451
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Abstract
Developmental origins of health and disease (DOHaD) is the study of how the early life environment can impact the risk of chronic diseases from childhood to adulthood and the mechanisms involved. Epigenetic modifications such as DNA methylation, histone modifications and non-coding RNAs are involved in mediating how early life environment impacts later health. This review is a summary of the Epigenetics and DOHaD workshop held at the 2016 DOHaD Society of Australia and New Zealand Conference. Our extensive knowledge of how the early life environment impacts later risk for chronic disease would not have been possible without animal models. In this review we highlight some animal model examples that demonstrate how an adverse early life exposure results in epigenetic and gene expression changes that may contribute to increased risk of chronic disease later in life. Type 2 diabetes and cardiovascular disease are chronic diseases with an increasing incidence due to the increased number of children and adults that are obese. Epigenetic changes such as DNA methylation have been shown to be associated with metabolic health measures and potentially predict future metabolic health status. Although more difficult to elucidate in humans, recent studies suggest that DNA methylation may be one of the epigenetic mechanisms that mediates the effects of early life exposures on later life risk of obesity and obesity related diseases. Finally, we discuss the role of the microbiome and how it is a new player in developmental programming and mediating early life exposures on later risk of chronic disease.
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452
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Huang JP, Ling K. EZH2 and histone deacetylase inhibitors induce apoptosis in triple negative breast cancer cells by differentially increasing H3 Lys 27 acetylation in the BIM gene promoter and enhancers. Oncol Lett 2017; 14:5735-5742. [PMID: 29113202 PMCID: PMC5661363 DOI: 10.3892/ol.2017.6912] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 03/30/2017] [Indexed: 11/21/2022] Open
Abstract
Enhancer of zeste homolog 2 (EZH2), a subunit of polycomb repressive complex 2, is a histone methyl-transferase and is considered to work cooperatively with histone deacetylases (HDACs) in the same protein complex to mediate gene transcription repression by increasing histone H3 Lys27 trimethylation (H3K27me3), in particular in the nucleosome (s). EZH2 is overexpressed in numerous types of cancer, including triple negative breast cancer (TNBC), a subtype of breast cancer, which there are no effective treatment options for. Thus, inhibition of EZH2 may be harnessed for targeted therapy of this disease. The present study demonstrated that co-treatment with an EZH2 inhibitor and a HDAC inhibitor additively induced apoptosis in two TNBC cell lines, namely MDA-MB-231 and MDA-MB-436. The increased rate of cell death was associated with an elevation of B cell lymphoma-2 like 11 (BIM) expression level, a pro-apoptotic protein at the protein and mRNA expression levels in these two cell lines. The expression of forkhead box O1 (FOXO1), a known upstream transcriptional activator of BIM, was upregulated in both cell lines by the HDAC inhibitor, and the effect was more pronounced in MDA-MB-436 cells with higher phosphorylation levels of protein kinase B, a negative regulator of FOXO1, compared with MDA-MB-231 cells. Conversely, FOXO1 expression was inhibited following treatment with the EZH2 inhibitor, suggesting that EZH2 and HDAC inhibitors induced BIM expression via a FOXO1-independent mechanism. The present study further revealed that the EZH2 inhibitor, but not the HDAC inhibitor, induced high levels of H3K27 acetylation (H3K27ac) in the BIM promoter. By contrast, compared with the effect of the EZH2 inhibitor, HDAC inhibitor treatment resulted in an increase in H3K27ac at two BIM enhancers. Collectively, the results of the present study indicated that EZH2 and HDACs act differentially on H3K27ac levels in the nucleosome at the promoter and enhancer regions of the BIM gene. Through the upregulation of BIM, co-treatment with EZH2 and HDAC inhibitors had a pronounced therapeutic effect on TNBC cells, suggesting that co-targeting EZH2 and HDAC proteins represents a viable therapeutic option for the treatment of TNBC.
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Affiliation(s)
- Julia P Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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453
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Affiliation(s)
- Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
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454
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Abstract
As an important epigenetic mark, lysine methylations play critical roles in the regulation of both chromatin and non-chromatin proteins. There are three levels of lysine methylation, mono-, di-, and trimethylation. Each one has turned out to be biologically distinctive. For the biochemical characterization of proteins with lysine methylation, multiple chemical biology methods have been developed. This concept article will highlight these developments and their applications in epigenetic investigation of protein functions.
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Affiliation(s)
- Zhipeng A. Wang
- Chemistry Department, Texas A&M University, College Station, TX, 77843, USA
| | - Wenshe R. Liu
- Chemistry Department, Texas A&M University, College Station, TX, 77843, USA
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455
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Staiber W. Germline-specific labeling of the somatic chromosomes by protein phosphatase 2A and histone H3S28 phosphorylation in Acricotopus lucidus. PROTOPLASMA 2017; 254:1983-1993. [PMID: 28265764 PMCID: PMC5610207 DOI: 10.1007/s00709-017-1092-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/22/2017] [Indexed: 06/06/2023]
Abstract
Additional chromosomes limited to the germline (=Ks) were established as a special form of germline-soma differentiation in the Orthocladiinae, a subfamily of the Chironomidae (Bauer and Beermann in Z Naturforsch 7b: 557-563, 1952). The Ks together with the somatic chromosomes (=Ss) pass through a complex chromosome cycle with elimination at mitosis and a monopolar migration of all Ks. The dissimilar behavior of Ks and Ss in these exceptional mitoses initiated the search for differential chromosome marks in the orthocladiid Acricotopus lucidus. The search, using immunofluorescence, revealed that in metaphases of male gonial mitoses, and both meiotic divisions, the Ss are fully labeled by protein phosphatase 2A (PP2A) and histone H3S28ph, while in metaphases of somatic cells both marks were detected only at the centromeres of the Ss. In another orthocladiid, Psectrocladius obvius, the same labeling pattern of the Ss as in A. lucidus was established for H3S28ph, but not for PP2A, which was localised solely at the centromeres. In Chironomus nuditaris, a species possessing no Ks, PP2A and H3S28ph signals were always restricted to the centromeres. High levels of H3K4me3, a marker of transcriptionally competent chromatin, were detected on the Ss in metaphases I of C. nuditaris, while in both orthocladiids, the Ss in metaphases I were devoid of H3K4me3 signals. This strongly supports an earlier idea of a silencing of the Ss in male meiosis of A. lucidus suggesting the possibility of extending this concept to the Orthocladiinae. The germline-soma differentiation in A. lucidus is not only made apparent by the occurrence of Ks but also by a germline-specific labeling of the Ss by PP2A and H3S28ph.
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Affiliation(s)
- Wolfgang Staiber
- Institute of Genetics (240), University of Hohenheim, Garbenstrasse 30, D-70599, Stuttgart, Germany.
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456
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Epigenetic Alterations in Human Papillomavirus-Associated Cancers. Viruses 2017; 9:v9090248. [PMID: 28862667 PMCID: PMC5618014 DOI: 10.3390/v9090248] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 08/25/2017] [Accepted: 08/25/2017] [Indexed: 12/15/2022] Open
Abstract
Approximately 15–20% of human cancers are caused by viruses, including human papillomaviruses (HPVs). Viruses are obligatory intracellular parasites and encode proteins that reprogram the regulatory networks governing host cellular signaling pathways that control recognition by the immune system, proliferation, differentiation, genomic integrity, and cell death. Given that key proteins in these regulatory networks are also subject to mutation in non-virally associated diseases and cancers, the study of oncogenic viruses has also been instrumental to the discovery and analysis of many fundamental cellular processes, including messenger RNA (mRNA) splicing, transcriptional enhancers, oncogenes and tumor suppressors, signal transduction, immune regulation, and cell cycle control. More recently, tumor viruses, in particular HPV, have proven themselves invaluable in the study of the cancer epigenome. Epigenetic silencing or de-silencing of genes can have cellular consequences that are akin to genetic mutations, i.e., the loss and gain of expression of genes that are not usually expressed in a certain cell type and/or genes that have tumor suppressive or oncogenic activities, respectively. Unlike genetic mutations, the reversible nature of epigenetic modifications affords an opportunity of epigenetic therapy for cancer. This review summarizes the current knowledge on epigenetic regulation in HPV-infected cells with a focus on those elements with relevance to carcinogenesis.
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457
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Wesche J, Kühn S, Kessler BM, Salton M, Wolf A. Protein arginine methylation: a prominent modification and its demethylation. Cell Mol Life Sci 2017; 74:3305-3315. [PMID: 28364192 PMCID: PMC11107486 DOI: 10.1007/s00018-017-2515-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/07/2017] [Accepted: 03/28/2017] [Indexed: 12/20/2022]
Abstract
Arginine methylation of histones is one mechanism of epigenetic regulation in eukaryotic cells. Methylarginines can also be found in non-histone proteins involved in various different processes in a cell. An enzyme family of nine protein arginine methyltransferases catalyses the addition of methyl groups on arginines of histone and non-histone proteins, resulting in either mono- or dimethylated-arginine residues. The reversibility of histone modifications is an essential feature of epigenetic regulation to respond to changes in environmental factors, signalling events, or metabolic alterations. Prominent histone modifications like lysine acetylation and lysine methylation are reversible. Enzyme family pairs have been identified, with each pair of lysine acetyltransferases/deacetylases and lysine methyltransferases/demethylases operating complementarily to generate or erase lysine modifications. Several analyses also indicate a reversible nature of arginine methylation, but the enzymes facilitating direct removal of methyl moieties from arginine residues in proteins have been discussed controversially. Differing reports have been seen for initially characterized putative candidates, like peptidyl arginine deiminase 4 or Jumonji-domain containing protein 6. Here, we review the most recent cellular, biochemical, and mass spectrometry work on arginine methylation and its reversible nature with a special focus on putative arginine demethylases, including the enzyme superfamily of Fe(II) and 2-oxoglutarate-dependent oxygenases.
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Affiliation(s)
- Juste Wesche
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Sarah Kühn
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Benedikt M Kessler
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Alexander Wolf
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
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458
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Gurrion C, Uriostegui M, Zurita M. Heterochromatin Reduction Correlates with the Increase of the KDM4B and KDM6A Demethylases and the Expression of Pericentromeric DNA during the Acquisition of a Transformed Phenotype. J Cancer 2017; 8:2866-2875. [PMID: 28928876 PMCID: PMC5604219 DOI: 10.7150/jca.19477] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/04/2017] [Indexed: 01/19/2023] Open
Abstract
Cancer cells have alterations in chromatin organization, mostly a reduction in heterochromatin. How this process occurs during transformation and if it participates in the maintenance of a cancerous phenotype is not well understood. Here, using a transformation-inducible cell line, we analyzed the changes that occur in heterochromatin during transformation to a cancerous phenotype. After transformation, there is a reduction in heterochromatin bodies and a nuclear reorganization of HP1α. These occurrences correlate with reductions in H3K9me3 and H3K27me3 levels and with some of the enzymes that introduce these modifications. At the same time, there are increases in the KDM4B and KDM6A/UTX demethylases and an enhancement in the transcription of pericentromeric DNA that correlate with the reduction of H3K9me3 and the recruitment of KDM4B to these elements. The depletion of KDM4B and KDM6A/UTX has a more deleterious effect in transformed cells than in their progenitors, suggesting an important role for these enzymes in the survival of cancerous cells. These results provide new insights into heterochromatin dynamics during transformation to a cancerous phenotype as well as some of the participating mechanisms.
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Affiliation(s)
- Cinthya Gurrion
- Departamento de Genética del Desarrollo y Fisiología Molecular. Instituto de Biotecnología, Universidad Nacional Autónoma de México. 62250 Cuernavaca Morelos, México
| | - Maritere Uriostegui
- Departamento de Genética del Desarrollo y Fisiología Molecular. Instituto de Biotecnología, Universidad Nacional Autónoma de México. 62250 Cuernavaca Morelos, México
| | - Mario Zurita
- Departamento de Genética del Desarrollo y Fisiología Molecular. Instituto de Biotecnología, Universidad Nacional Autónoma de México. 62250 Cuernavaca Morelos, México
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459
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Wei J, Antony J, Meng F, MacLean P, Rhind R, Laible G, Oback B. KDM4B-mediated reduction of H3K9me3 and H3K36me3 levels improves somatic cell reprogramming into pluripotency. Sci Rep 2017; 7:7514. [PMID: 28790329 PMCID: PMC5548918 DOI: 10.1038/s41598-017-06569-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 06/14/2017] [Indexed: 02/03/2023] Open
Abstract
Correct reprogramming of epigenetic marks is essential for somatic cells to regain pluripotency. Repressive histone (H) lysine (K) methylation marks are known to be stable and difficult to reprogram. In this study, we generated transgenic mice and mouse embryonic fibroblasts (MEFs) for the inducible expression of KDM4B, a demethylase that removes H3 K9 and H3K36 trimethylation (me3) marks (H3K9/36me3). Upon inducing Kdm4b, H3K9/36me3 levels significantly decreased compared to non-induced controls. Concurrently, H3K9me1 levels significantly increased, while H3K9me2 and H3K27me3 remained unchanged. The global transcriptional impact of Kdm4b-mediated reduction in H3K9/36me3 levels was examined by comparative microarray analysis and mRNA-sequencing of three independent transgenic MEF lines. We identified several commonly up-regulated targets, including the heterochromatin-associated zinc finger protein 37 and full-length endogenous retrovirus repeat elements. Following optimized zona-free somatic nuclear transfer, reduced H3K9/36me3 levels were restored within hours. Nevertheless, hypo-methylated Kdm4b MEF donors reprogrammed six-fold better into cloned blastocysts than non-induced donors. They also reprogrammed nine-fold better into induced pluripotent stem cells that gave rise to teratomas and chimeras. In summary, we firmly established H3K9/36me3 as a major roadblock to somatic cell reprogramming and identified transcriptional targets of derestricted chromatin that could contribute towards improving this process in mouse.
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Affiliation(s)
- Jingwei Wei
- AgResearch Ruakura Research Centre, Hamilton, New Zealand.,Animal Science Institute, Guangxi University, Nanning, P.R. China
| | - Jisha Antony
- AgResearch Ruakura Research Centre, Hamilton, New Zealand.,University of Otago, Department of Pathology, Dunedin, 9016, New Zealand
| | - Fanli Meng
- AgResearch Ruakura Research Centre, Hamilton, New Zealand
| | - Paul MacLean
- AgResearch Ruakura Research Centre, Hamilton, New Zealand
| | - Rebekah Rhind
- AgResearch Ruakura Research Centre, Hamilton, New Zealand
| | - Götz Laible
- AgResearch Ruakura Research Centre, Hamilton, New Zealand
| | - Björn Oback
- AgResearch Ruakura Research Centre, Hamilton, New Zealand.
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460
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Botchkarev VA, Mardaryev AN. Repressing the Keratinocyte Genome: How the Polycomb Complex Subunits Operate in Concert to Control Skin and Hair Follicle Development. J Invest Dermatol 2017; 136:1538-1540. [PMID: 27450498 DOI: 10.1016/j.jid.2016.04.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 04/27/2016] [Indexed: 01/10/2023]
Abstract
The Polycomb group proteins are transcriptional repressors that are critically important in the control of stem cell activity and maintenance of the identity of differentiated cells. Polycomb proteins interact with each other to form chromatin-associated repressive complexes (Polycomb repressive complexes 1 and 2) leading to chromatin compaction and gene silencing. However, the roles of the distinct components of the Polycomb repressive complex 2 in the control of skin development and keratinocyte differentiation remain obscure. Dauber et al. demonstrate the conditional ablations of three essential Polycomb repressive complex 2 subunits (EED, Suz12, or Ezh1/2) in the epidermal progenitors result in quite similar skin phenotypes including premature acquisition of a functional epidermal barrier, formation of ectopic Merkel cells, and defective postnatal hair follicle development. The reported data demonstrate that in skin epithelia, EED, Suz12, and Ezh1/2 function largely as subunits of the Polycomb repressive complex 2, which is important in the context of data demonstrating their independent activities in other cell types. The report provides an important platform for further analyses of the role of distinct Polycomb components in the control of gene expression programs in the disorders of epidermal differentiation, such as psoriasis and epidermal cancer.
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Affiliation(s)
- Vladimir A Botchkarev
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, UK; Department of Dermatology, Boston University School of Medicine, Boston, USA.
| | - Andrei N Mardaryev
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, UK
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461
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Tao J, Shi L, Huang L, Shi H, Chen H, Wang Y, Wang T. EZH2 is involved in silencing of WNT5A during epithelial-mesenchymal transition of colon cancer cell line. J Cancer Res Clin Oncol 2017; 143:2211-2219. [PMID: 28748258 DOI: 10.1007/s00432-017-2479-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/15/2017] [Indexed: 12/20/2022]
Abstract
PURPOSE Transforming growth factor-β (TGF-β) induction of epithelial-mesenchymal transition (EMT) in SW480 was established as a system for studies of colon cancer metastasis. However, the epigenetic mechanisms underlying this process remain unknown. In mammal, polycomb repressive complex-2 (PRC2) is a highly conserved histone methyltransferase involved in epigenetic regulations. Enhancer of zeste Homolog 2 (EZH2) is the catalytic subunit of PRC2, which catalyzes methylation of lysine 27 of histone H3 (H3K27). METHODS An inducible EMT system in colorectal cancer was utilized to study its mechanistic and phenotypic changes. Particularly, gene expression analysis was studied after immunoprecipitation. RESULTS In this study, we reported that EZH2 is significantly enriched in the promoter region of WNT5A after TGF-β induction in SW480 colon cancer cell line, which in turn silenced the expression of WNT5A. Furthermore, EZH2 inhibitor antagonized the TGF-β-induced morphological conversion associated with epithelial-mesenchymal transition (EMT). Conversely, inhibition of histone H3K27me3 reader CBX does not affect the WNT5A expression level during TGF-β-induced EMT. CONCLUSIONS Our results indicate that EZH2 was essential for the silencing of WNT5A during TGF-β-induced epithelial-mesenchymal transition of colon cancer cells.
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Affiliation(s)
- Jianxin Tao
- Department of Endoscopy Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214023, People's Republic of China
| | - Liping Shi
- Department of Endoscopy Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214023, People's Republic of China
| | - Longchang Huang
- Department of Endoscopy Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214023, People's Republic of China
| | - Haoze Shi
- Department of Endoscopy Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214023, People's Republic of China
| | - Hang Chen
- Department of Endoscopy Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214023, People's Republic of China
| | - Yixin Wang
- Department of Endoscopy Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214023, People's Republic of China
| | - Tong Wang
- Department of Endoscopy Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214023, People's Republic of China.
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462
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Arnal JF, Lenfant F, Metivier R, Flouriot G, Henrion D, Adlanmerini M, Fontaine C, Gourdy P, Chambon P, Katzenellenbogen B, Katzenellenbogen J. Membrane and Nuclear Estrogen Receptor Alpha Actions: From Tissue Specificity to Medical Implications. Physiol Rev 2017; 97:1045-1087. [DOI: 10.1152/physrev.00024.2016] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/19/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022] Open
Abstract
Estrogen receptor alpha (ERα) has been recognized now for several decades as playing a key role in reproduction and exerting functions in numerous nonreproductive tissues. In this review, we attempt to summarize the in vitro studies that are the basis of our current understanding of the mechanisms of action of ERα as a nuclear receptor and the key roles played by its two activation functions (AFs) in its transcriptional activities. We then depict the consequences of the selective inactivation of these AFs in mouse models, focusing on the prominent roles played by ERα in the reproductive tract and in the vascular system. Evidence has accumulated over the two last decades that ERα is also associated with the plasma membrane and activates non-nuclear signaling from this site. These rapid/nongenomic/membrane-initiated steroid signals (MISS) have been characterized in a variety of cell lines, and in particular in endothelial cells. The development of selective pharmacological tools that specifically activate MISS and the generation of mice expressing an ERα protein impeded for membrane localization have begun to unravel the physiological role of MISS in vivo. Finally, we discuss novel perspectives for the design of tissue-selective ER modulators based on the integration of the physiological and pathophysiological roles of MISS actions of estrogens.
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Affiliation(s)
- Jean-Francois Arnal
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Françoise Lenfant
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Raphaël Metivier
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Gilles Flouriot
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Daniel Henrion
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Marine Adlanmerini
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Coralie Fontaine
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Pierre Gourdy
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Pierre Chambon
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Benita Katzenellenbogen
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - John Katzenellenbogen
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
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463
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Shaul O. How introns enhance gene expression. Int J Biochem Cell Biol 2017; 91:145-155. [PMID: 28673892 DOI: 10.1016/j.biocel.2017.06.016] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 06/26/2017] [Accepted: 06/30/2017] [Indexed: 01/18/2023]
Abstract
In many eukaryotes, including mammals, plants, yeast, and insects, introns can increase gene expression without functioning as a binding site for transcription factors. This phenomenon was termed 'intron-mediated enhancement'. Introns can increase transcript levels by affecting the rate of transcription, nuclear export, and transcript stability. Moreover, introns can also increase the efficiency of mRNA translation. This review discusses the current knowledge about these processes. The role of splicing in IME and the significance of intron position relative to the sites of transcription and translation initiation are elaborated. Particular emphasis is placed on the question why different introns, present at the same location of the same genes and spliced at a similar high efficiency, can have very different impacts on expression - from almost no effect to considerable stimulation. This situation can be at least partly accounted for by the identification of splicing-unrelated intronic elements with a special ability to enhance mRNA accumulation or translational efficiency. The many factors that could lead to the large variation observed between the impact of introns in different genes and experimental systems are highlighted. It is suggested that there is no sole, definite answer to the question "how do introns enhance gene expression". Rather, each intron-gene combination might undergo its own unique mixture of processes that lead to the perceptible outcome.
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Affiliation(s)
- Orit Shaul
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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464
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Epigenetic regulation of TGF-β1 signalling in dilative aortopathy of the thoracic ascending aorta. Clin Sci (Lond) 2017; 130:1389-405. [PMID: 27389586 DOI: 10.1042/cs20160222] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 04/11/2016] [Indexed: 01/21/2023]
Abstract
The term 'epigenetics' refers to heritable, reversible DNA or histone modifications that affect gene expression without modifying the DNA sequence. Epigenetic modulation of gene expression also includes the RNA interference mechanism. Epigenetic regulation of gene expression is fundamental during development and throughout life, also playing a central role in disease progression. The transforming growth factor β1 (TGF-β1) and its downstream effectors are key players in tissue repair and fibrosis, extracellular matrix remodelling, inflammation, cell proliferation and migration. TGF-β1 can also induce cell switch in epithelial-to-mesenchymal transition, leading to myofibroblast transdifferentiation. Cellular pathways triggered by TGF-β1 in thoracic ascending aorta dilatation have relevant roles to play in remodelling of the vascular wall by virtue of their association with monogenic syndromes that implicate an aortic aneurysm, including Loeys-Dietz and Marfan's syndromes. Several studies and reviews have focused on the progression of aneurysms in the abdominal aorta, but research efforts are now increasingly being focused on pathogenic mechanisms of thoracic ascending aorta dilatation. The present review summarizes the most recent findings concerning the epigenetic regulation of effectors of TGF-β1 pathways, triggered by sporadic dilative aortopathy of the thoracic ascending aorta in the presence of a tricuspid or bicuspid aortic valve, a congenital malformation occurring in 0.5-2% of the general population. A more in-depth comprehension of the epigenetic alterations associated with TGF-β1 canonical and non-canonical pathways in dilatation of the ascending aorta could be helpful to clarify its pathogenesis, identify early potential biomarkers of disease, and, possibly, develop preventive and therapeutic strategies.
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465
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Soo BPC, Tay J, Ng S, Ho SCL, Yang Y, Chao SH. Correlation Between Expression of Recombinant Proteins and Abundance of H3K4Me3 on the Enhancer of Human Cytomegalovirus Major Immediate-Early Promoter. Mol Biotechnol 2017; 59:315-322. [DOI: 10.1007/s12033-017-0019-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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466
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Abstract
Chromosomes present one of most challenging of all substrates for biochemical study. This is because genomic DNA is physically associated with an astonishing collection of nuclear factors, which serve to not only store the nucleic acid in a stable form, but also grant access to the information it encodes when needed. Understanding this complex molecular choreography is central to the field of epigenetics. One of the great challenges in this area is to move beyond correlative type information, which is now in abundant supply, to the point where we can truly connect the dots at the molecular level. Establishing such causal relationships requires precise manipulation of the covalent structure of chromatin. Tools for this purpose are currently in short supply, creating an opportunity that, as we will argue in this Perspective, is well suited to the sensibilities of the chemist.
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Affiliation(s)
- Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Tom W Muir
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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467
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Turner AMW, Margolis DM. Chromatin Regulation and the Histone Code in HIV Latency
. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2017; 90:229-243. [PMID: 28656010 PMCID: PMC5482300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The formation of a latent reservoir of Human Immunodeficiency Virus (HIV) infection hidden from immune clearance remains a significant obstacle to approaches to eradicate HIV infection. Towards an understanding of the mechanisms of HIV persistence, there is a growing body of work implicating epigenetic regulation of chromatin in establishment and maintenance of this latent reservoir. Here we discuss recent advances in the field of chromatin regulation, specifically in our understanding of the histone code, and how these discoveries relate to our current knowledge of the chromatin mechanisms linked to HIV transcriptional repression and the reversal of latency. We also examine mechanisms unexplored in the context of HIV latency and briefly discuss current therapies aimed at the induction of proviral expression within latently infected cells. We aim to emphasize that a greater understanding of the epigenetic mechanisms which govern HIV latency could lead to new therapeutic targets for latency reversal and clearance cure strategies.
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Affiliation(s)
- Anne-Marie W. Turner
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - David M. Margolis
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC,Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC,To whom all correspondence should be addressed: David Margolis, University of North Carolina at Chapel Hill, 2016 Genetic Medicine Building, CB#7042, 120 Mason Farm Road, Chapel Hill, NC, 27599-7435, Tel: (919) 966-6388, .
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468
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Concomitant epigenetic targeting of LSD1 and HDAC synergistically induces mitochondrial apoptosis in rhabdomyosarcoma cells. Cell Death Dis 2017; 8:e2879. [PMID: 28617441 PMCID: PMC5520898 DOI: 10.1038/cddis.2017.239] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/29/2017] [Accepted: 04/26/2017] [Indexed: 12/22/2022]
Abstract
The lysine-specific demethylase 1 (LSD1) is overexpressed in several cancers including rhabdomyosarcoma (RMS). However, little is yet known about whether or not LSD1 may serve as therapeutic target in RMS. We therefore investigated the potential of LSD1 inhibitors alone or in combination with other epigenetic modifiers such as histone deacetylase (HDAC) inhibitors. Here, we identify a synergistic interaction of LSD1 inhibitors (i.e., GSK690, Ex917) and HDAC inhibitors (i.e., JNJ-26481585, SAHA) to induce cell death in RMS cells. By comparison, LSD1 inhibitors as single agents exhibit little cytotoxicity against RMS cells. Mechanistically, GSK690 acts in concert with JNJ-26481585 to upregulate mRNA levels of the proapoptotic BH3-only proteins BMF, PUMA, BIM and NOXA. This increase in mRNA levels is accompanied by a corresponding upregulation of BMF, PUMA, BIM and NOXA protein levels. Importantly, individual knockdown of either BMF, BIM or NOXA significantly reduces GSK690/JNJ-26481585-mediated cell death. Similarly, genetic silencing of BAK significantly rescues cell death upon GSK690/JNJ-26481585 cotreatment. Also, overexpression of antiapoptotic BCL-2 or MCL-1 significantly protects RMS cells from GSK690/JNJ-26481585-induced cell death. Furthermore, GSK690 acts in concert with JNJ-26481585 to increase activation of caspase-9 and -3. Consistently, addition of the pan-caspase inhibitor N-benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone (zVAD.fmk) significantly reduces GSK690/JNJ-26481585-mediated cell death. In conclusion, concomitant LSD1 and HDAC inhibition synergistically induces cell death in RMS cells by shifting the ratio of pro- and antiapoptotic BCL-2 proteins in favor of apoptosis, thereby engaging the intrinsic apoptotic pathway. This indicates that combined treatment with LSD1 and HDAC inhibitors is a promising new therapeutic approach in RMS.
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469
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Brici D, Zhang Q, Reinhardt S, Dahl A, Hartmann H, Schmidt K, Goveas N, Huang J, Gahurova L, Kelsey G, Anastassiadis K, Stewart AF, Kranz A. Setd1b, encoding a histone 3 lysine 4 methyltransferase, is a maternal effect gene required for the oogenic gene expression program. Development 2017; 144:2606-2617. [PMID: 28619824 DOI: 10.1242/dev.143347] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 06/02/2017] [Indexed: 12/16/2022]
Abstract
Germ cell development involves major reprogramming of the epigenome to prime the zygote for totipotency. Histone 3 lysine 4 (H3K4) methylations are universal epigenetic marks mediated in mammals by six H3K4 methyltransferases related to fly Trithorax, including two yeast Set1 orthologs: Setd1a and Setd1b. Whereas Setd1a plays no role in oogenesis, we report that Setd1b deficiency causes female sterility in mice. Oocyte-specific Gdf9-iCre conditional knockout (Setd1bGdf9 cKO) ovaries develop through all stages; however, follicular loss accumulated with age and unfertilized metaphase II (MII) oocytes exhibited irregularities of the zona pellucida and meiotic spindle. Most Setd1bGdf9 cKO zygotes remained in the pronuclear stage and displayed polyspermy in the perivitelline space. Expression profiling of Setd1bGdf9 cKO MII oocytes revealed (1) that Setd1b promotes the expression of the major oocyte transcription factors including Obox1, 2, 5, 7, Meis2 and Sall4; and (2) twice as many mRNAs were upregulated than downregulated, suggesting that Setd1b also promotes the expression of negative regulators of oocyte development with multiple Zfp-KRAB factors implicated. Together, these findings indicate that Setd1b serves as maternal effect gene through regulation of the oocyte gene expression program.
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Affiliation(s)
- David Brici
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Qinyu Zhang
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Susanne Reinhardt
- Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Dahl
- Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Hella Hartmann
- Light Microscopy Core Facility of the Biotechnology Center/Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Kerstin Schmidt
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Neha Goveas
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Jiahao Huang
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Lenka Gahurova
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Andrea Kranz
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
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470
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Abstract
More than 20% of adults worldwide experience different types of chronic pain, which are frequently associated with several comorbidities and a decrease in quality of life. Several approved painkillers are available, but current analgesics are often hampered by insufficient efficacy and/or severe adverse effects. Consequently, novel strategies for safe, highly efficacious treatments are highly desirable, particularly for chronic pain. Epigenetic mechanisms such as DNA methylation, histone modifications and microRNAs (miRNAs) strongly affect the regulation of gene expression, potentially for long periods over years or even generations, and have been associated with pathophysiological pain. Several studies, mostly in animals, revealed that inhibitors of DNA methylation, activators and inhibitors of histone modification and modulators of miRNAs reverse a number of pathological changes in the pain epigenome, which are associated with altered expression of pain-relevant genes. This epigenetic modulation might then reduce the nociceptive response and provide novel therapeutic options for analgesic therapy of chronic pain states. However, a number of challenges, such as nonspecific effects and poor delivery to target cells and tissues, hinder the rapid development of such analgesics. In this Review, we critically summarize data on epigenetics and pain, focusing on challenges in clinical development as well as possible new approaches to the drug modulation of the pain epigenome.
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Affiliation(s)
- Ellen Niederberger
- Pharmazentrum Frankfurt, Zentrum für Arzneimittelforschung Entwicklung und Sicherheit (ZAFES), Institut für Klinische Pharmakologie, Klinikum der Goethe-Universität Frankfurt, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Eduard Resch
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group for Translational Medicine &Pharmacology, Theodor Stern Kai 7, 60596 Frankfurt am Main, Germany
| | - Michael J Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group for Translational Medicine &Pharmacology, Theodor Stern Kai 7, 60596 Frankfurt am Main, Germany
| | - Gerd Geisslinger
- Pharmazentrum Frankfurt, Zentrum für Arzneimittelforschung Entwicklung und Sicherheit (ZAFES), Institut für Klinische Pharmakologie, Klinikum der Goethe-Universität Frankfurt, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group for Translational Medicine &Pharmacology, Theodor Stern Kai 7, 60596 Frankfurt am Main, Germany
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471
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Epigenetic Strategies to Boost Cancer Immunotherapies. Int J Mol Sci 2017; 18:ijms18061108. [PMID: 28545238 PMCID: PMC5485932 DOI: 10.3390/ijms18061108] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 01/22/2023] Open
Abstract
Recently, immunotherapeutic approaches have shown impressive responses in a subset of cancer patients. However, the rate of success is low and a large percentage of treated patients do not experience clinical benefits. Therefore, additional strategies are needed to improve responses and select responsive patients. Emerging data suggest that epigenetic drugs can improve the responses to immunotherapy. Understanding the mechanisms of resistance to immunotherapy and the epigenetic events that take place during immune evasion is critical to providing a rational combined use of immunotherapies and epigenetic drugs. This review focuses in the epigenetic mechanisms involved in the responses to immunotherapy and how current drugs that target epigenetic regulators impact on them.
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472
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Schreiner S, Nassal M. A Role for the Host DNA Damage Response in Hepatitis B Virus cccDNA Formation-and Beyond? Viruses 2017; 9:v9050125. [PMID: 28531167 PMCID: PMC5454437 DOI: 10.3390/v9050125] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 12/12/2022] Open
Abstract
Chronic hepatitis B virus (HBV) infection puts more than 250 million people at a greatly increased risk to develop end-stage liver disease. Like all hepadnaviruses, HBV replicates via protein-primed reverse transcription of a pregenomic (pg) RNA, yielding an unusually structured, viral polymerase-linked relaxed-circular (RC) DNA as genome in infectious particles. Upon infection, RC-DNA is converted into nuclear covalently closed circular (ccc) DNA. Associating with cellular proteins into an episomal minichromosome, cccDNA acts as template for new viral RNAs, ensuring formation of progeny virions. Hence, cccDNA represents the viral persistence reservoir that is not directly targeted by current anti-HBV therapeutics. Eliminating cccDNA will thus be at the heart of a cure for chronic hepatitis B. The low production of HBV cccDNA in most experimental models and the associated problems in reliable cccDNA quantitation have long hampered a deeper understanding of cccDNA molecular biology. Recent advancements including cccDNA-dependent cell culture systems have begun to identify select host DNA repair enzymes that HBV usurps for RC-DNA to cccDNA conversion. While this list is bound to grow, it may represent just one facet of a broader interaction with the cellular DNA damage response (DDR), a network of pathways that sense and repair aberrant DNA structures and in the process profoundly affect the cell cycle, up to inducing cell death if repair fails. Given the divergent interactions between other viruses and the DDR it will be intriguing to see how HBV copes with this multipronged host system.
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Affiliation(s)
- Sabrina Schreiner
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, D-85764 Munich, Germany.
| | - Michael Nassal
- Dept. of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Hugstetter Str. 55, D-79106 Freiburg, Germany.
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473
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A Novel Histone Crosstalk Pathway Important for Regulation of UV-Induced DNA Damage Repair in Saccharomyces cerevisiae. Genetics 2017; 206:1389-1402. [PMID: 28522541 DOI: 10.1534/genetics.116.195735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 05/16/2017] [Indexed: 02/04/2023] Open
Abstract
Histone post-translational modifications play vital roles in a variety of nuclear processes, including DNA repair. It has been previously shown that histone H3K79 methylation is important for the cellular response to DNA damage caused by ultraviolet (UV) radiation, with evidence that specific methylation states play distinct roles in UV repair. Here, we report that H3K79 methylation is reduced in response to UV exposure in Saccharomyces cerevisiae This reduction is specific to the dimethylated state, as trimethylation levels are minimally altered by UV exposure. Inhibition of this reduction has a deleterious effect on UV-induced sister chromatid exchange, suggesting that H3K79 dimethylation levels play a regulatory role in UV repair. Further evidence implicates an additional role for H3K79 dimethylation levels in error-free translesion synthesis, but not in UV-induced G1/S checkpoint activation or double-stranded break repair. Additionally, we find that H3K79 dimethylation levels are influenced by acetylatable lysines on the histone H4 N-terminal tail, which are hyperacetylated in response to UV exposure. Preclusion of H4 acetylation prevents UV-induced reduction of H3K79 dimethylation, and similarly has a negative effect on UV-induced sister chromatid exchange. These results point to the existence of a novel histone crosstalk pathway that is important for the regulation of UV-induced DNA damage repair.
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474
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The Regulatory Capacity of Bivalent Genes-A Theoretical Approach. Int J Mol Sci 2017; 18:ijms18051069. [PMID: 28513551 PMCID: PMC5454979 DOI: 10.3390/ijms18051069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 02/07/2023] Open
Abstract
Bivalent genes are frequently associated with developmental and lineage specification processes. Resolving their bivalency enables fast changes in their expression, which potentially can trigger cell fate decisions. Here, we provide a theoretical model of bivalency that allows for predictions on the occurrence, stability and regulatory capacity of this prominent modification state. We suggest that bivalency enables balanced gene expression heterogeneity that constitutes a prerequisite of robust lineage priming in somatic stem cells. Moreover, we demonstrate that interactions between the histone and DNA methylation machineries together with the proliferation activity control the stability of the bivalent state and can turn it into an unmodified state. We suggest that deregulation of these interactions underlies cell transformation processes as associated with acute myeloid leukemia (AML) and provide a model of AML blast formation following deregulation of the Ten-eleven Translocation (TET) pathway.
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475
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Maclary E, Hinten M, Harris C, Sethuraman S, Gayen S, Kalantry S. PRC2 represses transcribed genes on the imprinted inactive X chromosome in mice. Genome Biol 2017; 18:82. [PMID: 28468635 PMCID: PMC5415793 DOI: 10.1186/s13059-017-1211-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/11/2017] [Indexed: 12/29/2022] Open
Abstract
Background Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which marks many transcriptionally silent genes throughout the mammalian genome. Although H3K27me3 is associated with silenced gene expression broadly, it remains unclear why some but not other PRC2 target genes require PRC2 and H3K27me3 for silencing. Results Here we define the transcriptional and chromatin features that predict which PRC2 target genes require PRC2/H3K27me3 for silencing by interrogating imprinted mouse X-chromosome inactivation. H3K27me3 is enriched at promoters of silenced genes across the inactive X chromosome. To abrogate PRC2 function, we delete the core PRC2 protein EED in F1 hybrid trophoblast stem cells (TSCs), which undergo imprinted inactivation of the paternally inherited X chromosome. Eed–/– TSCs lack H3K27me3 and Xist lncRNA enrichment on the inactive X chromosome. Despite the absence of H3K27me3 and Xist RNA, only a subset of the inactivated X-linked genes is derepressed in Eed–/– TSCs. Unexpectedly, in wild-type (WT) TSCs these genes are transcribed and are enriched for active chromatin hallmarks on the inactive-X, including RNA PolII, H3K27ac, and H3K36me3, but not the bivalent mark H3K4me2. By contrast, PRC2 targets that remain repressed in Eed–/– TSCs are depleted for active chromatin characteristics in WT TSCs. Conclusions A comparative analysis of transcriptional and chromatin features of inactive X-linked genes in WT and Eed–/– TSCs suggests that PRC2 acts as a brake to prevent induction of transcribed genes on the inactive X chromosome, a mode of PRC2 function that may apply broadly. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1211-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emily Maclary
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Michael Hinten
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Clair Harris
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Shriya Sethuraman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Srimonta Gayen
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA.
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476
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Gallo A, Landi R, Rubino V, Di Cerbo A, Giovazzino A, Palatucci AT, Centenaro S, Guidetti G, Canello S, Cortese L, Ruggiero G, Alessandrini A, Terrazzano G. Oxytetracycline induces DNA damage and epigenetic changes: a possible risk for human and animal health? PeerJ 2017; 5:e3236. [PMID: 28462039 PMCID: PMC5410137 DOI: 10.7717/peerj.3236] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 03/27/2017] [Indexed: 01/26/2023] Open
Abstract
Background Oxytetracycline (OTC), which is largely employed in zootechnical and veterinary practices to ensure wellness of farmed animals, is partially absorbed within the gastrointestinal tract depositing in several tissues. Therefore, the potential OTC toxicity is relevant when considering the putative risk derived by the entry and accumulation of such drug in human and pet food chain supply. Despite scientific literature highlights several OTC-dependent toxic effects on human and animal health, the molecular mechanisms of such toxicity are still poorly understood. Methods Here, we evaluated DNA damages and epigenetic alterations by quantitative reverse transcription polymerase chain reaction, quantitative polymerase chain reaction, chromatin immuno-precipitation and Western blot analysis. Results We observed that human peripheral blood mononuclear cells (PBMCs) expressed DNA damage features (activation of ATM and p53, phosphorylation of H2AX and modifications of histone H3 methylation of lysine K4 in the chromatin) after the in vitro exposure to OTC. These changes are linked to a robust inflammatory response indicated by an increased expression of Interferon (IFN)-γ and type 1 superoxide dismutase (SOD1). Discussion Our data reveal an unexpected biological in vitro activity of OTC able to modify DNA and chromatin in cultured human PBMC. In this regard, OTC presence in foods of animal origin could represent a potential risk for both the human and animal health.
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Affiliation(s)
- Adriana Gallo
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Naples, Italy
| | - Rosaria Landi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Valentina Rubino
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Alessandro Di Cerbo
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena, Italy
| | - Angela Giovazzino
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | | | - Sara Centenaro
- Division of Research and Development, Sanypet SpA, Padova, Italy
| | | | - Sergio Canello
- Division of Research and Development, Sanypet SpA, Padova, Italy
| | - Laura Cortese
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Giuseppina Ruggiero
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Andrea Alessandrini
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena, Italy.,National Research Council (CNR), Nanoscience Istitute, Modena, Italy
| | - Giuseppe Terrazzano
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Department of Science, University of Basilicata, Potenza, Italy
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477
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Total chemical synthesis of methylated analogues of histone 3 revealed KDM4D as a potential regulator of H3K79me3. Bioorg Med Chem 2017; 25:4966-4970. [PMID: 28434780 DOI: 10.1016/j.bmc.2017.04.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/06/2017] [Accepted: 04/11/2017] [Indexed: 01/03/2023]
Abstract
Histone H3 methylation plays an important role in regulating gene expression. In histones in general, this mark is dynamically regulated via various demethylases, which found to control cell fate decisions as well as linked to several diseases, including neurological and cancer. Despite major progress in studying methylation mark at various positions in H3 histone proteins, less is known about the regulation of methylated H3 at Lys79. Methylation at this site is known to have direct cross-talk with monoubiquitination of histone H2B at positions Lys120 and 34, as well as with acetylated H3 at Lys9. Herein we applied convergent total chemical protein synthesis to prepare trimethylated H3 at Lys79 to perform initial studies related to the regulation of this mark. Our study enabled us to identify KDM4D lysine demethylase as a potential regulator for trimethylated H3 at Lys79.
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478
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Vörös Z, Yan Y, Kovari DT, Finzi L, Dunlap D. Proteins mediating DNA loops effectively block transcription. Protein Sci 2017; 26:1427-1438. [PMID: 28295806 PMCID: PMC5477534 DOI: 10.1002/pro.3156] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 12/17/2022]
Abstract
Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop‐mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription.
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Affiliation(s)
- Zsuzsanna Vörös
- Department of Physics, Emory University, Atlanta, Georgia, 30322
| | - Yan Yan
- Department of Physics, Emory University, Atlanta, Georgia, 30322
| | - Daniel T Kovari
- Department of Physics, Emory University, Atlanta, Georgia, 30322
| | - Laura Finzi
- Department of Physics, Emory University, Atlanta, Georgia, 30322
| | - David Dunlap
- Department of Physics, Emory University, Atlanta, Georgia, 30322
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479
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Ospelt C, Gay S, Klein K. Epigenetics in the pathogenesis of RA. Semin Immunopathol 2017; 39:409-419. [DOI: 10.1007/s00281-017-0621-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/09/2017] [Indexed: 01/02/2023]
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480
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481
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Abstract
INTRODUCTION Epigenetic regulators including writers, erasers, and readers of chromatin marks have been implicated in numerous diseases and are therefore subject of intense academic and pharmaceutical research. While several small-molecule inhibitors targeting writers or erasers are either approved drugs or are currently being evaluated in clinical trials, the targeting of epigenetic readers has lagged behind. Proof-of-principle that epigenetic readers are also relevant drug targets was provided by landmark discoveries of selective inhibitors targeting the BET family of acetyl-lysine readers. More recently, high affinity chemical probes for non-BET acetyl- and methyl-lysine reader domains have also been developed. Areas covered: This article covers recent advances with the identification and validation of inhibitors and chemical probes targeting epigenetic reader domains. Issues related to epigenetic reader druggability, quality requirements for chemical probes, interpretation of cellular action, unexpected cross-talk, and future challenges are also discussed. Expert opinion: Chemical probes provide a powerful means to unravel biological functions of epigenetic readers and evaluate their potential as drug targets. To yield meaningful results, potency, selectivity, and cellular target engagement of chemical probes need to be stringently validated. Future chemical probes will probably need to fulfil additional criteria such as strict target specificity or the targeting of readers within protein complexes.
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Affiliation(s)
- Holger Greschik
- a Urologische Klinik und Zentrale Klinische Forschung , Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg , Freiburg , Germany
| | - Roland Schüle
- a Urologische Klinik und Zentrale Klinische Forschung , Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg , Freiburg , Germany.,b Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg , Freiburg , Germany.,c BIOSS Centre of Biological Signalling Studies , Albert-Ludwigs-University Freiburg , Freiburg , Germany
| | - Thomas Günther
- a Urologische Klinik und Zentrale Klinische Forschung , Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg , Freiburg , Germany
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482
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Weirich S, Kudithipudi S, Jeltsch A. Somatic cancer mutations in the MLL1 histone methyltransferase modulate its enzymatic activity and dependence on the WDR5/RBBP5/ASH2L complex. Mol Oncol 2017; 11:373-387. [PMID: 28182322 PMCID: PMC5527479 DOI: 10.1002/1878-0261.12041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/28/2017] [Accepted: 02/02/2017] [Indexed: 12/19/2022] Open
Abstract
Somatic missense mutations in the mixed lineage leukemia 1 (MLL1) histone H3K4 methyltransferase are often observed in cancers. MLL1 forms a complex with WDR5, RBBP5, and ASH2L (WRA) which stimulates its activity. The MM‐102 compound prevents the interaction between MLL1 and WDR5 and functions as an MLL1 inhibitor. We have studied the effects of four cancer mutations in the catalytic SET domain of MLL1 on the enzymatic activity of MLL1 and MLL1–WRA complexes. In addition, we studied the interaction of the MLL1 mutants with the WRA proteins and inhibition of MLL1–WRA complexes by MM‐102. All four investigated mutations had strong effects on the activity of MLL1. R3903H was inactive and S3865F showed reduced activity both alone and in complex with WRA, but its activity was stimulated by the WRA complex. By contrast, R3864C and R3841W were both more active than wild‐type MLL1, but still less active than the wild‐type MLL1–WRA complex. Both mutants were not stimulated by complex formation with WRA, although no differences in the interaction with the complex proteins were observed. These results indicate that both mutants are in an active conformation even in the absence of the WRA complex and their normal control of activity by the WRA complex is altered. In agreement with this observation, the activity of R3864C and R3841W was not reduced by addition of the MM‐102 inhibitor. We show that different cancer mutations in MLL1 lead to a loss or increase in activity, illustrating the complex and tumor‐specific role of MLL1 in carcinogenesis. Our data exemplify that biochemical investigations of somatic tumor mutations are required to decipher their pathological role. Moreover, our data indicate that MM‐102 may not be used as an MLL1 inhibitor if the R3864C and R3841W mutations are present. More generally, the efficacy of any enzyme inhibitor must be experimentally confirmed for mutant enzymes before an application can be considered.
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Affiliation(s)
- Sara Weirich
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Germany
| | - Srikanth Kudithipudi
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Germany
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483
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NEUROD2 Regulates Stim1 Expression and Store-Operated Calcium Entry in Cortical Neurons. eNeuro 2017; 4:eN-NWR-0255-16. [PMID: 28303257 PMCID: PMC5343279 DOI: 10.1523/eneuro.0255-16.2017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/18/2017] [Accepted: 01/25/2017] [Indexed: 12/26/2022] Open
Abstract
Calcium signaling controls many key processes in neurons, including gene expression, axon guidance, and synaptic plasticity. In contrast to calcium influx through voltage- or neurotransmitter-gated channels, regulatory pathways that control store-operated calcium entry (SOCE) in neurons are poorly understood. Here, we report a transcriptional control of Stim1 (stromal interaction molecule 1) gene, which is a major sensor of endoplasmic reticulum (ER) calcium levels and a regulator of SOCE. By using a genome-wide chromatin immunoprecipitation and sequencing approach in mice, we find that NEUROD2, a neurogenic transcription factor, binds to an intronic element within the Stim1 gene. We show that NEUROD2 limits Stim1 expression in cortical neurons and consequently fine-tunes the SOCE response upon depletion of ER calcium. Our findings reveal a novel mechanism that regulates neuronal calcium homeostasis during cortical development.
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484
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Nishimura K, Aizawa S, Nugroho FL, Shiomitsu E, Tran YTH, Bui PL, Borisova E, Sakuragi Y, Takada H, Kurisaki A, Hayashi Y, Fukuda A, Nakanishi M, Hisatake K. A Role for KLF4 in Promoting the Metabolic Shift via TCL1 during Induced Pluripotent Stem Cell Generation. Stem Cell Reports 2017; 8:787-801. [PMID: 28262547 PMCID: PMC5355680 DOI: 10.1016/j.stemcr.2017.01.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/26/2017] [Accepted: 01/27/2017] [Indexed: 01/08/2023] Open
Abstract
Reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) is accompanied by morphological, functional, and metabolic alterations before acquisition of full pluripotency. Although the genome-wide effects of the reprogramming factors on gene expression are well documented, precise mechanisms by which gene expression changes evoke phenotypic responses remain to be determined. We used a Sendai virus-based system that permits reprogramming to progress in a strictly KLF4-dependent manner to screen for KLF4 target genes that are critical for the progression of reprogramming. The screening identified Tcl1 as a critical target gene that directs the metabolic shift from oxidative phosphorylation to glycolysis. KLF4-induced TCL1 employs a two-pronged mechanism, whereby TCL1 activates AKT to enhance glycolysis and counteracts PnPase to diminish oxidative phosphorylation. These regulatory mechanisms described here highlight a central role for a reprogramming factor in orchestrating the metabolic shift toward the acquisition of pluripotency during iPSC generation. KLF4 upregulates Tcl1 expression by directly binding to its enhancer and promoter TCL1 enhances glycolysis by activating AKT during reprogramming TCL1 reduces oxidative phosphorylation by counteracting PnPase during reprogramming TCL1 promotes the metabolic shift to facilitate reprogramming
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Affiliation(s)
- Ken Nishimura
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.
| | - Shiho Aizawa
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Fransiska Liliani Nugroho
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Emi Shiomitsu
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yen Thi Hai Tran
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Phuong Linh Bui
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Evgeniia Borisova
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yuta Sakuragi
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Hitomi Takada
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Akira Kurisaki
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Yohei Hayashi
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Aya Fukuda
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Mahito Nakanishi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Koji Hisatake
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.
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485
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Nishihara M, Kanda GN, Suzuki T, Yamakado S, Harashima H, Kamiya H. Enhanced transgene expression by plasmid-specific recruitment of histone acetyltransferase. J Biosci Bioeng 2017; 123:277-280. [DOI: 10.1016/j.jbiosc.2016.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/10/2016] [Accepted: 09/14/2016] [Indexed: 12/31/2022]
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486
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Hatch SB, Yapp C, Montenegro RC, Savitsky P, Gamble V, Tumber A, Ruda GF, Bavetsias V, Fedorov O, Atrash B, Raynaud F, Lanigan R, Carmichael L, Tomlin K, Burke R, Westaway SM, Brown JA, Prinjha RK, Martinez ED, Oppermann U, Schofield CJ, Bountra C, Kawamura A, Blagg J, Brennan PE, Rossanese O, Müller S. Assessing histone demethylase inhibitors in cells: lessons learned. Epigenetics Chromatin 2017; 10:9. [PMID: 28265301 PMCID: PMC5333395 DOI: 10.1186/s13072-017-0116-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/21/2017] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Histone lysine demethylases (KDMs) are of interest as drug targets due to their regulatory roles in chromatin organization and their tight associations with diseases including cancer and mental disorders. The first KDM inhibitors for KDM1 have entered clinical trials, and efforts are ongoing to develop potent, selective and cell-active 'probe' molecules for this target class. Robust cellular assays to assess the specific engagement of KDM inhibitors in cells as well as their cellular selectivity are a prerequisite for the development of high-quality inhibitors. Here we describe the use of a high-content cellular immunofluorescence assay as a method for demonstrating target engagement in cells. RESULTS A panel of assays for the Jumonji C subfamily of KDMs was developed to encompass all major branches of the JmjC phylogenetic tree. These assays compare compound activity against wild-type KDM proteins to a catalytically inactive version of the KDM, in which residues involved in the active-site iron coordination are mutated to inactivate the enzyme activity. These mutants are critical for assessing the specific effect of KDM inhibitors and for revealing indirect effects on histone methylation status. The reported assays make use of ectopically expressed demethylases, and we demonstrate their use to profile several recently identified classes of KDM inhibitors and their structurally matched inactive controls. The generated data correlate well with assay results assessing endogenous KDM inhibition and confirm the selectivity observed in biochemical assays with isolated enzymes. We find that both cellular permeability and competition with 2-oxoglutarate affect the translation of biochemical activity to cellular inhibition. CONCLUSIONS High-content-based immunofluorescence assays have been established for eight KDM members of the 2-oxoglutarate-dependent oxygenases covering all major branches of the JmjC-KDM phylogenetic tree. The usage of both full-length, wild-type and catalytically inactive mutant ectopically expressed protein, as well as structure-matched inactive control compounds, allowed for detection of nonspecific effects causing changes in histone methylation as a result of compound toxicity. The developed assays offer a histone lysine demethylase family-wide tool for assessing KDM inhibitors for cell activity and on-target efficacy. In addition, the presented data may inform further studies to assess the cell-based activity of histone lysine methylation inhibitors.
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Affiliation(s)
- Stephanie B. Hatch
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Clarence Yapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Raquel C. Montenegro
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
- Medical Faculty, Research and Drug Development Center, Federal University of Ceará, Rua Cel. Nunes de Melo n.1000—Rodolfo Teófilo, 60, Fortaleza, CE 430-270 Brazil
| | - Pavel Savitsky
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
| | - Vicki Gamble
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Anthony Tumber
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Gian Filippo Ruda
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Vassilios Bavetsias
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Butrus Atrash
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Florence Raynaud
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Rachel Lanigan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - LeAnne Carmichael
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Kathy Tomlin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Rosemary Burke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Susan M. Westaway
- Epigenetics Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, SG1 2NY UK
| | - Jack A. Brown
- Epigenetics Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, SG1 2NY UK
| | - Rab K. Prinjha
- Epigenetics Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, SG1 2NY UK
| | - Elisabeth D. Martinez
- Hamon Center for Therapeutic Oncology Research, and Department of Pharmacology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390 USA
| | - Udo Oppermann
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, OX3 7LD UK
| | | | - Chas Bountra
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Akane Kawamura
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Paul E. Brennan
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Olivia Rossanese
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Susanne Müller
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
- Buchmann Institute for Molecular Life Science, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
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487
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Ellis SE, Gupta S, Moes A, West AB, Arking DE. Exaggerated CpH methylation in the autism-affected brain. Mol Autism 2017; 8:6. [PMID: 28316770 PMCID: PMC5351204 DOI: 10.1186/s13229-017-0119-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/09/2017] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The etiology of autism, a complex, heritable, neurodevelopmental disorder, remains largely unexplained. Given the unexplained risk and recent evidence supporting a role for epigenetic mechanisms in the development of autism, we explored the role of CpG and CpH (H = A, C, or T) methylation within the autism-affected cortical brain tissue. METHODS Reduced representation bisulfite sequencing (RRBS) was completed, and analysis was carried out in 63 post-mortem cortical brain samples (Brodmann area 19) from 29 autism-affected and 34 control individuals. Analyses to identify single sites that were differentially methylated and to identify any global methylation alterations at either CpG or CpH sites throughout the genome were carried out. RESULTS We report that while no individual site or region of methylation was significantly associated with autism after multi-test correction, methylated CpH dinucleotides were markedly enriched in autism-affected brains (~2-fold enrichment at p < 0.05 cutoff, p = 0.002). CONCLUSIONS These results further implicate epigenetic alterations in pathobiological mechanisms that underlie autism.
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Affiliation(s)
- Shannon E. Ellis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Simone Gupta
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Anna Moes
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Andrew B. West
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Dan E. Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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488
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Ponnaluri VKC, Ehrlich KC, Zhang G, Lacey M, Johnston D, Pradhan S, Ehrlich M. Association of 5-hydroxymethylation and 5-methylation of DNA cytosine with tissue-specific gene expression. Epigenetics 2017; 12:123-138. [PMID: 27911668 PMCID: PMC5330441 DOI: 10.1080/15592294.2016.1265713] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/10/2016] [Accepted: 11/21/2016] [Indexed: 12/15/2022] Open
Abstract
Differentially methylated or hydroxymethylated regions (DMRs) in mammalian DNA are often associated with tissue-specific gene expression but the functional relationships are still being unraveled. To elucidate these relationships, we studied 16 human genes containing myogenic DMRs by analyzing profiles of their epigenetics and transcription and quantitatively assaying 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) at specific sites in these genes in skeletal muscle (SkM), myoblasts, heart, brain, and diverse other samples. Although most human promoters have little or no methylation regardless of expression, more than half of the genes that we chose to study-owing to their myogenic DMRs-overlapped tissue-specific alternative or cryptic promoters displaying corresponding tissue-specific differences in histone modifications. The 5mC levels in myoblast DMRs were significantly associated with 5hmC levels in SkM at the same site. Hypermethylated myogenic DMRs within CDH15, a muscle- and cerebellum-specific cell adhesion gene, and PITX3, a homeobox gene, were used for transfection in reporter gene constructs. These intragenic DMRs had bidirectional tissue-specific promoter activity that was silenced by in vivo-like methylation. The CDH15 DMR, which was previously associated with an imprinted maternal germline DMR in mice, had especially strong promoter activity in myogenic host cells. These findings are consistent with the controversial hypothesis that intragenic DNA methylation can facilitate transcription and is not just a passive consequence of it. Our results support varied roles for tissue-specific 5mC- or 5hmC-enrichment in suppressing inappropriate gene expression from cryptic or alternative promoters and in increasing the plasticity of gene expression required for development and rapid responses to tissue stress or damage.
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Affiliation(s)
| | - Kenneth C. Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA, USA
| | | | - Michelle Lacey
- Department of Mathematics, Tulane Health Sciences Center and Tulane University, New Orleans, LA, USA
| | - Douglas Johnston
- Department of Microbiology, Immunology and Parasitology, LSU Health Sciences Center, New Orleans, LA, USA
| | | | - Melanie Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA, USA
- Hayward Genetics Center and Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA, USA
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489
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Pang J, Yang YW, Huang Y, Yang J, Zhang H, Chen R, Dong L, Huang Y, Wang D, Liu J, Li B. P110β Inhibition Reduces Histone H3K4 Di-Methylation in Prostate Cancer. Prostate 2017; 77:299-308. [PMID: 27800642 DOI: 10.1002/pros.23271] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/05/2016] [Indexed: 12/27/2022]
Abstract
INTRODUCTION AND AIMS Epigenetic alteration plays a major role in the development and progression of human cancers, including prostate cancer. Histones are the key factors in modulating gene accessibility to transcription factors and post-translational modification of the histone N-terminal tail including methylation is associated with either transcriptional activation (H3K4me2) or repression (H3K9me3). Furthermore, phosphoinositide 3-kinase (PI3 K) signaling and the androgen receptor (AR) are the key determinants in prostate cancer development and progression. We recently showed that prostate-targeted nano-micelles loaded with PI3 K/p110beta specific inhibitor TGX221 blocked prostate cancer growth in vitro and in vivo. Our objective of this study was to determine the role of PI3 K signaling in histone methylation in prostate cancer, with emphasis on histone H3K4 methylation. METHODS PI3 K non-specific inhibitor LY294002 and p110beta-specific inhibitor TGX221 were used to block PI3 K/p110beta signaling. The global levels of H3K4 and H3K9 methylation in prostate cancer cells and tissue specimens were evaluated by Western blot assay and immunohistochemical staining. A synthetic androgen R1881 was used to stimulate AR activity in prostate cancer cells. A castration-resistant prostate cancer (CRPC) specific human tissue microarray (TMA) was used to assess the global levels of H3K4me2 methylation by immunostaining approach. RESULTS Our data revealed that H3K4me2 levels were significantly elevated after androgen stimulation. With RNA silencing and pharmacology approaches, we further defined that inhibition of PI3 K/p110beta activity through gene-specific knocking down and small chemical inhibitor TGX221 abolished androgen-stimulated H3K4me2 methylation. Consistently, prostate cancer-targeted delivery of TGX221 in vivo dramatically reduced the global levels of H3K4me2 as assessed by immunohistochemical staining on tissue section of mouse xenografts from CRPC cell lines 22RV1 and C4-2. Finally, immunostaining data revealed a strong H3K4me2 immunosignal in CRPC tissues compared to primary tumors and benign prostate tissues. CONCLUSIONS Taken together, our results suggest that PI3 K/p110beta-dependent signaling is involved in androgen-stimulated H3K4me2 methylation in prostate cancer, which might be used as a novel biomarker for disease prognosis and targeted therapy. Prostate 77:299-308, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jun Pang
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yue-Wu Yang
- Department of Traditional Chinese Medicine, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yiling Huang
- Department of Urology, The University of Kansas Medical Center, Kansas City, Kansas
- Department of Pathology, China Three Gorges University School of Medicine, Yichang, China
| | - Jun Yang
- Department of Urology, The University of Kansas Medical Center, Kansas City, Kansas
- Department of Urology, Tongji Hospital, Huanzhong University of Science and Technology, Wuhan, China
| | - Hao Zhang
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ruibao Chen
- Department of Urology, The University of Kansas Medical Center, Kansas City, Kansas
- Department of Urology, Tongji Hospital, Huanzhong University of Science and Technology, Wuhan, China
| | - Liang Dong
- Department of Urology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Yan Huang
- Department of Urology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Dongying Wang
- Department of Urology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Huanzhong University of Science and Technology, Wuhan, China
| | - Benyi Li
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Urology, The University of Kansas Medical Center, Kansas City, Kansas
- Department of Pathology, China Three Gorges University School of Medicine, Yichang, China
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490
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Teste B, Champ J, Londono-Vallejo A, Descroix S, Malaquin L, Viovy JL, Draskovic I, Mottet G. Chromatin immunoprecipitation in microfluidic droplets: towards fast and cheap analyses. LAB ON A CHIP 2017; 17:530-537. [PMID: 28092380 DOI: 10.1039/c6lc01535b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Genetic organization is governed by the interaction of DNA with histone proteins, and differential modifications of these proteins is a fundamental mechanism of gene regulation. Histone modifications are primarily studied through chromatin immunoprecipitation (ChIP) assays, however conventional ChIP procedures are time consuming, laborious and require a large number of cells. Here we report for the first time the development of ChIP in droplets based on a microfluidic platform combining nanoliter droplets, magnetic beads (MB) and magnetic tweezers (MT). The droplet approach enabled compartmentalization and improved mixing, while reducing the consumption of samples and reagents in an integrated workflow. Anti-histone antibodies grafted to MB were used as a solid support to capture and transfer the target chromatin from droplets to droplets in order to perform chromatin immunoprecipitation, washing, elution and purification of DNA. We designed a new ChIP protocol to investigate four different types of modified histones with known roles in gene activation or repression. We evaluated the performances of this new ChIP in droplet assay in comparison with conventional methods. The proposed technology dramatically reduces analytical time from a few days to 7 hours, simplifies the ChIP protocol and decreases the number of cells required by 100 fold while maintaining a high degree of sensitivity and specificity. Therefore this droplet-based ChIP assay represents a new, highly advantageous and convenient approach to epigenetic analyses.
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Affiliation(s)
- Bruno Teste
- Institut Curie, PSL Research University, CNRS UMR 168, 6 Rue Calvin, 75005 Paris, France. and Institut Pierre-Gilles de Gennes, MMBM group, 75005 Paris, France
| | - Jerome Champ
- Institut Curie, PSL Research University, CNRS UMR 168, 6 Rue Calvin, 75005 Paris, France. and Institut Pierre-Gilles de Gennes, MMBM group, 75005 Paris, France
| | - Arturo Londono-Vallejo
- CNRS, UMR 3244, Telomeres and Cancer Laboratory, Institut Curie, PSL Research University, F-75248, Paris, France and CNRS, UMR3244, Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France
| | - Stéphanie Descroix
- Institut Curie, PSL Research University, CNRS UMR 168, 6 Rue Calvin, 75005 Paris, France. and Institut Pierre-Gilles de Gennes, MMBM group, 75005 Paris, France
| | - Laurent Malaquin
- Institut Curie, PSL Research University, CNRS UMR 168, 6 Rue Calvin, 75005 Paris, France. and Institut Pierre-Gilles de Gennes, MMBM group, 75005 Paris, France
| | - Jean-Louis Viovy
- Institut Curie, PSL Research University, CNRS UMR 168, 6 Rue Calvin, 75005 Paris, France. and Institut Pierre-Gilles de Gennes, MMBM group, 75005 Paris, France
| | - Irena Draskovic
- CNRS, UMR 3244, Telomeres and Cancer Laboratory, Institut Curie, PSL Research University, F-75248, Paris, France and CNRS, UMR3244, Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France
| | - Guillaume Mottet
- Institut Curie, PSL Research University, CNRS UMR 168, 6 Rue Calvin, 75005 Paris, France. and Institut Pierre-Gilles de Gennes, MMBM group, 75005 Paris, France
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491
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Hemstedt TJ, Lattal KM, Wood MA. Reconsolidation and extinction: Using epigenetic signatures to challenge conventional wisdom. Neurobiol Learn Mem 2017; 142:55-65. [PMID: 28119018 DOI: 10.1016/j.nlm.2017.01.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/15/2017] [Accepted: 01/16/2017] [Indexed: 12/17/2022]
Abstract
Epigenetic mechanisms have the potential to give rise to lasting changes in cell function that ultimately can affect behavior persistently. This concept is especially interesting with respect to fear reconsolidation and fear memory extinction. These two behavioral approaches are used in the laboratory to investigate how fear memory can be attenuated, which becomes important when searching for therapeutic intervention to treat anxiety disorders and post-traumatic stress disorder. Here we review the role of several key epigenetic mechanisms in reconsolidation and extinction of learned fear and their potential to persistently alter behavioral responses to conditioned cues. We also briefly discuss how epigenetic mechanisms may establish persistent behaviors that challenge our definitions of extinction and reconsolidation.
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Affiliation(s)
- Thekla J Hemstedt
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA; Center for the Neurobiology of Learning and Memory, Irvine, CA, USA
| | - K Matthew Lattal
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA; Center for the Neurobiology of Learning and Memory, Irvine, CA, USA.
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492
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Haddad N, Jost D, Vaillant C. Perspectives: using polymer modeling to understand the formation and function of nuclear compartments. Chromosome Res 2017; 25:35-50. [PMID: 28091870 PMCID: PMC5346151 DOI: 10.1007/s10577-016-9548-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/18/2016] [Accepted: 12/21/2016] [Indexed: 12/20/2022]
Abstract
Compartmentalization is a ubiquitous feature of cellular function. In the nucleus, early observations revealed a non-random spatial organization of the genome with a large-scale segregation between transcriptionally active—euchromatin—and silenced—heterochromatin—parts of the genome. Recent advances in genome-wide mapping and imaging techniques have strikingly improved the resolution at which nuclear genome folding can be analyzed and have revealed a multiscale spatial compartmentalization with increasing evidences that such compartment may indeed result from and participate to genome function. Understanding the underlying mechanisms of genome folding and in particular the link to gene regulation requires a cross-disciplinary approach that combines the new high-resolution techniques with computational modeling of chromatin and chromosomes. In this perspective article, we first present how the copolymer theoretical framework can account for the genome compartmentalization. We then suggest, in a second part, that compartments may act as a “nanoreactor,” increasing the robustness of either activation or repression by enhancing the local concentration of regulators. We conclude with the need to develop a new framework, namely the “living chromatin” model that will allow to explicitly investigate the coupling between spatial compartmentalization and gene regulation.
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Affiliation(s)
- N Haddad
- CNRS, Laboratoire de Physique, University of Lyon, ENS de Lyon, University of Claude Bernard, 69007, Lyon, France
| | - D Jost
- University Grenoble-Alpes, CNRS, TIMC-IMAG lab, UMR 5525, Grenoble, France.
| | - C Vaillant
- CNRS, Laboratoire de Physique, University of Lyon, ENS de Lyon, University of Claude Bernard, 69007, Lyon, France.
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493
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Liu XF, Hummel M, Abecassis M. Epigenetic regulation of cellular and cytomegalovirus genes during myeloid cell development. ACTA ACUST UNITED AC 2017; 3. [PMID: 28707002 DOI: 10.18103/imr.v3i3.385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Myeloid cells are important cell types that carry human cytomegalovirus. Latent viral DNA is present in CD34+ progenitor cells and their derived monocytes. However, differentiation of latently infected monocytes to mature macrophages or dendritic cells causes reactivation of latent viruses. During hematopoietic development, pluripotent genes are repressed, and lineage specific genes are activated in a step-wise manner. This process is governed by cell-type specific chromatin states. Enhancers in the hematopoietic system are highly dynamic and established by pioneer (first tier) transcription factors (TFs), which set the stage for second and third tier TF binding. In this review, we examine the epigenetic mechanisms that regulate myeloid cell development, cell identity, and activation with a special focus on factors that regulate viral gene expression and the status of viral infection in myeloid cells.
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Affiliation(s)
- Xue-Feng Liu
- Comprehensive Transplant Center, Division of Organ Transplantation, Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611
| | - Mary Hummel
- Comprehensive Transplant Center, Division of Organ Transplantation, Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611
| | - Michael Abecassis
- Comprehensive Transplant Center, Division of Organ Transplantation, Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611
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494
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Rademacher A, Erdel F, Trojanowski J, Schumacher S, Rippe K. Real-time observation of light-controlled transcription in living cells. J Cell Sci 2017. [DOI: 10.1242/jcs.205534] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
Gene expression is tightly regulated in space and time. To dissect this process with high temporal resolution, we introduce an optogenetic tool termed BLInCR (Blue Light-Induced Chromatin Recruitment) that combines rapid and reversible light-dependent recruitment of effector proteins with a real-time readout for transcription. We used BLInCR to control the activity of a reporter gene cluster in the human osteosarcoma cell line U2OS by reversibly recruiting the viral transactivator VP16. RNA production was detectable ∼2 minutes after VP16 recruitment and readily decreased when VP16 dissociated from the cluster in the absence of light. Quantitative assessment of the activation process revealed biphasic activation kinetics with a pronounced early phase in cells treated with the histone deacetylase inhibitor SAHA. Comparison with kinetic models for transcription activation suggests that the gene cluster undergoes a maturation process when activated. We anticipate that BLInCR will facilitate the study of transcription dynamics in living cells.
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Affiliation(s)
- Anne Rademacher
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Fabian Erdel
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jorge Trojanowski
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sabrina Schumacher
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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495
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Bernstein D, Golson ML, Kaestner KH. Epigenetic control of β-cell function and failure. Diabetes Res Clin Pract 2017; 123:24-36. [PMID: 27918975 PMCID: PMC5250585 DOI: 10.1016/j.diabres.2016.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 11/15/2016] [Indexed: 12/21/2022]
Abstract
Type 2 diabetes is a highly heritable disease, but only ∼15% of this heritability can be explained by known genetic variant loci. In fact, body mass index is more predictive of diabetes than any of the common risk alleles identified by genome-wide association studies. This discrepancy may be explained by epigenetic inheritance, whereby changes in gene regulation can be passed along to offspring. Epigenetic changes throughout an organism's lifetime, based on environmental factors such as chemical exposures, diet, physical activity, and age, can also affect gene expression and susceptibility to diabetes. Recently, novel genome-wide assays of epigenetic marks have resulted in a greater understanding of how genetics, epigenetics, and the environment interact in the development and inheritance of diabetes.
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Affiliation(s)
- Diana Bernstein
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria L Golson
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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496
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Rabhi N, Hannou SA, Froguel P, Annicotte JS. Cofactors As Metabolic Sensors Driving Cell Adaptation in Physiology and Disease. Front Endocrinol (Lausanne) 2017; 8:304. [PMID: 29163371 PMCID: PMC5675844 DOI: 10.3389/fendo.2017.00304] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/19/2017] [Indexed: 12/21/2022] Open
Abstract
Chromatin architectures and epigenetic fingerprint regulation are fundamental for genetically determined biological processes. Chemical modifications of the chromatin template sensitize the genome to intracellular metabolism changes to set up diverse functional adaptive states. Accumulated evidence suggests that the action of epigenetic modifiers is sensitive to changes in dietary components and cellular metabolism intermediates, linking nutrition and energy metabolism to gene expression plasticity. Histone posttranslational modifications create a code that acts as a metabolic sensor, translating changes in metabolism into stable gene expression patterns. These observations support the notion that epigenetic reprograming-linked energy input is connected to the etiology of metabolic diseases and cancer. In the present review, we introduce the role of epigenetic cofactors and their relation with nutrient intake and we question the links between epigenetic regulation and the development of metabolic diseases.
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Affiliation(s)
- Nabil Rabhi
- Lille University, UMR 8199—EGID, Lille, France
- CNRS, UMR 8199, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Sarah Anissa Hannou
- Lille University, UMR 8199—EGID, Lille, France
- CNRS, UMR 8199, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Philippe Froguel
- Lille University, UMR 8199—EGID, Lille, France
- CNRS, UMR 8199, Lille, France
- Institut Pasteur de Lille, Lille, France
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Jean-Sébastien Annicotte
- Lille University, UMR 8199—EGID, Lille, France
- CNRS, UMR 8199, Lille, France
- Institut Pasteur de Lille, Lille, France
- *Correspondence: Jean-Sébastien Annicotte,
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497
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Pirih N, Kunej T. Toward a Taxonomy for Multi-Omics Science? Terminology Development for Whole Genome Study Approaches by Omics Technology and Hierarchy. ACTA ACUST UNITED AC 2017; 21:1-16. [DOI: 10.1089/omi.2016.0144] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Nina Pirih
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
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498
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Kudrin RA, Mironov AA, Stavrovskaya ED. Chromatin and Polycomb: Biology and bioinformatics. Mol Biol 2017. [DOI: 10.1134/s0026893316060121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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499
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Epigenetic Changes in Chronic Inflammatory Diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 106:139-189. [DOI: 10.1016/bs.apcsb.2016.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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500
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Jost D, Vaillant C, Meister P. Coupling 1D modifications and 3D nuclear organization: data, models and function. Curr Opin Cell Biol 2016; 44:20-27. [PMID: 28040646 DOI: 10.1016/j.ceb.2016.12.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 12/17/2022]
Abstract
Over the past decade, advances in molecular methods have strikingly improved the resolution at which nuclear genome folding can be analyzed. This revealed a wealth of conserved features organizing the one dimensional DNA molecule into tridimensional nuclear domains. In this review, we briefly summarize the main findings and highlight how models based on polymer physics shed light on the principles underlying the formation of these domains. Finally, we discuss the mechanistic similarities allowing self-organization of these structures and the functional importance of these in the maintenance of transcriptional programs.
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Affiliation(s)
- Daniel Jost
- University Grenoble Alpes, CNRS, TIMC-IMAG lab, UMR 5525, Grenoble, F-38706 La Tronche, France
| | - Cédric Vaillant
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, F-69007 Lyon, France
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland.
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