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Silva-Carvalho AÉ, Filiú-Braga LDC, Bogéa GMR, de Assis AJB, Pittella-Silva F, Saldanha-Araujo F. GLP and G9a histone methyltransferases as potential therapeutic targets for lymphoid neoplasms. Cancer Cell Int 2024; 24:243. [PMID: 38997742 PMCID: PMC11249034 DOI: 10.1186/s12935-024-03441-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 07/08/2024] [Indexed: 07/14/2024] Open
Abstract
Histone methyltransferases (HMTs) are enzymes that regulate histone methylation and play an important role in controlling transcription by altering the chromatin structure. Aberrant activation of HMTs has been widely reported in certain types of neoplastic cells. Among them, G9a/EHMT2 and GLP/EHMT1 are crucial for H3K9 methylation, and their dysregulation has been associated with tumor initiation and progression in different types of cancer. More recently, it has been shown that G9a and GLP appear to play a critical role in several lymphoid hematologic malignancies. Importantly, the key roles played by both enzymes in various diseases made them attractive targets for drug development. In fact, in recent years, several groups have tried to develop small molecule inhibitors targeting their epigenetic activities as potential anticancer therapeutic tools. In this review, we discuss the physiological role of GLP and G9a, their oncogenic functions in hematologic malignancies of the lymphoid lineage, and the therapeutic potential of epigenetic drugs targeting G9a/GLP for cancer treatment.
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Affiliation(s)
| | | | | | - Alan Jhones Barbosa de Assis
- Laboratory of Molecular Pathology of Cancer, Faculty of Health Sciences and Medicine, University of Brasilia, Brasília, Brazil
| | - Fábio Pittella-Silva
- Laboratory of Molecular Pathology of Cancer, Faculty of Health Sciences and Medicine, University of Brasilia, Brasília, Brazil
| | - Felipe Saldanha-Araujo
- Hematology and Stem Cells Laboratory, Faculty of Health Sciences, University of Brasília, Brasilia, Brazil.
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2
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Larue AEM, Atlasi Y. The epigenetic landscape in intestinal stem cells and its deregulation in colorectal cancer. Stem Cells 2024; 42:509-525. [PMID: 38597726 PMCID: PMC11177158 DOI: 10.1093/stmcls/sxae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Epigenetic mechanisms play a pivotal role in controlling gene expression and cellular plasticity in both normal physiology and pathophysiological conditions. These mechanisms are particularly important in the regulation of stem cell self-renewal and differentiation, both in embryonic development and within adult tissues. A prime example of this finely tuned epigenetic control is observed in the gastrointestinal lining, where the small intestine undergoes renewal approximately every 3-5 days. How various epigenetic mechanisms modulate chromatin functions in intestinal stem cells (ISCs) is currently an active area of research. In this review, we discuss the main epigenetic mechanisms that control ISC differentiation under normal homeostasis. Furthermore, we explore the dysregulation of these mechanisms in the context of colorectal cancer (CRC) development. By outlining the main epigenetic mechanisms contributing to CRC, we highlight the recent therapeutics development and future directions for colorectal cancer research.
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Affiliation(s)
- Axelle E M Larue
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, United Kingdom
| | - Yaser Atlasi
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, United Kingdom
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3
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Low R, Ha SD, Sleapnicov N, Maneesh P, Kim SO. Prolonged Inhibition of the MEK1/2-ERK Signaling Axis Primes Interleukin-1 Beta Expression through Histone 3 Lysine 9 Demethylation in Murine Macrophages. Int J Mol Sci 2023; 24:14428. [PMID: 37833877 PMCID: PMC10572145 DOI: 10.3390/ijms241914428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Macrophages undergo different cellular states upon activation that can be hyporesponsive (tolerated) or hyperresponsive (primed or trained) to subsequent stimuli. Epigenetic modifications are known to play key roles in determining these cellular states. However, little is known about the role of signaling pathways that lead to these epigenetic modifications. Here, we examined the effects of various inhibitors targeting key signaling pathways induced by lipopolysaccharide (LPS) on tolerance and priming in murine macrophages. We found that a prolonged inhibition (>18 h) of the mitogen-activated protein kinase (MEK)1/2-extracellular signal-regulated kinase (ERK)1/2 signaling axis reversed tolerance and primed cells in expressing interleukin (IL)-1β and other inflammatory cytokines such as IL-6, tumor necrosis factor (TNF)α, and CXCL10. The ectopic expression of catalytically active and inactive MEK1 mutants suppressed and enhanced IL-1β expression, respectively. A transcriptomic analysis showed that cells primed by the MEK1/2 inhibitor U0126 expressed higher levels of gene sets associated with immune responses and cytokine/chemokine production, but expressed lower levels of genes with cell cycle progression, chromosome organization, and heterochromatin formation than non-primed cells. Of interest, the mRNA expressions of the histone 3 lysine 9 (H3K9) methyltransferase Suv39h1 and the H3K9 methylation reader Cbx5 were substantially suppressed, whereas the H3K9 demethylase Kdm7a was enhanced, suggesting a role of the MEK1/2-ERK signaling axis in H3K9 demethylation. The H3K9 trimethylation levels in the genomic regions of IL-1β, TNFα, and CXCL10 were decreased by U0126. Also, the H3K9 methyltransferase inhibitor BIX01294 mimicked the U0126 training effects and the overexpression of chromobox homolog (CBX)5 prevented the U0126 training effects in both RAW264.7 cells and bone-marrow-derived macrophages. Collectively, these data suggest that the prolonged inhibition of the MEK1/2-ERK signaling axis reverses tolerance and primed macrophages likely through decreasing the H3K9 methylation levels.
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Affiliation(s)
| | | | | | | | - Sung Ouk Kim
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6G 2V4, Canada; (R.L.); (S.-D.H.); (N.S.); (P.M.)
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4
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Djeghloul D, Dimond A, Cheriyamkunnel S, Kramer H, Patel B, Brown K, Montoya A, Whilding C, Wang YF, Futschik ME, Veland N, Montavon T, Jenuwein T, Merkenschlager M, Fisher AG. Loss of H3K9 trimethylation alters chromosome compaction and transcription factor retention during mitosis. Nat Struct Mol Biol 2023; 30:489-501. [PMID: 36941433 PMCID: PMC10113154 DOI: 10.1038/s41594-023-00943-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/13/2023] [Indexed: 03/23/2023]
Abstract
Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases and polycomb repressor complexes, binds to chromosomes throughout mitosis and their depletion results in increased chromosome size. In the present study, we show that enzymes that catalyze H3K9 methylation, such as Suv39h1, Suv39h2, G9a and Glp, are also retained on mitotic chromosomes. Surprisingly, however, mutants lacking histone 3 lysine 9 trimethylation (H3K9me3) have unusually small and compact mitotic chromosomes associated with increased histone H3 phospho Ser10 (H3S10ph) and H3K27me3 levels. Chromosome size and centromere compaction in these mutants were rescued by providing exogenous first protein lysine methyltransferase Suv39h1 or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wild-type versus Suv39h1/Suv39h2 double-null mouse embryonic stem cells revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.
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Affiliation(s)
- Dounia Djeghloul
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK.
| | - Andrew Dimond
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Sherry Cheriyamkunnel
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Bhavik Patel
- Flow Cytometry Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Karen Brown
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Chad Whilding
- Microscopy Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Yi-Fang Wang
- Bioinformatics, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Matthias E Futschik
- Bioinformatics, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Nicolas Veland
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Thomas Montavon
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Jenuwein
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK.
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5
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Qu J, Wang Q, Sun X, Li Y. The environment and female reproduction: Potential mechanism of cadmium poisoning to the growth and development of ovarian follicle. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 244:114029. [PMID: 36055045 DOI: 10.1016/j.ecoenv.2022.114029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd) is ubiquitous in our environment and can easily bioaccumulate into the organism after passage through the respiratory and digestive tracts. Long-term exposure to Cd can result in the significant bioaccumulation in organism because of its long biological high-life (10-30 years), which exerts irreversible damages on the health of animals and humans. Although there are increased evidence of impeding the normal function of female reproduction resulted from Cd exposure, the mechanism of the negative action of Cd on the growth and development of ovarian follicle remains enigmatic. Thus, the purpose of the presented study is to summarize available literature which describing Cd-related toxicity involved in the adverse effects on the growth and development of the ovarian follicle. In conclusion, it is suggested that Cd causes damage to the folliculogenesis of mammalians, which results in the decline in the number and quality of ovulated oocytes and the failure in the fertilization. The mechanism behinds that may be linked to the interference to the production of reproductive hormones and the augment of reactive oxygen species (ROS). Furthermore, the enhanced ROS, in turn, impairs various molecules including proteins, lipids and DNA, as well as the balance of the antioxidant defense system, mitochondrial homeostasis, endoplasmic reticulum, autophagy and epigenetic modification. This review is expected to elaborate the toxic mechanism of Cd exposure to the growth and development of ovarian follicles and provide essential remediation strategies to alleviate the damage of Cd to female reproductive health.
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Affiliation(s)
- Jingwen Qu
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Department of Animal Science, University of Vermont, Burlington, VT 05405, USA.
| | - Qiang Wang
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Xiaomei Sun
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Yongjun Li
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
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6
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Angre T, Kumar A, Singh AK, Thareja S, Kumar P. Role of collagen regulators in cancer treatment: A comprehensive review. Anticancer Agents Med Chem 2022; 22:2956-2984. [DOI: 10.2174/1871520622666220501162351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/13/2022] [Accepted: 03/25/2022] [Indexed: 12/24/2022]
Abstract
Abstract:
Collagen is the most important structural protein and also a main component of extra-cellular matrix (ECM). It plays a role in tumor progression. Collagen can be regulated by altering it’s biosynthesis pathway through various signaling pathways, receptors and genes. Activity of cancer cells can also be regulated by other ECM components like metalloproteinases, hyaluronic acid, fibronectin and so on. Hypoxia is also one of the condition which leads to cancer progression by stimulating the expression of procollagen lysine as a collagen crosslinker, which increases the size of collagen fibres promoting cancer spread. The collagen content in cancerous cells leads to resistance in chemotherapy. So, to reduce this resistance, some of the collagen regulating therapies are introduced, which include inhibiting its biosynthesis, disturbing cancer cell signaling pathway, mediating ECM components and directly utilizing collagenase. This study is an effort to compile the strategies reported to control the collagen level and different collagen inhibitors reported so far. More research is needed in this area, growing understandings of collagen’s structural features and its role in cancer progression will aid in the advancement of newer chemotherapies.
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Affiliation(s)
- Tanuja Angre
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
| | - Adarsh Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
| | - Ankit Kumar Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
| | - Pradeep Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
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7
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Gao W, Liu JL, Lu X, Yang Q. Epigenetic regulation of energy metabolism in obesity. J Mol Cell Biol 2021; 13:480-499. [PMID: 34289049 PMCID: PMC8530523 DOI: 10.1093/jmcb/mjab043] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/24/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Obesity has reached epidemic proportions globally. Although modern adoption of a sedentary lifestyle coupled with energy-dense nutrition is considered to be the main cause of obesity epidemic, genetic preposition contributes significantly to the imbalanced energy metabolism in obesity. However, the variants of genetic loci identified from large-scale genetic studies do not appear to fully explain the rapid increase in obesity epidemic in the last four to five decades. Recent advancements of next-generation sequencing technologies and studies of tissue-specific effects of epigenetic factors in metabolic organs have significantly advanced our understanding of epigenetic regulation of energy metabolism in obesity. The epigenome, including DNA methylation, histone modifications, and RNA-mediated processes, is characterized as mitotically or meiotically heritable changes in gene function without alteration of DNA sequence. Importantly, epigenetic modifications are reversible. Therefore, comprehensively understanding the landscape of epigenetic regulation of energy metabolism could unravel novel molecular targets for obesity treatment. In this review, we summarize the current knowledge on the roles of DNA methylation, histone modifications such as methylation and acetylation, and RNA-mediated processes in regulating energy metabolism. We also discuss the effects of lifestyle modifications and therapeutic agents on epigenetic regulation of energy metabolism in obesity.
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Affiliation(s)
- Wei Gao
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory for Aging & Disease, Nanjing Medical University, Nanjing 211166, China
| | - Jia-Li Liu
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory for Aging & Disease, Nanjing Medical University, Nanjing 211166, China
| | - Xiang Lu
- Department of Geriatrics, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory for Aging & Disease, Nanjing Medical University, Nanjing 211166, China
| | - Qin Yang
- Department of Medicine, Physiology and Biophysics, UC Irvine Diabetes Center, University of California Irvine, Irvine, CA 92697, USA
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8
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Sinha S, Molla S, Kundu CN. PARP1-modulated chromatin remodeling is a new target for cancer treatment. Med Oncol 2021; 38:118. [PMID: 34432161 DOI: 10.1007/s12032-021-01570-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022]
Abstract
Cancer progression requires certain tumorigenic mutations in genes encoding for different cellular and nuclear proteins. Altered expressions of these mutated genes are mediated by post-translational modifications and chromatin remodeling. Chromatin remodeling is mainly regulated by the chromatin remodeling enzyme complexes and histone modifications. Upon DNA damage, Poly-(ADP-ribose) Polymerase1 (PARP1) plays a very important role in the induction of chromatin modifications and activation of DNA repair pathways to repair the DNA lesion. It has been targeted to develop different anti-cancer therapeutic interventions and PARP inhibitors have been approved by the U.S. Food and Drug Administration (FDA) for clinical use. But it has been found that the cancer cells often develop resistance to these PARP inhibitors and chromatin remodeling helps in enhancing this process. Hence, it may be beneficial to target PARP1-mediated chromatin remodeling, which may allow to reverse the drug resistance. In the current review, we have discussed the role of chromatin remodeling in DNA repair, how PARP1 regulates modifications of chromatin dynamics, and the role of chromatin modifications in cancer. It has also been discussed how the PARP1-mediated chromatin remodeling can be targeted by PARP inhibitors alone or in combination with other chemotherapeutic agents to establish novel anti-cancer therapeutics. We have also considered the use of PARG inhibitors that may enhance the action of PARP inhibitors to target different types of cancers.
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Affiliation(s)
- Saptarshi Sinha
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Sefinew Molla
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Chanakya Nath Kundu
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India.
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9
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Weirich S, Khella MS, Jeltsch A. Structure, Activity and Function of the Suv39h1 and Suv39h2 Protein Lysine Methyltransferases. Life (Basel) 2021; 11:life11070703. [PMID: 34357075 PMCID: PMC8303541 DOI: 10.3390/life11070703] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/01/2021] [Accepted: 07/13/2021] [Indexed: 12/26/2022] Open
Abstract
SUV39H1 and SUV39H2 were the first protein lysine methyltransferases that were identified more than 20 years ago. Both enzymes introduce di- and trimethylation at histone H3 lysine 9 (H3K9) and have important roles in the maintenance of heterochromatin and gene repression. They consist of a catalytically active SET domain and a chromodomain, which binds H3K9me2/3 and has roles in enzyme targeting and regulation. The heterochromatic targeting of SUV39H enzymes is further enhanced by the interaction with HP1 proteins and repeat-associated RNA. SUV39H1 and SUV39H2 recognize an RKST motif with additional residues on both sides, mainly K4 in the case of SUV39H1 and G12 in the case of SUV39H2. Both SUV39H enzymes methylate different non-histone proteins including RAG2, DOT1L, SET8 and HupB in the case of SUV39H1 and LSD1 in the case of SUV39H2. Both enzymes are expressed in embryonic cells and have broad expression profiles in the adult body. SUV39H1 shows little tissue preference except thymus, while SUV39H2 is more highly expressed in the brain, testis and thymus. Both enzymes are connected to cancer, having oncogenic or tumor-suppressive roles depending on the tumor type. In addition, SUV39H2 has roles in the brain during early neurodevelopment.
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Affiliation(s)
- Sara Weirich
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany; (S.W.); (M.S.K.)
| | - Mina S. Khella
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany; (S.W.); (M.S.K.)
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Abbassia, Cairo 11566, Egypt
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany; (S.W.); (M.S.K.)
- Correspondence:
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10
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Ummarino S, Hausman C, Di Ruscio A. The PARP Way to Epigenetic Changes. Genes (Basel) 2021; 12:446. [PMID: 33804735 PMCID: PMC8003872 DOI: 10.3390/genes12030446] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/22/2022] Open
Abstract
ADP-ribosylation, is a reversible post-translational modification implicated in major biological functions. Poly ADP-ribose polymerases (PARP) are specialized enzymes that catalyze the addition of ADP ribose units from "nicotinamide adenine dinucleotide-donor molecules" to their target substrates. This reaction known as PARylation modulates essential cellular processes including DNA damage response, chromatin remodeling, DNA methylation and gene expression. Herein, we discuss emerging roles of PARP1 in chromatin remodeling and epigenetic regulation, focusing on its therapeutic implications for cancer treatment and beyond.
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Affiliation(s)
- Simone Ummarino
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
- Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA;
| | - Clinton Hausman
- Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA;
| | - Annalisa Di Ruscio
- Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA;
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
- Beth Israel Deaconess Medical Center, Cancer Research Institute, Boston, MA 02215, USA
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11
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Wang Z, Liu D, Xu B, Tian R, Zuo Y. Modular arrangements of sequence motifs determine the functional diversity of KDM proteins. Brief Bioinform 2020; 22:5912575. [PMID: 32987405 DOI: 10.1093/bib/bbaa215] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Histone lysine demethylases (KDMs) play a vital role in regulating chromatin dynamics and transcription. KDM proteins are given modular activities by its sequence motifs with obvious roles division, which endow the complex and diverse functions. In our review, according to functional features, we classify sequence motifs into four classes: catalytic motifs, targeting motifs, regulatory motifs and potential motifs. JmjC, as the main catalytic motif, combines to Fe2+ and α-ketoglutarate by residues H-D/E-H and S-N-N/Y-K-N/Y-T/S. Targeting motifs make catalytic motifs recognize specific methylated lysines, such as PHD that helps KDM5 to demethylate H3K4me3. Regulatory motifs consist of a functional network. For example, NLS, Ser-rich, TPR and JmjN motifs regulate the nuclear localization. And interactions through the CW-type-C4H2C2-SWIRM are necessary to the demethylase activity of KDM1B. Additionally, many conservative domains that have potential functions but no deep exploration are reviewed for the first time. These conservative domains are usually amino acid-rich regions, which have great research value. The arrangements of four types of sequence motifs generate that KDM proteins diversify toward modular activities and biological functions. Finally, we draw a blueprint of functional mechanisms to discuss the modular activity of KDMs.
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Affiliation(s)
- Zerong Wang
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Dongyang Liu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. He is now studying for a master's degree at the institute of botany of the Chinese Academy of Sciences. His research interests include bioinformatics and computational genomics
| | - Baofang Xu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Ruixia Tian
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Yongchun Zuo
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. His research interests include bioinformatics and integration analysis of multiomics in cell reprogramming
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12
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Mitra S, Bodor DL, David AF, Abdul-Zani I, Mata JF, Neumann B, Reither S, Tischer C, Jansen LET. Genetic screening identifies a SUMO protease dynamically maintaining centromeric chromatin. Nat Commun 2020; 11:501. [PMID: 31980633 PMCID: PMC6981222 DOI: 10.1038/s41467-019-14276-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 12/18/2019] [Indexed: 12/27/2022] Open
Abstract
Centromeres are defined by a self-propagating chromatin structure based on stable inheritance of CENP-A containing nucleosomes. Here, we present a genetic screen coupled to pulse-chase labeling that allow us to identify proteins selectively involved in deposition of nascent CENP-A or in long-term transmission of chromatin-bound CENP-A. These include factors with known roles in DNA replication, repair, chromatin modification, and transcription, revealing a broad set of chromatin regulators that impact on CENP-A dynamics. We further identify the SUMO-protease SENP6 as a key factor, not only controlling CENP-A stability but virtually the entire centromere and kinetochore. Loss of SENP6 results in hyper-SUMOylation of CENP-C and CENP-I but not CENP-A itself. SENP6 activity is required throughout the cell cycle, suggesting that a dynamic SUMO cycle underlies a continuous surveillance of the centromere complex that in turn ensures stable transmission of CENP-A chromatin.
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Affiliation(s)
- Sreyoshi Mitra
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Dani L Bodor
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
- MRC-Laboratory for Molecular Cell Biology, UCL, London, WC1E 6BT, UK
| | - Ana F David
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
- Institute of Molecular Biotechnology, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Izma Abdul-Zani
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - João F Mata
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Beate Neumann
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117, Heidelberg, Germany
| | - Sabine Reither
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117, Heidelberg, Germany
| | - Christian Tischer
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117, Heidelberg, Germany
| | - Lars E T Jansen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal.
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13
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Barve A, Vega A, Shah PP, Ghare S, Casson L, Wunderlich M, Siskind LJ, Beverly LJ. Perturbation of Methionine/S-adenosylmethionine Metabolism as a Novel Vulnerability in MLL Rearranged Leukemia. Cells 2019; 8:cells8111322. [PMID: 31717699 PMCID: PMC6912509 DOI: 10.3390/cells8111322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022] Open
Abstract
Leukemias bearing mixed lineage leukemia (MLL) rearrangement (MLL-R) resulting in expression of oncogenic MLL fusion proteins (MLL-FPs) represent an especially aggressive disease subtype with the worst overall prognoses and chemotherapeutic response. MLL-R leukemias are uniquely dependent on the epigenetic function of the H3K79 methyltransferase DOT1L, which is misdirected by MLL-FPs activating gene expression, driving transformation and leukemogenesis. Given the functional necessity of these leukemias to maintain adequate methylation potential allowing aberrant activating histone methylation to proceed, driving leukemic gene expression, we investigated perturbation of methionine (Met)/S-adenosylmethionine (SAM) metabolism as a novel therapeutic paradigm for MLL-R leukemia. Disruption of Met/SAM metabolism, by either methionine deprivation or pharmacologic inhibition of downstream metabolism, reduced overall cellular methylation potential, reduced relative cell numbers, and induced apoptosis selectively in established MLL-AF4 cell lines or MLL-AF6-expressing patient blasts but not in BCR-ABL-driven K562 cells. Global histone methylation dynamics were altered, with a profound loss of requisite H3K79 methylation, indicating inhibition of DOT1L function. Relative occupancy of the repressive H3K27me3 modification was increased at the DOT1L promoter in MLL-R cells, and DOT1L mRNA and protein expression was reduced. Finally, pharmacologic inhibition of Met/SAM metabolism significantly prolonged survival in an advanced, clinically relevant patient–derived MLL-R leukemia xenograft model, in combination with cytotoxic induction chemotherapy. Our findings provide support for further investigation into the development of highly specific allosteric inhibitors of enzymatic mediators of Met/SAM metabolism or dietary manipulation of methionine levels. Such inhibitors may lead to enhanced treatment outcomes for MLL-R leukemia, along with cytotoxic chemotherapy or DOT1L inhibitors.
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Affiliation(s)
- Aditya Barve
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA; (A.B.); (L.J.S.)
| | - Alexis Vega
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA;
| | - Parag P. Shah
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA;
| | - Smita Ghare
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (S.G.); (L.C.)
| | - Lavona Casson
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (S.G.); (L.C.)
| | - Mark Wunderlich
- Department of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
| | - Leah J. Siskind
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA; (A.B.); (L.J.S.)
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA;
| | - Levi J. Beverly
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA; (A.B.); (L.J.S.)
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA;
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (S.G.); (L.C.)
- Correspondence: ; Tel.: +01-502-852-8968
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14
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Blanquart C, Linot C, Cartron PF, Tomaselli D, Mai A, Bertrand P. Epigenetic Metalloenzymes. Curr Med Chem 2019; 26:2748-2785. [PMID: 29984644 DOI: 10.2174/0929867325666180706105903] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022]
Abstract
Epigenetics controls the expression of genes and is responsible for cellular phenotypes. The fundamental basis of these mechanisms involves in part the post-translational modifications (PTMs) of DNA and proteins, in particular, the nuclear histones. DNA can be methylated or demethylated on cytosine. Histones are marked by several modifications including acetylation and/or methylation, and of particular importance are the covalent modifications of lysine. There exists a balance between addition and removal of these PTMs, leading to three groups of enzymes involved in these processes: the writers adding marks, the erasers removing them, and the readers able to detect these marks and participating in the recruitment of transcription factors. The stimulation or the repression in the expression of genes is thus the result of a subtle equilibrium between all the possibilities coming from the combinations of these PTMs. Indeed, these mechanisms can be deregulated and then participate in the appearance, development and maintenance of various human diseases, including cancers, neurological and metabolic disorders. Some of the key players in epigenetics are metalloenzymes, belonging mostly to the group of erasers: the zinc-dependent histone deacetylases (HDACs), the iron-dependent lysine demethylases of the Jumonji family (JMJ or KDM) and for DNA the iron-dependent ten-eleven-translocation enzymes (TET) responsible for the oxidation of methylcytosine prior to the demethylation of DNA. This review presents these metalloenzymes, their importance in human disease and their inhibitors.
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Affiliation(s)
- Christophe Blanquart
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France.,Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Camille Linot
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France
| | - Pierre-François Cartron
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France.,Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Daniela Tomaselli
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy.,Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Philippe Bertrand
- Réseau Epigénétique du Cancéropôle Grand Ouest, France.,Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, 4 rue Michel Brunet, TSA 51106, B27, 86073, Poitiers cedex 09, France
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15
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Zhu JQ, Liu Y, Zhang JH, Liu YF, Cao JQ, Huang ZT, Yuan Y, Bian JC, Liu ZP. Cadmium Exposure of Female Mice Impairs the Meiotic Maturation of Oocytes and Subsequent Embryonic Development. Toxicol Sci 2019; 164:289-299. [PMID: 29684212 DOI: 10.1093/toxsci/kfy089] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cadmium is one major pollutant that is highly toxic to animals and humans. The mechanism of cadmium toxicity on the female reproductive system, particularly oocyte maturation and fertility, remains to be clarified. In this study, we used a mouse model to investigate the effects of cadmium in the drinking water on the meiotic maturation of oocytes and subsequent embryonic development, and the underlying mechanisms associated with the impairment of oocyte maturation such as mitochondrial distribution and histone modifications. Our results show that cadmium exposure decreased the number of ovulated oocytes and impaired oocyte meiotic maturation rate both in vivo and in vitro. The embryonic development after fertilization was also impaired even when the potential hazards of cadmium on the spermatozoa or the genital tract have been excluded by fertilization and embryonic development in culture. Cadmium exposure disrupted meiotic spindle morphology and actin filament, which are responsible for successful chromosome segregation and the polar body extrusion during oocyte maturation and fertilization. ATP contents, which are required for proper meiotic spindle assembly in the oocyte, were decreased, consistent with altered mitochondrial distribution after cadmium exposure. Finally, cadmium exposure affected the levels of H3K9me2 and H4K12ac in the oocyte, which are closely associated with the acquisition of oocyte developmental competence and subsequent embryonic development. In conclusion, cadmium exposure in female mice impaired meiotic maturation of oocytes and subsequent embryonic development by affecting the cytoskeletal organization, mitochondrial function, and histone modifications.
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Affiliation(s)
- Jia-Qiao Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, People's Republic of China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Yang Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Jiang-Hong Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Yan-Fang Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Jiang-Qin Cao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Zhu-Tao Huang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Yan Yuan
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, People's Republic of China
| | - Jian-Chun Bian
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Zong-Ping Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, People's Republic of China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
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16
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Ligresti G, Caporarello N, Meridew JA, Jones DL, Tan Q, Choi KM, Haak AJ, Aravamudhan A, Roden AC, Prakash YS, Lomberk G, Urrutia RA, Tschumperlin DJ. CBX5/G9a/H3K9me-mediated gene repression is essential to fibroblast activation during lung fibrosis. JCI Insight 2019; 5:127111. [PMID: 31095524 DOI: 10.1172/jci.insight.127111] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Pulmonary fibrosis is a devastating disease characterized by accumulation of activated fibroblasts and scarring in the lung. While fibroblast activation in physiological wound repair reverses spontaneously, fibroblast activation in fibrosis is aberrantly sustained. Here we identified histone 3 lysine 9 methylation (H3K9me) as a critical epigenetic modification that sustains fibroblast activation by repressing the transcription of genes essential to returning lung fibroblasts to an inactive state. We show that the histone methyltransferase G9a (EHMT2) and chromobox homolog 5 (CBX5, also known as HP1α), which deposit H3K9me marks and assemble an associated repressor complex respectively, are essential to initiation and maintenance of fibroblast activation specifically through epigenetic repression of peroxisome proliferator-activated receptor gamma coactivator 1 alpha gene (PPARGC1A, encoding PGC1α). Both TGFβ and increased matrix stiffness potently inhibit PGC1α expression in lung fibroblasts through engagement of the CBX5/G9a pathway. Inhibition of CBX5/G9a pathway in fibroblasts elevates PGC1α, attenuates TGFβ- and matrix stiffness-promoted H3K9 methylation, and reduces collagen accumulation in the lungs following bleomycin injury. Our results demonstrate that epigenetic silencing mediated by H3K9 methylation is essential for both biochemical and biomechanical fibroblast activation, and that targeting this epigenetic pathway may provide therapeutic benefit by returning lung fibroblasts to quiescence.
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Affiliation(s)
| | | | | | | | - Qi Tan
- Department of Physiology and Biomedical Engineering
| | | | | | | | | | - Y S Prakash
- Department of Physiology and Biomedical Engineering.,Department of Anesthesiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Gwen Lomberk
- Division of Research,Department of Surgery and Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Wauwatosa, Wisconsin, USA
| | - Raul A Urrutia
- Division of Research,Department of Surgery and Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Wauwatosa, Wisconsin, USA
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17
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The effects of 2-hydroxyglutarate on the tumorigenesis of gliomas. Contemp Oncol (Pozn) 2018; 22:215-222. [PMID: 30783384 PMCID: PMC6377424 DOI: 10.5114/wo.2018.82642] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/25/2018] [Indexed: 12/19/2022] Open
Abstract
Mutation of the isocitrate-dehydrogenase (IDH) enzymes is one of the central research topics regarding gliomagenesis. Indeed, 70% of gliomas are associated with a gain-of-function IDH mutation and consequently synthesize the oncometabolite, 2-hydroxyglutarate (2-HG). This review aims to elucidate the effects of 2-HG on gliomagenesis. 2-HG promotes tumorigenesis by impacting metabolism, vascularization and altering the epigenome of glioma cells. Glioma metabolism and vascularization is altered by 2-HG's effect on the stability of hypoxia-inducible factor (HIF) and inhibition of endostatin. However, 2-HG's impacts on epigenetic mechanisms are more profound to gliomagenesis. Through competitive inhibition of JHDMs and TET proteins, 2-HG orchestrates histone and DNA hypermethylation, which is associated with gene silencing and dedifferentiation of cells. The hypermethylator phenotype induced by 2-HG also results in alterations of the interaction of the immune system with the tumour. Additionally, this study reviews 2-HG promotion of tumorigenesis by inhibiting repair of DNA alkylation damage through competitive inhibition of AlkB proteins.
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18
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Abstract
The timely and precise repair of DNA damage, or more specifically DNA double-strand breaks (DSBs) - the most deleterious DNA lesions, is crucial for maintaining genome integrity and cellular homeostasis. An appropriate cellular response to DNA DSBs requires the integration of various factors, including the post-translational modifications (PTMs) of chromatin and chromatin-associated proteins. Notably, the PTMs of histones have been shown to play a fundamental role in initiating and regulating cellular responses to DNA DSBs. Here we review the role of the major histone PTMs, including phosphorylation, ubiquitination, methylation and acetylation, and their interactions during DNA DSB-induced responses.
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Affiliation(s)
- Hieu T Van
- a Department of Epigenetics and Molecular Carcinogenesis , University of Texas M.D. Anderson Cancer Center , Houston , TX , USA
| | - Margarida A Santos
- a Department of Epigenetics and Molecular Carcinogenesis , University of Texas M.D. Anderson Cancer Center , Houston , TX , USA
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19
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Gruber T. Synthetic Receptors for the Recognition and Discrimination of Post-Translationally Methylated Lysines. Chembiochem 2018; 19:2324-2340. [DOI: 10.1002/cbic.201800398] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Tobias Gruber
- School of Pharmacy; University of Lincoln; Joseph Banks Laboratories; Green Lane Lincoln LN6 7DL UK
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20
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A regulatory circuitry comprising TP53, miR-29 family, and SETDB1 in non-small cell lung cancer. Biosci Rep 2018; 38:BSR20180678. [PMID: 30054425 PMCID: PMC6137244 DOI: 10.1042/bsr20180678] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 12/30/2022] Open
Abstract
Lung cancer is a malignant tumor with high fatality rate and causes great harm to human economic life. Non-small cell lung cancer (NSCLC) is the most common type of lung cancer. With the rapid development of epigenetic study in the last decade, the understanding of the pathogenesis of lung cancer and the development of personalized treatment of lung cancer are picking up pace. Previous studies showed that miR-29 family members (miR-29s; miR-29a, -29b, and -29c) are down-regulated in most human cancers, including NSCLC, but their biological roles in tumorigenesis and their regulation mechanism are still not fully elucidated. Herein, we reported that the miR-29a, -29b and, -29c were coincidently down-regulated in NSCLC, and the histone H3K9 methyltransferase SET domain, bifurcated 1 (SETDB1) was directly targetted by miR-29s. Moreover, SETDB1 negatively regulated the expression of TP53 and overexpression of SETDB1 down-regulating the expression of miR-29s, while TP53 positively regulated the expression of miR-29s and overexpression of TP53 down-regulated the expression of SETDB1. On the other side, as a downstream target of TP53, the H3K9 methyltransferase Suv39h1 was also down-regulated by miR-29s via up-regulating TP53 expression. The further detection of H3K9 methylation status after changes in miR-29s expression revealed that they negatively regulated the levels of H3K9 di- and trimethylation in NSCLC. Collectively, our findings highlight a TP53/miR-29s/SETDB1 regulatory circuitry and assign a role of H3K9 methylation regulator to miR-29s, which may be a potential therapeutic target in the treatment of NSCLC.
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21
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Wang S, Zhang Q, Wang Q, Shen Q, Chen X, Li Z, Zhou Y, Hou J, Xu B, Li N, Cao X. NEAT1 paraspeckle promotes human hepatocellular carcinoma progression by strengthening IL-6/STAT3 signaling. Oncoimmunology 2018; 7:e1503913. [PMID: 30377567 DOI: 10.1080/2162402x.2018.1503913] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023] Open
Abstract
The formation of paraspeckle, a stress-induced nuclear body, increases in response to viral infection or proinflammatory stimuli. Paraspeckle consists of lncRNA (nuclear paraspeckle assembly transcript 1, NEAT1) and protein components including NONO, SFPQ, PSPC1, etc., which are shown to be involved in viral infection and cancer. Both NEAT1 and NONO expression increase in human hepatocellular carcinoma (HCC) samples according to TCGA data. However, the role of paraspeckle in HCC progression needs further identification. IL-6 signaling is well known to contribute to HCC progression. Here we reported that IL-6 signaling increased paraspeckle formation in HCC cells. Destruction of paraspeckle formation by silencing the paraspeckle essential components NEAT1_2 or NONO could suppress IL-6-induced STAT3 phosphorylation in HCC cells, and consequently repressed IL-6-promoted in vitro HCC cell invasion, cell cycle progression and survival. Mechanistically, paraspeckle promotes IL-6-induced STAT3 phosphorylation by binding and trapping peroxiredoxin-5 (PRDX5) mRNA in nucleus, decreasing protein level of PRDX5 which can directly interact with STAT3 and inhibit STAT3 phosphorylation. Besides, glutathione S-transferase P (GSTP1) protein, which inhibits DNA damage and apoptosis through its detoxification and anti-oxidation function, was also trapped within paraspeckles under IL-6 stimulation. Paraspeckle-trapping of both PRDX5 mRNA and GSTP1 protein contributes to IL-6-increased DNA damage in HCC cells. Our results demonstrate that paraspeckle can nuclear entrap the inhibitors of IL-6/STAT3 signaling as well as DNA damage, and then strengthen the promoting effect on HCC progression by IL-6. Therefore, paraspeckle contributes to the inflammation-related HCC progression and might be a potential therapeutic target for HCC.
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Affiliation(s)
- Shuai Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Qian Zhang
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Qinlan Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Qicong Shen
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Xiang Chen
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Zhenyang Li
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Ye Zhou
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Jin Hou
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Bowen Xu
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Nan Li
- National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Xuetao Cao
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China.,National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, Shanghai, China
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22
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Abstract
Puberty involves a series of morphological, physiological and behavioural changes during the last part of the juvenile period that culminates in the attainment of fertility. The activation of the pituitary-gonadal axis by increased hypothalamic secretion of gonadotrophin-releasing hormone (GnRH) is an essential step in the process. The current hypothesis postulates that a loss of transsynaptic inhibition and a rise in excitatory inputs are responsible for the activation of GnRH release. Similarly, a shift in the balance in the expression of puberty activating and puberty inhibitory genes exists during the pubertal transition. In addition, recent evidence suggests that the epigenetic machinery controls this genetic balance, giving rise to the tantalising possibility that epigenetics serves as a relay of environmental signals known for many years to modulate pubertal development. Here, we review the contribution of epigenetics as a regulatory mechanism in the hypothalamic control of female puberty.
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Affiliation(s)
- C A Toro
- Primate Genetics Section/Division of Neuroscience, Oregon National Primate Research Center/Oregon Health & Science University, Beaverton, OR, USA
| | - C F Aylwin
- Primate Genetics Section/Division of Neuroscience, Oregon National Primate Research Center/Oregon Health & Science University, Beaverton, OR, USA
| | - A Lomniczi
- Primate Genetics Section/Division of Neuroscience, Oregon National Primate Research Center/Oregon Health & Science University, Beaverton, OR, USA
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23
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Abstract
Protein lysine methylation is a distinct posttranslational modification that causes minimal changes in the size and electrostatic status of lysine residues. Lysine methylation plays essential roles in regulating fates and functions of target proteins in an epigenetic manner. As a result, substrates and degrees (free versus mono/di/tri) of protein lysine methylation are orchestrated within cells by balanced activities of protein lysine methyltransferases (PKMTs) and demethylases (KDMs). Their dysregulation is often associated with neurological disorders, developmental abnormalities, or cancer. Methyllysine-containing proteins can be recognized by downstream effector proteins, which contain methyllysine reader domains, to relay their biological functions. While numerous efforts have been made to annotate biological roles of protein lysine methylation, limited work has been done to uncover mechanisms associated with this modification at a molecular or atomic level. Given distinct biophysical and biochemical properties of methyllysine, this review will focus on chemical and biochemical aspects in addition, recognition, and removal of this posttranslational mark. Chemical and biophysical methods to profile PKMT substrates will be discussed along with classification of PKMT inhibitors for accurate perturbation of methyltransferase activities. Semisynthesis of methyllysine-containing proteins will also be covered given the critical need for these reagents to unambiguously define functional roles of protein lysine methylation.
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Affiliation(s)
- Minkui Luo
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
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24
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Ding H, Liu J, Liu B, Zeng Y, Chen P, Su Y. Long noncoding RNA PVT1 inhibits interferon-α mediated therapy for hepatocellular carcinoma cells by interacting with signal transducer and activator of transcription 1. Biochem Biophys Res Commun 2018; 500:973-980. [PMID: 29715456 DOI: 10.1016/j.bbrc.2018.04.219] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 04/27/2018] [Indexed: 02/07/2023]
Abstract
Long noncoding RNA (LncRNA) PVT1 has recently been reported to be involved in the development of hepatocellular carcinoma (HCC) and hsigh expression of oncogenic PVT1 is associated with poor prognosis of HCC. Interferon-α (IFN-α) has been used in clinic for HCC therapy. However, whether PVT1 is involved in the IFN-α therapy for HCC is completely unknown. Our study found that high PVT1 expression in HCC cells is associated with high unmethylation in PVT1 promoter region. IFN-α treatment further increases PVT1 expression in HCC cells by enhancing H3K4me3 modification on the promoter. Furthermore, PVT1 knockdown enhances IFN-α-induced HCC cell apoptosis by promoting phosphorylation of signal transducer and activator of transcription 1 (STAT1) and upregulating IFN-stimulated genes expression. Moreover, PVT1 specifically interacts with STAT1 in HCC cells. Taken together, these results for the first time indicate that IFN-α treatment promotes oncogenic PVT1 expression in HCC cells, which interacts with STAT1 to inhibit IFN-α signaling, ultimately blocking IFN-α-induced cells apoptosis, suggesting that lncRNA PVT1 may be a potential target to improve IFN-α-mediated HCC immunotherapies.
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Affiliation(s)
- Hongda Ding
- Department of the Fifth General Surgery, ShengJing Hospital of China Medical University, No. 36 Sanhao Road, Shenyang, 110004, China
| | - Junpeng Liu
- Department of the Fifth General Surgery, ShengJing Hospital of China Medical University, No. 36 Sanhao Road, Shenyang, 110004, China
| | - Baiming Liu
- Department of the Fifth General Surgery, ShengJing Hospital of China Medical University, No. 36 Sanhao Road, Shenyang, 110004, China
| | - Yongchao Zeng
- Department of the Fifth General Surgery, ShengJing Hospital of China Medical University, No. 36 Sanhao Road, Shenyang, 110004, China
| | - Pengrui Chen
- Department of the Fifth General Surgery, ShengJing Hospital of China Medical University, No. 36 Sanhao Road, Shenyang, 110004, China
| | - Yang Su
- Department of the Fifth General Surgery, ShengJing Hospital of China Medical University, No. 36 Sanhao Road, Shenyang, 110004, China.
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25
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Toro CA, Wright H, Aylwin CF, Ojeda SR, Lomniczi A. Trithorax dependent changes in chromatin landscape at enhancer and promoter regions drive female puberty. Nat Commun 2018; 9:57. [PMID: 29302059 PMCID: PMC5754362 DOI: 10.1038/s41467-017-02512-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/01/2017] [Indexed: 12/24/2022] Open
Abstract
Polycomb group (PcG) proteins control the timing of puberty by repressing the Kiss1 gene in hypothalamic arcuate nucleus (ARC) neurons. Here we identify two members of the Trithorax group (TrxG) of modifiers, mixed-lineage leukemia 1 (MLL1), and 3 (MLL3), as central components of an activating epigenetic machinery that dynamically counteracts PcG repression. Preceding puberty, MLL1 changes the chromatin configuration at the promoters of Kiss1 and Tac3, two genes required for puberty to occur, from repressive to permissive. Concomitantly, MLL3 institutes a chromatin structure that changes the functional status of a Kiss1 enhancer from poised to active. RNAi-mediated, ARC-specific Mll1 knockdown reduced Kiss1 and Tac3 expression, whereas CRISPR-Cas9-directed epigenome silencing of the Kiss1 enhancer selectively reduced Kiss1 activity. Both interventions delay puberty and disrupt reproductive cyclicity. Our results demonstrate that an epigenetic switch from transcriptional repression to activation is crucial to the regulatory mechanism controlling the timing of mammalian puberty.
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Affiliation(s)
- Carlos A Toro
- Primate Genetics Section/Division of Neuroscience, Oregon National Primate Research Center/Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA
| | - Hollis Wright
- Primate Genetics Section/Division of Neuroscience, Oregon National Primate Research Center/Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA
| | - Carlos F Aylwin
- Primate Genetics Section/Division of Neuroscience, Oregon National Primate Research Center/Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA
| | - Sergio R Ojeda
- Division of Neuroscience, Oregon National Primate Research Center/Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA.
| | - Alejandro Lomniczi
- Primate Genetics Section/Division of Neuroscience, Oregon National Primate Research Center/Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA.
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26
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Jurkowska RZ, Qin S, Kungulovski G, Tempel W, Liu Y, Bashtrykov P, Stiefelmaier J, Jurkowski TP, Kudithipudi S, Weirich S, Tamas R, Wu H, Dombrovski L, Loppnau P, Reinhardt R, Min J, Jeltsch A. H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1. Nat Commun 2017; 8:2057. [PMID: 29234025 PMCID: PMC5727127 DOI: 10.1038/s41467-017-02259-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 11/14/2017] [Indexed: 12/18/2022] Open
Abstract
SETDB1 is an essential H3K9 methyltransferase involved in silencing of retroviruses and gene regulation. We show here that its triple Tudor domain (3TD) specifically binds to doubly modified histone H3 containing K14 acetylation and K9 methylation. Crystal structures of 3TD in complex with H3K14ac/K9me peptides reveal that peptide binding and K14ac recognition occurs at the interface between Tudor domains (TD) TD2 and TD3. Structural and biochemical data demonstrate a pocket switch mechanism in histone code reading, because K9me1 or K9me2 is preferentially recognized by the aromatic cage of TD3, while K9me3 selectively binds to TD2. Mutations in the K14ac/K9me binding sites change the sub-nuclear localization of 3TD. ChIP-seq analyses show that SETDB1 is enriched at H3K9me3 regions and K9me3/K14ac is enriched at SETDB1 binding sites overlapping with LINE elements, suggesting that recruitment of the SETDB1 complex to K14ac/K9me regions has a role in silencing of active genomic regions.
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Affiliation(s)
- Renata Z Jurkowska
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada.,Life Science Research Center, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Goran Kungulovski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Yanli Liu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Pavel Bashtrykov
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Judith Stiefelmaier
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Tomasz P Jurkowski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Srikanth Kudithipudi
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Sara Weirich
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Raluca Tamas
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Ludmila Dombrovski
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Richard Reinhardt
- Max-Planck-Genomzentrum Köln, Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada. .,Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.
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27
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Lysine Possesses the Optimal Chain Length for Histone Lysine Methyltransferase Catalysis. Sci Rep 2017; 7:16148. [PMID: 29170487 PMCID: PMC5700997 DOI: 10.1038/s41598-017-16128-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 11/08/2017] [Indexed: 12/21/2022] Open
Abstract
Histone lysine methyltransferases (KMTs) represent an important class of epigenetic enzymes that play essential roles in regulation of gene expression in humans. Members of the KMT family catalyze the transfer of the methyl group from S-adenosylmethionine (SAM) to lysine residues in histone tails and core histones. Here we report combined MALDI-TOF MS experiments, NMR analyses and quantum mechanical/molecular dynamics studies on human KMT-catalyzed methylation of the most related shorter and longer lysine analogues, namely ornithine and homolysine, in model histone peptides. Our experimental work demonstrates that while lysine is an excellent natural substrate for KMTs, ornithine and homolysine are not. This study reveals that ornithine does not undergo KMT-catalyzed methylation reactions, whereas homolysine can be methylated by representative examples of human KMTs. The results demonstrate that the specificity of KMTs is highly sensitive to the side chain length of the residue to be methylated. The origin for the degree of the observed activities of KMTs on ornithine and homolysine is discussed.
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28
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Pinzón JH, Reed AR, Shalaby NA, Buszczak M, Rodan AR, Rothenfluh A. Alcohol-Induced Behaviors Require a Subset of Drosophila JmjC-Domain Histone Demethylases in the Nervous System. Alcohol Clin Exp Res 2017; 41:2015-2024. [PMID: 28940624 DOI: 10.1111/acer.13508] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 09/15/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND Long-lasting transcriptional changes underlie a number of adaptations that contribute to alcohol use disorders (AUD). Chromatin remodeling, including histone methylation, can confer distinct, long-lasting transcriptional changes, and histone methylases are known to play a role in the development of addiction. Conversely, little is known about the relevance of Jumonji (JmjC) domain-containing demethylases in AUDs. We systematically surveyed the alcohol-induced phenotypes of null mutations in all 13 Drosophila JmjC genes. METHODS We used a collection of JmjC mutants, the majority of which we generated by homologous recombination, and assayed them in the Booze-o-mat to determine their naïve sensitivity to sedation and their tolerance (change in sensitivity upon repeat exposure). Mutants with reproducible phenotypes had their phenotypes rescued with tagged genomic transgenes, and/or phenocopied by nervous system-specific knockdown using RNA interference (RNAi). RESULTS Four of the 13 JmjC genes (KDM3, lid, NO66, and HSPBAP1) showed reproducible ethanol (EtOH) sensitivity phenotypes. Some of the phenotypes were observed across doses, for example, the enhanced EtOH sensitivity of KDM3KO and NO66KO , but others were dose dependent, such as the reduced EtOH sensitivity of HSPBAP1KO , or the enhanced EtOH tolerance of NO66KO . These phenotypes were rescued by their respective genomic transgenes in KDM3KO and NO66KO mutants. While we were unable to rescue lidk mutants, knockdown of lid in the nervous system recapitulated the lidk phenotype, as was observed for KDM3KO and NO66KO RNAi-mediated knockdown. CONCLUSIONS Our study reveals that the Drosophila JmjC-domain histone demethylases Lid, KDM3, NO66, and HSPBAP1 are required for normal EtOH-induced sedation and tolerance. Three of 3 tested of those 4 JmjC genes are required in the nervous system for normal alcohol-induced behavioral responses, suggesting that this gene family is an intriguing avenue for future research.
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Affiliation(s)
- Jorge H Pinzón
- Department of Psychiatry, Southwestern Medical Center, University of Texas, Dallas, Texas.,Molecular Biology, Southwestern Medical Center, University of Texas, Dallas, Texas
| | - Addison R Reed
- Department of Psychiatry, University of Utah, Salt Lake City, Utah
| | - Nevine A Shalaby
- Molecular Biology, Southwestern Medical Center, University of Texas, Dallas, Texas
| | - Michael Buszczak
- Molecular Biology, Southwestern Medical Center, University of Texas, Dallas, Texas
| | - Aylin R Rodan
- Departments of Internal Medicine/Division of Nephrology, Molecular Medicine Program, University of Utah, Salt Lake City, Utah
| | - Adrian Rothenfluh
- Department of Psychiatry, Southwestern Medical Center, University of Texas, Dallas, Texas.,Department of Psychiatry, University of Utah, Salt Lake City, Utah
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29
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Mauser R, Kungulovski G, Keup C, Reinhardt R, Jeltsch A. Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state. Epigenetics Chromatin 2017; 10:45. [PMID: 28946896 PMCID: PMC5613355 DOI: 10.1186/s13072-017-0153-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/18/2017] [Indexed: 12/14/2022] Open
Abstract
Background Histone post-translational modifications (PTMs) play central roles in chromatin-templated processes. Combinations of two or more histone PTMs form unique interfaces for readout and recruitment of chromatin interacting complexes, but the genome-wide mapping of coexisting histone PTMs remains an experimentally difficult task. Results We introduce here a novel type of affinity reagents consisting of two fused recombinant histone modification interacting domains (HiMIDs) for direct detection of doubly modified chromatin. To develop the method, we fused the MPP8 chromodomain and DNMT3A PWWP domain which have a binding specificity for H3K9me3 and H3K36me2/3, respectively. We validate the novel reagent biochemically and in ChIP applications and show its specific interaction with H3K9me3–H3K36me2/3 doubly modified chromatin. Modification specificity was confirmed using mutant double-HiMIDs with inactivated methyllysine binding pockets. Using this novel tool, we mapped coexisting H3K9me3–H3K36me2/3 marks in human cells by chromatin interacting domain precipitation (CIDOP). CIDOP-seq data were validated by qPCR, sequential CIDOP/ChIP and by comparison with CIDOP- and ChIP-seq data obtained with single modification readers and antibodies. The genome-wide distribution of H3K9me3–H3K36me2/3 indicates that it represents a novel bivalent chromatin state, which is enriched in weakly transcribed chromatin segments and at ZNF274 and SetDB1 binding sites. Conclusions The application of double-HiMIDs allows the single-step study of co-occurrence and distribution of combinatorial chromatin marks. Our discovery of a novel H3K9me3–H3K36me2/3 bivalent chromatin state illustrates the power of this approach, and it will stimulate numerous follow-up studies on its biological functions. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0153-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rebekka Mauser
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Goran Kungulovski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Corinna Keup
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Richard Reinhardt
- Max-Planck-Genomzentrum Köln, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.
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30
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In silico probing and biological evaluation of SETDB1/ESET-targeted novel compounds that reduce tri-methylated histone H3K9 (H3K9me3) level. J Comput Aided Mol Des 2017; 31:877-889. [PMID: 28879500 DOI: 10.1007/s10822-017-0052-3] [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: 04/28/2017] [Accepted: 08/22/2017] [Indexed: 10/18/2022]
Abstract
ERG-associated protein with the SET domain (ESET/SET domain bifurcated 1/SETDB1/KMT1E) is a histone lysine methyltransferase (HKMT) and it preferentially tri-methylates lysine 9 of histone H3 (H3K9me3). SETDB1/ESET leads to heterochromatin condensation and epigenetic gene silencing. These functional changes are reported to correlate with Huntington's disease (HD) progression and mood-related disorders which make SETDB1/ESET a viable drug target. In this context, the present investigation was performed to identify novel peptide-competitive small molecule inhibitors of the SETDB1/ESET by a combined in silico-in vitro approach. A ligand-based pharmacophore model was built and employed for the virtual screening of ChemDiv and Asinex database. Also, a human SETDB1/ESET homology model was constructed to supplement the data further. Biological evaluation of the selected 21 candidates singled out 5 compounds exhibiting a notable reduction of the H3K9me3 level via inhibitory potential of SETDB1/ESET activity in SETDB1/ESET-inducible cell line and HD striatal cells. Later on, we identified two compounds as final hits that appear to have neuronal effects without cytotoxicity based on the result from MTT assay. These compounds hold the calibre to become the future lead compounds and can provide structural insights into more SETDB1/ESET-focused drug discovery research. Moreover, these SETDB1/ESET inhibitors may be applicable for the preclinical study to ameliorate neurodegenerative disorders via epigenetic regulation.
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31
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Structure based design, synthesis and activity studies of small hybrid molecules as HDAC and G9a dual inhibitors. Oncotarget 2017; 8:63187-63207. [PMID: 28968981 PMCID: PMC5609913 DOI: 10.18632/oncotarget.18730] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/23/2017] [Indexed: 12/18/2022] Open
Abstract
Aberrant enzymatic activities or expression profiles of epigenetic regulations are therapeutic targets for cancers. Among these, histone 3 lysine 9 methylation (H3K9Me2) and global de-acetylation on histone proteins are associated with multiple cancer phenotypes including leukemia, prostatic carcinoma, hepatocellular carcinoma and pulmonary carcinoma. Here, we report the discovery of the first small molecule capable of acting as a dual inhibitor targeting both G9a and HDAC. Our structure based design, synthesis, and screening for the dual activity of the small molecules led to the discovery of compound 14 which displays promising inhibition of both G9a and HDAC in low micro-molar range in cell based assays.
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32
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Kudithipudi S, Schuhmacher MK, Kebede AF, Jeltsch A. The SUV39H1 Protein Lysine Methyltransferase Methylates Chromatin Proteins Involved in Heterochromatin Formation and VDJ Recombination. ACS Chem Biol 2017; 12:958-968. [PMID: 28169523 DOI: 10.1021/acschembio.6b01076] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SUV39H1 is an H3K9 methyltransferase involved in the formation of heterochromatin. We investigated its substrate specificity profile and show recognition of H3 residues between K4 and G12 with highly specific readout of R8. The specificity profile of SUV39H1 is distinct from its paralog SUV39H2, indicating that they can have different additional substrates. Using the specificity profile, several novel SUV39H1 candidate substrates were identified. We observed methylation of 19 novel substrates at the peptide level and for six of them at the protein level. Methylation of RAG2, SET8, and DOT1L was confirmed in cells, which all have important roles in chromatin regulation. Methylation of SET8 allosterically stimulates its H4K20 monomethylation activity connecting SUV39H1 to the generation of increased H4K20me3 levels, another heterochromatic modification. Methylation of RAG2 alters its subnuclear localization, indicating that SUV39H1 might regulate VDJ recombination. Taken together, our results indicate that beyond the generation of H3K9me3, SUV39H1 has additional roles in chromatin biology by direct stimulation of the establishment of H4K20me3 and the regulation of chromatin binding of RAG2.
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Affiliation(s)
- Srikanth Kudithipudi
- Institute
of Biochemistry, Stuttgart University, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | | | - Adam Fiseha Kebede
- School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Albert Jeltsch
- Institute
of Biochemistry, Stuttgart University, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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33
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The Role of Epigenetic Regulation in Transcriptional Memory in the Immune System. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 106:43-69. [DOI: 10.1016/bs.apcsb.2016.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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34
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Liu XY, Li H. Reduced Histone H3 Lysine 9 Methylation Contributes to the Pathogenesis of Latent Autoimmune Diabetes in Adults via Regulation of SUV39H2 and KDM4C. J Diabetes Res 2017; 2017:8365762. [PMID: 28396876 PMCID: PMC5370514 DOI: 10.1155/2017/8365762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/01/2017] [Accepted: 03/02/2017] [Indexed: 01/19/2023] Open
Abstract
Aims. Latent autoimmune diabetes in adults (LADA) is an autoimmune disease of which the mechanism is not clear. Emerging evidence suggests that histone methylation contributes to autoimmunity. Methods. Blood CD4+ T lymphocytes from 26 LADA patients and 26 healthy controls were isolated to detect histone H3 lysine 4 and H3 lysine 9 methylation status. Results. Reduced global H3 lysine 9 methylation was observed in LADA patients' CD4+ T lymphocytes, compared to healthy controls (P < 0.05). H3 lysine 4 methylation was not statistically different. The reduced H3 lysine 9 methylation was associated with GADA titer but not correlated with glycosylated hemoglobin (HbA1c). When the LADA patient group was divided into those with complication and those without, relatively reduced global H3 lysine 9 methylation was observed in LADA patients with complication (P < 0.05). The expression of histone methyltransferase SUV39H2 for H3 lysine 9 methylation was downregulated in LADA patients, and the expression of histone demethylase KDM4C which made H3 lysine 9 demethylation was upregulated. Conclusion. The reduction of histone H3 lysine 9 methylation which may due to the downregulation of methyltransferase SUV39H2 and the upregulation of demethylase KDM4C was found in CD4+ T lymphocytes of LADA patients.
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Affiliation(s)
- Xi-yu Liu
- Department of Endocrinology, Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Hong Li
- Department of Endocrinology, Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Department of Endocrinology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- *Hong Li:
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35
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Histone H3 Methyltransferase Suv39h1 Prevents Myogenic Terminal Differentiation by Repressing MEF2 Activity in Muscle Cells. Int J Mol Sci 2016; 17:ijms17121908. [PMID: 27916793 PMCID: PMC5187760 DOI: 10.3390/ijms17121908] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 11/05/2016] [Accepted: 11/08/2016] [Indexed: 11/16/2022] Open
Abstract
The myogenic regulatory factors (MRFs) and myocyte enhancer factor 2 (MEF2) transcription factors have been extensively studied as key transcription factors that regulate myogenic gene expression. However, few reports on the molecular mechanism that modulates chromatin remodeling during skeletal muscle differentiation are available. We reported here that the expression of the H3-K9 methyltransferase Suv39h1 was decreased during myoblast differentiation. Ectopic expression of Suv39h1 could inhibit myoblast differentiation, increasing H3-K9 methylation levels, whereas knockdown of Suv39h1 stimulated myoblast differentiation. Furthermore, Suv39h1 interacted with MEF2C directly and inhibited MEF2 transcription activity in a dose-dependent manner. Together, our studies revealed a molecular mechanism wherein Suv39h1 modulated myogenic gene expression and activation during skeletal muscle differentiation.
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36
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Ciccarone F, Zampieri M, Caiafa P. PARP1 orchestrates epigenetic events setting up chromatin domains. Semin Cell Dev Biol 2016; 63:123-134. [PMID: 27908606 DOI: 10.1016/j.semcdb.2016.11.010] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/05/2016] [Accepted: 11/24/2016] [Indexed: 01/18/2023]
Abstract
Epigenetic events include reversible modifications of DNA and histone tails driving chromatin organization and thus transcription. The epigenetic regulation is a highly integrated process underlying the plasticity of the genomic information both in the context of complex physiological and pathological processes. The global regulatory aspects of epigenetic events are largely unknown. PARylation and PARP1 are recently emerging as multi-level regulatory effectors that modulate the topology of chromatin by orchestrating very different processes. This review focuses in particular on the role of PARP1 in epigenetics, trying to build a comprehensive perspective of its involvement in the regulation of epigenetic modifications of histones and DNA, contextualizing it in the global organization of chromatin domains in the nucleus.
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Affiliation(s)
- Fabio Ciccarone
- Department of Biology, Faculty of Mathematics, Physics and Natural Sciences, University of Rome 'Tor Vergata', Rome, Italy
| | - Michele Zampieri
- Department of Cellular Biotechnologies and Haematology, Faculty of Pharmacy and Medicine, 'Sapienza' University of Rome, Rome, Italy; Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Haematology, Faculty of Pharmacy and Medicine, 'Sapienza' University of Rome, Rome, Italy; Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy.
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37
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Lin SH, Ho WT, Wang YT, Chuang CT, Chuang LY, Guh JY. Histone methyltransferase Suv39h1 attenuates high glucose-induced fibronectin and p21 WAF1 in mesangial cells. Int J Biochem Cell Biol 2016; 78:96-105. [DOI: 10.1016/j.biocel.2016.06.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 06/09/2016] [Accepted: 06/29/2016] [Indexed: 12/13/2022]
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38
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Schuhmacher MK, Kudithipudi S, Jeltsch A. Investigation of H2AX methylation by the SUV39H2 protein lysine methyltransferase. FEBS Lett 2016; 590:1713-9. [PMID: 27177470 DOI: 10.1002/1873-3468.12216] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 04/29/2016] [Accepted: 05/05/2016] [Indexed: 12/21/2022]
Abstract
The H3K9 protein lysine methyltransferase SUV39H2 was reported to methylate K134 of H2AX and stimulate H2AX phosphorylation during DNA damage response [Sone K et al. (2014) Nat Commun 5, 5691]. However, the sequence context of H2AX-K134 differs from the specificity of SUV39H2. We performed in vitro methylation reactions with SUV39H2 (and its homolog SUV39H1) using H2AX protein and peptides, but no methylation at K134 or any other lysine in H2AX was detected. Positive controls demonstrated the functionality of the assays. While our data cannot finally exclude H2AX methylation of SUV39H2 in cells, additional experimental evidence is required to validate this claim.
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Affiliation(s)
| | | | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, Germany
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39
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Park SY, Park JW, Chun YS. Jumonji histone demethylases as emerging therapeutic targets. Pharmacol Res 2016; 105:146-51. [PMID: 26816087 DOI: 10.1016/j.phrs.2016.01.026] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 11/28/2022]
Abstract
The methylation status of lysine residues in histones determines the transcription of surrounding genes by modulating the chromatin architecture. Jumonji domain-containing histone-lysine demethylases (Jmj-KDMs) remove the methyl moiety from lysine residues in histones by utilizing Fe(2+) and α-ketoglutarate. Since genetic alterations in Jmj-KDMs occur in various human cancers, the roles of Jmj-KDMs in cancer development and progression have been investigated, but still controversial. The KDM7 subfamily, which belongs to the Jmj-KDM family, is an emerging class of transcriptional coactivators because its members erase the repressive marks H3K9me2/1, H3K27me2/1, and H4K20 me1. Recently, KDM7C (alternatively named PHF2) was discovered as a new KDM7 member and identified to play a tumor-suppressive role through the reinforcement of p53-driven growth arrest and apoptosis. In this article, we generally reviewed the roles of Jmj-KDMs in human cancers and more discussed the molecular functions and the clinical significances of KDM7C.
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Affiliation(s)
- Sung Yeon Park
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Jong-Wan Park
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Yang-Sook Chun
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea; Department of Physiology, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea.
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40
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Lomniczi A, Wright H, Castellano JM, Matagne V, Toro CA, Ramaswamy S, Plant TM, Ojeda SR. Epigenetic regulation of puberty via Zinc finger protein-mediated transcriptional repression. Nat Commun 2015; 6:10195. [PMID: 26671628 PMCID: PMC4703871 DOI: 10.1038/ncomms10195] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 11/16/2015] [Indexed: 11/09/2022] Open
Abstract
In primates, puberty is unleashed by increased GnRH release from the hypothalamus following an interval of juvenile quiescence. GWAS implicates Zinc finger (ZNF) genes in timing human puberty. Here we show that hypothalamic expression of several ZNFs decreased in agonadal male monkeys in association with the pubertal reactivation of gonadotropin secretion. Expression of two of these ZNFs, GATAD1 and ZNF573, also decreases in peripubertal female monkeys. However, only GATAD1 abundance increases when gonadotropin secretion is suppressed during late infancy. Targeted delivery of GATAD1 or ZNF573 to the rat hypothalamus delays puberty by impairing the transition of a transcriptional network from an immature repressive epigenetic configuration to one of activation. GATAD1 represses transcription of two key puberty-related genes, KISS1 and TAC3, directly, and reduces the activating histone mark H3K4me2 at each promoter via recruitment of histone demethylase KDM1A. We conclude that GATAD1 epitomizes a subset of ZNFs involved in epigenetic repression of primate puberty.
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Affiliation(s)
- Alejandro Lomniczi
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Hollis Wright
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Juan Manuel Castellano
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA.,Department of Cell Biology, Physiology and Immunology, University of Cordoba; CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III; and Instituto Maimónides de Investigación Biomédica (IMIBIC)/Hospital Universitario Reina Sofia (HURS), Cordoba 14004, Spain
| | - Valerie Matagne
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Carlos A Toro
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Suresh Ramaswamy
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Tony M Plant
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Sergio R Ojeda
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
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Méndez C, Ahlenstiel CL, Kelleher AD. Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus. World J Virol 2015; 4:219-244. [PMID: 26279984 PMCID: PMC4534814 DOI: 10.5501/wjv.v4.i3.219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/24/2015] [Accepted: 04/29/2015] [Indexed: 02/05/2023] Open
Abstract
While human immunodeficiency virus 1 (HIV-1) infection is controlled through continuous, life-long use of a combination of drugs targeting different steps of the virus cycle, HIV-1 is never completely eradicated from the body. Despite decades of research there is still no effective vaccine to prevent HIV-1 infection. Therefore, the possibility of an RNA interference (RNAi)-based cure has become an increasingly explored approach. Endogenous gene expression is controlled at both, transcriptional and post-transcriptional levels by non-coding RNAs, which act through diverse molecular mechanisms including RNAi. RNAi has the potential to control the turning on/off of specific genes through transcriptional gene silencing (TGS), as well as fine-tuning their expression through post-transcriptional gene silencing (PTGS). In this review we will describe in detail the canonical RNAi pathways for PTGS and TGS, the relationship of TGS with other silencing mechanisms and will discuss a variety of approaches developed to suppress HIV-1 via manipulation of RNAi. We will briefly compare RNAi strategies against other approaches developed to target the virus, highlighting their potential to overcome the major obstacle to finding a cure, which is the specific targeting of the HIV-1 reservoir within latently infected cells.
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Chase KA, Rosen C, Rubin LH, Feiner B, Bodapati AS, Gin H, Hu E, Sharma RP. Evidence of a sex-dependent restrictive epigenome in schizophrenia. J Psychiatr Res 2015; 65:87-94. [PMID: 25935252 PMCID: PMC4439370 DOI: 10.1016/j.jpsychires.2015.04.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 03/24/2015] [Accepted: 04/09/2015] [Indexed: 01/07/2023]
Abstract
When compared to women, men have a higher incidence of schizophrenia, with increases in negative and cognitive symptoms, and an overall poorer disease course. Schizophrenia is conceptualized as a disorder of aberrant gene transcription and regulation. Thus, epigenetics, the study of environmentally induced changes in gene regulation, could advance our understanding of the molecular underpinnings of schizophrenia. Peripheral histone methyltransferase (HMT) mRNA levels have been previously shown to be significantly increased in patients with schizophrenia and correlate with symptomology. In this independent study, peripheral lymphocytes were extracted and clinical symptoms were measured on 74 participants, (40 patients with schizophrenia (19 women, 21 men) and 34 healthy individuals (19 women, 15 men)). HMT (G9α, SETDB1 and GLP) mRNA levels and their resulting histone modification H3K9me2 were measured with RT-PCR and ELISA respectively. Plasma estradiol levels were also measured via ELISA and correlated with HMT mRNA. Clinical symptoms were measured utilizing the Positive and Negative Syndrome Scale (PANSS) and the Heinrichs Carpenter Quality of Life Scale (QLS). The results indicate that men with schizophrenia expressed the highest levels of G9α, SETDB1 mRNA and H3K9me2 protein levels. Additionally, higher levels of symptom presentation and an overall poorer quality of life were correlated with higher HMT mRNA and H3K9me2 protein levels in a sex-dependent pattern. These data support the hypothesis of a sex-dependent restrictive epigenome contributing towards the etiology of schizophrenia. The histone methyltransferases measured here could be potential future therapeutic targets for small molecule pharmacology.
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Affiliation(s)
- Kayla A. Chase
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612,Corresponding author: Rajiv P. Sharma MD, Professor, Psychiatric Institute, 1601 West Taylor Street, Chicago, IL 60612, Tel.: (312) 413-4508; Fax: (312) 413-4503.
| | - Cherise Rosen
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612
| | - Leah H. Rubin
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612
| | - Benjamin Feiner
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612
| | - Anjuli S. Bodapati
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612
| | - Hannah Gin
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612
| | - Edward Hu
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612
| | - Rajiv P. Sharma
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612,Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL 60612
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43
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Kim EJ, Ma X, Cerutti H. Gene silencing in microalgae: mechanisms and biological roles. BIORESOURCE TECHNOLOGY 2015; 184:23-32. [PMID: 25466994 DOI: 10.1016/j.biortech.2014.10.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/22/2014] [Accepted: 10/24/2014] [Indexed: 05/18/2023]
Abstract
Microalgae exhibit enormous diversity and can potentially contribute to the production of biofuels and high value compounds. However, for most species, our knowledge of their physiology, metabolism, and gene regulation is fairly limited. In eukaryotes, gene silencing mechanisms play important roles in both the reversible repression of genes that are required only in certain contexts and the suppression of genome invaders such at transposons. The recent sequencing of several algal genomes is providing insights into the complexity of these mechanisms in microalgae. Collectively, glaucophyte, red, and green microalgae contain the machineries involved in repressive histone H3 lysine methylation, DNA cytosine methylation, and RNA interference. However, individual species often only have subsets of these gene silencing mechanisms. Moreover, current evidence suggests that algal silencing systems function in transposon and transgene repression but their role(s) in gene regulation or other cellular processes remains virtually unexplored, hindering rational genetic engineering efforts.
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Affiliation(s)
- Eun-Jeong Kim
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Xinrong Ma
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Heriberto Cerutti
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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44
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Accari SL, Fisher PR. Emerging Roles of JmjC Domain-Containing Proteins. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 319:165-220. [DOI: 10.1016/bs.ircmb.2015.07.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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45
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Lomniczi A, Wright H, Ojeda SR. Epigenetic regulation of female puberty. Front Neuroendocrinol 2015; 36:90-107. [PMID: 25171849 PMCID: PMC6824271 DOI: 10.1016/j.yfrne.2014.08.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/15/2014] [Accepted: 08/20/2014] [Indexed: 12/18/2022]
Abstract
Substantial progress has been made in recent years toward deciphering the molecular and genetic underpinnings of the pubertal process. The availability of powerful new methods to interrogate the human genome has led to the identification of genes that are essential for puberty to occur. Evidence has also emerged suggesting that the initiation of puberty requires the coordinated activity of gene sets organized into functional networks. At a cellular level, it is currently thought that loss of transsynaptic inhibition, accompanied by an increase in excitatory inputs, results in the pubertal activation of GnRH release. This concept notwithstanding, a mechanism of epigenetic repression targeting genes required for the pubertal activation of GnRH neurons was recently identified as a core component of the molecular machinery underlying the central restraint of puberty. In this chapter we will discuss the potential contribution of various mechanisms of epigenetic regulation to the hypothalamic control of female puberty.
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Affiliation(s)
- Alejandro Lomniczi
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Ave, Beaverton, OR 97006, USA.
| | - Hollis Wright
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Ave, Beaverton, OR 97006, USA
| | - Sergio R Ojeda
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Ave, Beaverton, OR 97006, USA.
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Sun L, Huang Y, Wei Q, Tong X, Cai R, Nalepa G, Ye X. Cyclin E-CDK2 protein phosphorylates plant homeodomain finger protein 8 (PHF8) and regulates its function in the cell cycle. J Biol Chem 2014; 290:4075-85. [PMID: 25548279 DOI: 10.1074/jbc.m114.602532] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclin E-CDK2 is a key regulator in G1/S transition. Previously, we identified a number of CDK2-interacting proteins, including PHF8 (plant homeodomain finger protein 8). In this report, we confirmed that PHF8 is a novel cyclin E-CDK2 substrate. By taking the approach of mass spectrometry, we identified that PHF8 Ser-844 is phosphorylated by cyclin E-CDK2. Immunoblotting analysis indicated that WT PHF8 demethylates histone H3K9me2 more efficiently than the cyclin E-CDK2 phosphorylation-deficient PHF8-S844A mutant. Furthermore, flow cytometry analysis showed that WT PHF8 promotes S phase progression more robustly than PHF8-S844A. Real-time PCR results demonstrated that PHF8 increases transcription of cyclin E, E2F3, and E2F7 to significantly higher levels compared with PHF8-S844A. Further analysis by ChIP assay indicated that PHF8 binds to the cyclin E promoter stronger than PHF8-S844A and reduces the H3K9me2 level at the cyclin E promoter more efficiently than PHF8-S844A. In addition, we found that cyclin E-CDK2-mediated phosphorylation of PHF8 Ser-844 promotes PHF8-dependent rRNA transcription in luciferase reporter assays and real-time PCR. Taken together, these results indicate that cyclin E-CDK2 phosphorylates PHF8 to stimulate its demethylase activity to promote rRNA transcription and cell cycle progression.
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Affiliation(s)
- Liping Sun
- From the Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100101, China, and
| | - Yan Huang
- From the Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100101, China, and
| | - Qian Wei
- From the Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100101, China, and
| | - Xiaomei Tong
- From the Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rong Cai
- From the Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100101, China, and
| | - Grzegorz Nalepa
- the Department of Pediatrics and Division of Pediatric Hematology-Oncology, Herman B. Wells Center for Pediatric Research, and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Xin Ye
- From the Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,
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Transcriptional repression is epigenetically marked by H3K9 methylation during SV40 replication. Clin Epigenetics 2014; 6:21. [PMID: 25395994 PMCID: PMC4230732 DOI: 10.1186/1868-7083-6-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 10/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We have recently shown that T-antigen binding to Site I results in the replication-dependent introduction of H3K9me1 into SV40 chromatin late in infection. Since H3K9me2 and H3K9me3 are also present late in infection, we determined whether their presence was also related to the status of ongoing transcription and replication. Transcription was either inhibited with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidizole (DRB) or stimulated with sodium butyrate and the effects on histone modifications early and late in infection determined. The role of DNA replication was determined by concomitant inhibition of replication with aphidicolin. RESULTS We observed that H3K9me2/me3 was specifically introduced when transcription was inhibited during active replication. The introduction of H3K9me2/me3 that occurred when transcription was inhibited was partially blocked when replication was also inhibited. The introduction of H3K9me2/me3 did not require the presence of H3K9me1 since similar results were obtained with the mutant cs1085 whose chromatin contains very little H3K9me1. CONCLUSIONS Our data suggest that methylation of H3K9 can occur either as a consequence of a specific repressive event such as T-antigen binding to Site I or as a result of a general repression of transcription in the presence of active replication. The results suggest that the nonproductive generation of transcription complexes as occurs following DRB treatment may be recognized by a 'proof reading' mechanism, which leads to the specific introduction of H3K9me2 and H3K9me3.
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Škugor A, Krasnov A, Andersen Ø. Genome-wide microarray analysis of Atlantic cod (Gadus morhua) oocyte and embryo. BMC Genomics 2014; 15:594. [PMID: 25023375 PMCID: PMC4124161 DOI: 10.1186/1471-2164-15-594] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 07/09/2014] [Indexed: 01/06/2023] Open
Abstract
Background Regulation of gene expression plays a central role in embryonic development. Early stages are controlled by gametic transcripts, which are subsequently substituted with transcripts from the genome of the zygote. Transcriptomic analyses provide an efficient approach to explore the temporal gene expression profiles in embryos and to search for the developmental regulators. We report a study of early Atlantic cod development that used a genome-wide oligonucleotide microarray to examine the composition and putative roles of polyadenylated transcripts. Results The analyses were carried out in unfertilized oocytes, newly fertilized oocytes and embryos at the stages of mid-blastula transition and segmentation. Numerous genes transcribed in oocytes are involved in multiple aspects of cell maintenance and protection, including metabolism, signal perception and transduction, RNA processing, cell cycle, defense against pathogens and DNA damage. Transcripts found in unfertilized oocytes also encoded a large number of proteins implicated in cell adherence, tight junction and focal adhesion, suggesting high complexity in terms of structure and cellular interactions in embryos prior to midblastula transition (MBT). Prezygotic transcripts included multiple regulators that are most likely involved in developmental processes that take place long after fertilization, such as components of ErbB, hedgehog, notch, retinoid, TGFb, VEGF and Wnt signaling pathways, as well as transcripts involved in the development of nervous system. The major event of MBT was the activation of a large group of histones and other genes that modify chromatin structure preceding massive gene expression changes. A hallmark of events observed during segmentation was the induction of multiple transcription factors, including a large group of homeobox proteins in pace with decay of a large fraction of maternal transcripts. Microarray analyses detected a suite of master developmental regulators that control differentiation and maintenance of diverse cell lineages. Conclusions Transcriptome profiling of the early stages in Atlantic cod revealed the presence of transcripts involved in patterning and development of tissues and organs long before activation of the zygotic genome. The switch from maternal to zygotic developmental programs is associated with large-scale modification of chromosomes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-594) contains supplementary material, which is available to authorized users.
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Theillet FX, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley PB, Gierasch L, Pielak GJ, Elcock AH, Gershenson A, Selenko P. Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chem Rev 2014; 114:6661-714. [PMID: 24901537 PMCID: PMC4095937 DOI: 10.1021/cr400695p] [Citation(s) in RCA: 338] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Francois-Xavier Theillet
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Andres Binolfi
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Tamara Frembgen-Kesner
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Karan Hingorani
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Mohona Sarkar
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Ciara Kyne
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Conggang Li
- Key Laboratory
of Magnetic Resonance in Biological Systems, State Key Laboratory
of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center
for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P.R. China
| | - Peter B. Crowley
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Lila Gierasch
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Gary J. Pielak
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Adrian H. Elcock
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Anne Gershenson
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Philipp Selenko
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
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Molecular basis for substrate recognition by lysine methyltransferases and demethylases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1404-15. [PMID: 24946978 DOI: 10.1016/j.bbagrm.2014.06.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 05/16/2014] [Accepted: 06/09/2014] [Indexed: 11/24/2022]
Abstract
Lysine methylation has emerged as a prominent covalent modification in histones and non-histone proteins. This modification has been implicated in numerous genomic processes, including heterochromatinization, cell cycle progression, DNA damage response, DNA replication, genome stability, and epigenetic gene regulation that underpins developmental programs defining cell identity and fate. The site and degree of lysine methylation is dynamically modulated through the enzymatic activities of protein lysine methyltransferases (KMTs) and protein lysine demethylases (KDMs). These enzymes display distinct substrate specificities that in part define their biological functions. This review explores recent progress in elucidating the molecular basis of these specificities, highlighting structural and functional studies of the methyltransferases SUV4-20H1 (KMT5B), SUV4-20H2 (KMT5C), and ATXR5, and the demethylases UTX (KDM6A), JMJD3 (KDM6B), and JMJD2D (KDM4D). We conclude by examining these findings in the context of related KMTs and KDMs and by exploring unresolved questions regarding the specificities and functions of these enzymes.
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