–589Wiley Online LibraryCASPubMedWeb of Science®Google Scholar Cohen-Carmon D, Meshorer E (2012) Polyglutamine (polyQ) disorders: the chromatin connection. Nucleus 3: 433–441CrossrefPubMedWeb of Science®Google Scholar Guan JS, Haggarty SJ, Giacometti E, Dannenberg JH, Joseph N, Gao J, Nieland TJ, Zhou Y, Wang X, Mazitschek R, Bradner JE, DePinho RA, Jaenisch R, Tsai LH (2009) HDAC2 negatively regulates memory formation and synaptic plasticity. Nature 459: 55–60CrossrefCASPubMedWeb of Science®Google Scholar Haberland M, Montgomery RL, Olson EN (2009) The many roles of histone deacetylases in development and physiology: implications for disease and therapy. Nat Rev Genet 10: 32–42CrossrefCASPubMedWeb of Science®Google Scholar Hezroni H, Tzchori I, Davidi A, Mattout A, Biran A, Nissim-Rafinia M, Westphal H, Meshorer E (2011) H3K9 histone acetylation predicts pluripotency and reprogramming capacity of ES cells. Nucleus 2: 300–309CrossrefPubMedWeb of Science®Google Scholar Joshi P, Greco TM, Guise AJ, Luo Y, Yu F, Nesvizhskii AI, Cristea IM (2013) The functional interactome landscape of the human histone deacetylase family. Mol Syst Biol 9: 672 accession:10.1038/msb201326 Wiley Online LibraryPubMedWeb of Science®Google Scholar McFarland KN, Das S, Sun TT, Leyfer D, Xia E, Sangrey GR, Kuhn A, Luthi-Carter R, Clark TW, Sadri-Vakili G, Cha JH (2012) Genome-wide histone acetylation is altered in a transgenic mouse model of Huntington's disease. PLoS ONE 7: e41423CrossrefCASPubMedWeb of Science®Google Scholar Reichert N, Choukrallah MA, Matthias P (2012) Multiple roles of class I HDACs in proliferation, differentiation, and development. Cell Mol Life Sci 69: 2173–2187CrossrefCASPubMedWeb of Science®Google Scholar Sailaja BS, Cohen-Carmon D, Zimmerman G, Soreq H, Meshorer E (2012) Stress-induced epigenetic transcriptional memory of acetylcholinesterase by HDAC4. Proc Natl Acad Sci USA 109: E3687–E3695CrossrefCASPubMedWeb of Science®Google Scholar Telles ES, Seto E (2012) Modulation of cell cycle regulators by HDACs. Front Biosci 4: 831–839Google Scholar Previous ArticleNext Article Volume 9Issue 11 January 2013In this issue FiguresReferencesRelatedDetailsLoading ...

Stress-induced epigenetic transcriptional memory of acetylcholinesterase by HDAC4

Stress induces long-lasting changes in neuronal gene expression and cholinergic neurotransmission, but the underlying mechanism(s) are incompletely understood. Here, we report that chromatin structure and histone modifications are causally involved in this transcriptional memory. Specifically, the AChE gene encoding the acetylcholine-hydrolyzing enzyme acetylcholinesterase is known to undergo long-lasting transcriptional and alternative splicing changes after stress. In mice subjected to stress, we identified two alternative 5' exons that were down-regulated after stress in the hippocampus, accompanied by reduced acetylation and elevated trimethylation of H3K9 at the corresponding promoter. These effects were reversed completely by daily administration of the histone deacetylase (HDAC) inhibitor sodium butyrate for 1 wk after stress. H3K9 hypoacetylation was associated with a selective, sodium butyrate-reversible promoter accumulation of HDAC4. Hippocampal suppression of HDAC4 in vivo completely abolished the long-lasting AChE-related and behavioral stress effects. Our findings demonstrate long-lasting stress-inducible changes in AChE's promoter choices, identify the chromatin changes that support this long-term transcriptional memory, and reveal HDAC4 as a mediator of these effects in the hippocampus.

MK3 controls Polycomb target gene expression via negative feedback on ERK

BackgroundGene-environment interactions are mediated by epigenetic mechanisms. Polycomb Group proteins constitute part of an epigenetic cellular transcriptional memory system that is subject to dynamic modulation during differentiation. Molecular insight in processes that control dynamic chromatin association and dissociation of Polycomb repressive complexes during and beyond development is limited. We recently showed that MK3 interacts with Polycomb repressive complex 1 (PRC1). The functional relevance of this interaction, however, remained poorly understood. MK3 is activated downstream of mitogen- and stress-activated protein kinases (M/SAPKs), all of which fulfill crucial roles during development. We here use activation of the immediate-early response gene ATF3, a bona fide PRC1 target gene, as a model to study how MK3 and its effector kinases MAPK/ERK and SAPK/P38 are involved in regulation of PRC1-dependent ATF3 transcription.ResultsOur current data show that mitogenic signaling through ERK, P38 and MK3 regulates ATF3 expression by PRC1/chromatin dissociation and epigenetic modulation. Mitogenic stimulation results in transient P38-dependent H3S28 phosphorylation and ERK-driven PRC1/chromatin dissociation at PRC1 targets. H3S28 phosphorylation by itself appears not sufficient to induce PRC1/chromatin dissociation, nor ATF3 transcription, as inhibition of MEK/ERK signaling blocks BMI1/chromatin dissociation and ATF3 expression, despite induced H3S28 phosphorylation. In addition, we establish that concomitant loss of local H3K27me3 promoter marking is not required for ATF3 activation. We identify pERK as a novel signaling-induced binding partner of PRC1, and provide evidence that MK3 controls ATF3 expression in cultured cells via negative regulatory feedback on M/SAPKs. Dramatically increased ectopic wing vein formation in the absence of Drosophila MK in a Drosophila ERK gain-of-function wing vein patterning model, supports the existence of MK-mediated negative feedback regulation on pERK.ConclusionWe here identify and characterize important actors in a PRC1-dependent epigenetic signal/response mechanism, some of which appear to be nonspecific global responses, whereas others provide modular specificity. Our findings provide novel insight into a Polycomb-mediated epigenetic mechanism that dynamically controls gene transcription and support a direct link between PRC1 and cellular responses to changes in the microenvironment.

Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates

BackgroundWithin chromatin, the histone variant H2A.Z plays a role in many diverse nuclear processes including transcription, preventing the spread of heterochromatin and epigenetic transcriptional memory. The molecular mechanisms of how H2A.Z mediates its effects are not entirely understood. However, it is now known that H2A.Z has two protein isoforms in vertebrates, H2A.Z-1 and H2A.Z-2, which are encoded by separate genes and differ by 3 amino acid residues.ResultsWe report that H2A.Z-1 and H2A.Z-2 are expressed across a wide range of human tissues, they are both acetylated at lysine residues within the N-terminal region and they exhibit similar, but nonidentical, distributions within chromatin. Our results suggest that H2A.Z-2 preferentially associates with H3 trimethylated at lysine 4 compared to H2A.Z-1. The phylogenetic analysis of the promoter regions of H2A.Z-1 and H2A.Z-2 indicate that they have evolved separately during vertebrate evolution.ConclusionsOur biochemical, gene expression, and phylogenetic data suggest that the H2A.Z-1 and H2A.Z-2 variants function similarly yet they may have acquired a degree of functional independence.

The DNA-binding Polycomb-group protein Pleiohomeotic maintains both active and repressed transcriptional states through a single site

Although epigenetic maintenance of either the active or repressed transcriptional state often involves overlapping regulatory elements, the underlying basis of this is not known. Epigenetic and pairing-sensitive silencing are related properties of Polycomb-group proteins, whereas their activities are generally opposed by the trithorax group. Both groups modify chromatin structure, but how their opposing activities are targeted to allow differential maintenance remains a mystery. Here, we identify a strong pairing-sensitive silencing (PSS) element at the 3' border of the Drosophila even skipped (eve) locus. This element can maintain repression during embryonic as well as adult eye development. Transgenic dissection revealed that silencing activity depends on a binding site for the Polycomb-group protein Pleiohomeotic (Pho) and on pho gene function. Binding sites for the trithorax-group protein GAGA factor also contribute, whereas sites for the known Polycomb response element binding factors Zeste and Dsp1 are dispensible. Normally, eve expression in the nervous system is maintained throughout larval stages. An enhancer that functions fully in embryos does not maintain expression, but the adjacent PSS element confers maintenance. This positive activity also depends on pho gene activity and on Pho binding. Thus, a DNA-binding complex requiring Pho is differentially regulated to facilitate epigenetic transcriptional memory of both the active and the repressed state.

The multidomain protein Brpf1 binds histones and is required for Hox gene expression and segmental identity

The Trithorax group (TrxG) is composed of diverse, evolutionary conserved proteins that form chromatin-associated complexes accounting for epigenetic transcriptional memory. However, the molecular mechanisms by which particular loci are marked for reactivation after mitosis are only partially understood. Here, based on genetic analyses in zebrafish, we identify the multidomain protein Brpf1 as a novel TrxG member with a central role during development. brpf1 mutants display anterior transformations of pharyngeal arches due to progressive loss of anterior Hox gene expression. Brpf1 functions in association with the histone acetyltransferase Moz (Myst3), an interaction mediated by the N-terminal domain of Brpf1, and promotes histone acetylation in vivo. Brpf1 recruits Moz to distinct sites of active chromatin and remains at chromosomes during mitosis, mediated by direct histone binding of its bromodomain, which has a preference for acetylated histones, and its PWWP domain, which binds histones independently of their acetylation status. This is the first demonstration of histone binding for PWWP domains. Mutant analyses further show that the PWWP domain is absolutely essential for Brpf1 function in vivo. We conclude that Brpf1, coordinated by its particular set of domains, acts by multiple mechanisms to mediate Moz-dependent histone acetylation and to mark Hox genes for maintained expression throughout vertebrate development.

SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster

Post-translational modification of nucleosomal histones has been suggested to contribute to epigenetic transcriptional memory. We describe a case of transcriptional memory in yeast where the rate of transcriptional induction of GAL1 is regulated by the prior expression state. This epigenetic state is inherited by daughter cells, but does not require the histone acetyltransferase, Gcn5p, the histone ubiquitinylating enzyme, Rad6p, or the histone methylases, Dot1p, Set1p, or Set2p. In contrast, we show that the ATP-dependent chromatin remodeling enzyme, SWI/SNF, is essential for transcriptional memory at GAL1. Genetic studies indicate that SWI/SNF controls transcriptional memory by antagonizing ISWI-like chromatin remodeling enzymes.