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Liu Z, Deng C, Zhou Z, Xiao Y, Jiang S, Zhu B, Naler LB, Jia X, Yao DD, Lu C. Epigenomic tomography for probing spatially defined chromatin state in the brain. Cell Rep Methods 2024; 4:100738. [PMID: 38508188 PMCID: PMC10985265 DOI: 10.1016/j.crmeth.2024.100738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 12/24/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024]
Abstract
Spatially resolved epigenomic profiling is critical for understanding biology in the mammalian brain. Single-cell spatial epigenomic assays were developed recently for this purpose, but they remain costly and labor intensive for examining brain tissues across substantial dimensions and surveying a collection of brain samples. Here, we demonstrate an approach, epigenomic tomography, that maps spatial epigenomes of mouse brain at the scale of centimeters. We individually profiled neuronal and glial fractions of mouse neocortex slices with 0.5 mm thickness. Tri-methylation of histone 3 at lysine 27 (H3K27me3) or acetylation of histone 3 at lysine 27 (H3K27ac) features across these slices were grouped into clusters based on their spatial variation patterns to form epigenomic brain maps. As a proof of principle, our approach reveals striking dynamics in the frontal cortex due to kainic-acid-induced seizure, linked with transmembrane ion transporters, exocytosis of synaptic vesicles, and secretion of neurotransmitters. Epigenomic tomography provides a powerful and cost-effective tool for characterizing brain disorders based on the spatial epigenome.
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Affiliation(s)
- Zhengzhi Liu
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, USA
| | - Chengyu Deng
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ya Xiao
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Shan Jiang
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Xiaoting Jia
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, USA
| | | | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA.
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2
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Van Moortel L, Verhee A, Thommis J, Houtman R, Melchers D, Delhaye L, Van Leene C, Hellemans M, Gevaert K, Eyckerman S, De Bosscher K. Selective Modulation of the Human Glucocorticoid Receptor Compromises GR Chromatin Occupancy and Recruitment of p300/CBP and the Mediator Complex. Mol Cell Proteomics 2024; 23:100741. [PMID: 38387774 PMCID: PMC10957501 DOI: 10.1016/j.mcpro.2024.100741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 02/24/2024] Open
Abstract
Exogenous glucocorticoids are frequently used to treat inflammatory disorders and as adjuncts for the treatment of solid cancers. However, their use is associated with severe side effects and therapy resistance. Novel glucocorticoid receptor (GR) ligands with a patient-validated reduced side effect profile have not yet reached the clinic. GR is a member of the nuclear receptor family of transcription factors and heavily relies on interactions with coregulator proteins for its transcriptional activity. To elucidate the role of the GR interactome in the differential transcriptional activity of GR following treatment with the selective GR agonist and modulator dagrocorat compared to classic (ant)agonists, we generated comprehensive interactome maps by high-confidence proximity proteomics in lung epithelial carcinoma cells. We found that dagrocorat and the antagonist RU486 both reduced GR interaction with CREB-binding protein/p300 and the mediator complex compared to the full GR agonist dexamethasone. Chromatin immunoprecipitation assays revealed that these changes in GR interactome were accompanied by reduced GR chromatin occupancy with dagrocorat and RU486. Our data offer new insights into the role of differential coregulator recruitment in shaping ligand-specific GR-mediated transcriptional responses.
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Affiliation(s)
- Laura Van Moortel
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Annick Verhee
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jonathan Thommis
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | | | - Louis Delhaye
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Chloé Van Leene
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Madeleine Hellemans
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB-UGent Inflammation Research Center, VIB Institute, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
| | - Karolien De Bosscher
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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3
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Becker PB. Cell-free genomics: transcription factor interactions in reconstituted naïve embryonic chromatin. Biochem Soc Trans 2024; 52:423-429. [PMID: 38329186 DOI: 10.1042/bst20230878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Extracts from Drosophila preblastoderm embryos (DREX) form the basis of a powerful in vitro chromatin reconstitution system that assembles entire genomes into complex chromatin with physiological nucleosome spacing and polymer condensation. As the zygotic genome has not yet been activated in preblastoderm embryos, the reconstitution extract lacks endogenous transcription factors (TFs) and the RNA polymerase machinery. At the same time, it contains high levels of ATP-dependent nucleosome sliding enzymes that render the reconstituted chromatin dynamic. The naïve chromatin can be used to determine the intrinsic DNA binding properties of exogenous, usually recombinant TFs (or DNA binding proteins in general) in a complex chromatin context. Recent applications of the system include the description of cooperation and competition of Drosophila pioneer TFs for composite binding sites, and the characterization of nucleosome interactions of mammalian pioneer TFs in the heterologous system.
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Affiliation(s)
- Peter B Becker
- Biomedical Center, Molecular Biology Division, Faculty of Medicine, LMU, Munich, Germany
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4
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Zhou P, Ouyang L, Jiang T, Tian Y, Deng W, Wang H, Kong S, Lu Z. Progesterone and cAMP synergistically induce SHP2 expression via PGR and CREB1 during uterine stromal decidualization. FEBS J 2024; 291:142-157. [PMID: 37786383 DOI: 10.1111/febs.16966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/31/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Decidualization of endometrial stroma is a key step in embryo implantation and its abnormality often leads to pregnancy failure. Stromal decidualization is a very complex process that is co-regulated by estrogen, progesterone and many local factors. The signaling protein SHP2 encoded by PTPN11 is dynamically expressed in decidualized endometrial stroma and mediates and integrates various signals to govern the decidualization. In the present study, we investigate the mechanism of PTPN11 gene transcription. Estrogen, progesterone and cAMP co-induced decidualization of human endometrial stromal cell in vitro, but only progesterone and cAMP induced SHP2 expression. Using the luciferase reporter, we refined a region from -229 bp to +1 bp in the PTPN11 gene promoter comprising the transcriptional core regions that respond to progesterone and cAMP. Progesterone receptor (PGR) and cAMP-responsive element-binding protein 1 (CREB1) were predicted to be transcription factors in this core region by bioinformatic methods. The direct binding of PGR and CREB1 on the PTPN11 promoter was confirmed by electrophoretic mobility and chromatin immunoprecipitation in vitro. Knockdown of PGR and CREB1 protein significantly inhibited the expression of SHP2 induced by medroxyprogesterone acetate and cAMP. These results demonstrate that transcription factors PGR and CREB1 bind to the PTPN11 promoter to regulate the expression of SHP2 in response to decidual signals. Our results explain the transcriptional expression mechanism of SHP2 during decidualization and promote the understanding of the mechanism of decidualization of stromal cells.
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Affiliation(s)
- Peiyi Zhou
- Xiamen City Key Laboratory of Metabolism, School of Pharmaceutical Sciences, Xiamen University, China
| | - Liqun Ouyang
- Xiamen City Key Laboratory of Metabolism, School of Pharmaceutical Sciences, Xiamen University, China
| | - Ting Jiang
- Xiamen City Key Laboratory of Metabolism, School of Pharmaceutical Sciences, Xiamen University, China
| | - Yingpu Tian
- Xiamen City Key Laboratory of Metabolism, School of Pharmaceutical Sciences, Xiamen University, China
| | - Wenbo Deng
- Reproductive Medical Centre, The First Affiliated Hospital of Xiamen University, China
- Fujian Provincial Key Laboratory of Reproductive Health Research, Medical College of Xiamen University, China
| | - Haibin Wang
- Reproductive Medical Centre, The First Affiliated Hospital of Xiamen University, China
- Fujian Provincial Key Laboratory of Reproductive Health Research, Medical College of Xiamen University, China
| | - Shuangbo Kong
- Reproductive Medical Centre, The First Affiliated Hospital of Xiamen University, China
- Fujian Provincial Key Laboratory of Reproductive Health Research, Medical College of Xiamen University, China
| | - Zhongxian Lu
- Xiamen City Key Laboratory of Metabolism, School of Pharmaceutical Sciences, Xiamen University, China
- Fujian Provincial Key Laboratory of Reproductive Health Research, Medical College of Xiamen University, China
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5
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Khamwachirapithak P, Guillaume-Schoepfer D, Chansongkrow P, Teichmann SA, Wigge PA, Charoensawan V. Characterizing Different Modes of Interplay Between Rap1 and H3 Using Inducible H3-depletion Yeast. J Mol Biol 2023; 435:168355. [PMID: 37935256 DOI: 10.1016/j.jmb.2023.168355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
Histones and transcription factors (TFs) are two important DNA-binding proteins that interact, compete, and together regulate transcriptional processes in response to diverse internal and external stimuli. Condition-specific depletion of histones in Saccharomyces cerevisiae using a galactose-inducible H3 promoter provides a suitable framework for examining transcriptional alteration resulting from reduced nucleosome content. However, the effect on DNA binding activities of TFs is yet to be fully explored. In this work, we combine ChIP-seq of H3 with RNA-seq to elucidate the genome-scale relationships between H3 occupancy patterns and transcriptional dynamics before and after global H3 depletion. ChIP-seq of Rap1 is also conducted in the H3-depletion and control treatments, to investigate the interplay between this master regulator TF and nucleosomal H3, and to explore the impact on diverse transcriptional responses of different groups of target genes and functions. Ultimately, we propose a working model and testable hypotheses regarding the impact of global and local H3 depletion on transcriptional changes. We also demonstrate different potential modes of interaction between Rap1 and H3, which sheds light on the potential multifunctional regulatory capabilities of Rap1 and potentially other pioneer factors.
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Affiliation(s)
- Peerapat Khamwachirapithak
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok, Thailand; Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Pakkanan Chansongkrow
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - Philip A Wigge
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom; University Potsdam, Institute for Biochemistry and Biology, Molecular Biology, Karl-Liebknecht-Str, Potsdam-Golm, Germany; Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany.
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand; Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom; Systems Biology of Diseases Research Unit, Faculty of Science, Mahidol University, Bangkok, Thailand; Integrative Computational BioScience (ICBS) center, Mahidol University, Nakhon Pathom, Thailand; School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand.
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6
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Petrie MV, He Y, Gan Y, Ostrow AZ, Aparicio OM. Broadly Applicable Control Approaches Improve Accuracy of ChIP-Seq Data. Int J Mol Sci 2023; 24:ijms24119271. [PMID: 37298223 DOI: 10.3390/ijms24119271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Chromatin ImmunoPrecipitation (ChIP) is a widely used method for the analysis of protein-DNA interactions in vivo; however, ChIP has pitfalls, particularly false-positive signal enrichment that permeates the data. We have developed a new approach to control for non-specific enrichment in ChIP that involves the expression of a non-genome-binding protein targeted in the IP alongside the experimental target protein due to the sharing of epitope tags. ChIP of the protein provides a "sensor" for non-specific enrichment that can be used for the normalization of the experimental data, thereby correcting for non-specific signals and improving data quality as validated against known binding sites for several proteins that we tested, including Fkh1, Orc1, Mcm4, and Sir2. We also tested a DNA-binding mutant approach and showed that, when feasible, ChIP of a site-specific DNA-binding mutant of the target protein is likely an ideal control. These methods vastly improve our ChIP-seq results in S. cerevisiae and should be applicable in other systems.
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Affiliation(s)
- Meghan V Petrie
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA
| | - Yiwei He
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA
| | - Yan Gan
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew Zachary Ostrow
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA
| | - Oscar M Aparicio
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA
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7
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Orchard KJA, Akbar M, Crowe LAN, Cole J, Millar NL, Raleigh SM. Characterization of Histone Modifications in Late-Stage Rotator Cuff Tendinopathy. Genes (Basel) 2023; 14:496. [PMID: 36833423 PMCID: PMC9956879 DOI: 10.3390/genes14020496] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
The development and progression of rotator cuff tendinopathy (RCT) is multifactorial and likely to manifest through a combination of extrinsic, intrinsic, and environmental factors, including genetics and epigenetics. However, the role of epigenetics in RCT, including the role of histone modification, is not well established. Using chromatin immunoprecipitation sequencing, differences in the trimethylation status of H3K4 and H3K27 histones in late-stage RCT compared to control were investigated in this study. For H3K4, 24 genomic loci were found to be significantly more trimethylated in RCT compared to control (p < 0.05), implicating genes such as DKK2, JAG2, and SMOC2 in RCT. For H3K27, 31 loci were shown to be more trimethylated (p < 0.05) in RCT compared to control, inferring a role for EPHA3, ROCK1, and DEFβ115. Furthermore, 14 loci were significantly less trimethylated (p < 0.05) in control compared to RCT, implicating EFNA5, GDF6, and GDF7. Finally, the TGFβ signaling, axon guidance, and regulation of focal adhesion assembly pathways were found to be enriched in RCT. These findings suggest that the development and progression of RCT is, at least in part, under epigenetic control, highlighting the influence of histone modifications in this disorder and paving the way to further understand the role of epigenome in RCT.
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Affiliation(s)
- Kayleigh J. A. Orchard
- Centre for Sports, Exercise and Life Sciences, Coventry University, Coventry CV1 5FB, UK
| | - Moeed Akbar
- School of Infection and Immunity, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Lindsay A. N. Crowe
- School of Infection and Immunity, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - John Cole
- School of Infection and Immunity, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Neal L. Millar
- School of Infection and Immunity, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Stuart M. Raleigh
- Centre for Sports, Exercise and Life Sciences, Coventry University, Coventry CV1 5FB, UK
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8
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Shirahama Y, Yamamoto K. The E2F6 Transcription Factor is Associated with the Mammalian SUZ12-Containing Polycomb Complex. Kurume Med J 2023; 67:171-183. [PMID: 36464274 DOI: 10.2739/kurumemedj.ms674006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The Polycomb group protein (PcG) SUZ12 forms Polycomb repressive complexes together with histone methyltransferase EZH2. Although the complexes have been demonstrated to be involved in epigenetic maintenance of gene expression in a transcriptional repressive state, it is unclear how they are recruited to the target genes. Here we report that SUZ12 directly interacts with site-specific transcriptional repressor E2F6 and forms a complex together with EZH2. SUZ12 interacts with E2F6 selectively among the E2F family proteins and E2F6- containing SUZ12-EZH2 complex was biochemically purified from HEK293 cells stably expressing Flag-tagged SUZ12. Chromatin immunoprecipitation assays revealed the target genes of the E2F6-SUZ12-EZH2 complex. Contrary to expectation, the promoter regions of these genes are not or only weakly tri-methylated at histone H3-K27, and their expression is down-regulated by depletion of EZH2. Given that the transactivation function of SUZ12-EZH2 has been previously reported, the inhibitory effect on E2F6-mediated transcriptional repression by physical interaction can be considered a candidate mechanism of gene activation by these PcGs.
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Affiliation(s)
- Yuko Shirahama
- Department of Medical Biochemistry, Kurume University School of Medicine
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine
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9
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Gyenis A, Chang J, Demmers JJPG, Bruens ST, Barnhoorn S, Brandt RMC, Baar MP, Raseta M, Derks KWJ, Hoeijmakers JHJ, Pothof J. Genome-wide RNA polymerase stalling shapes the transcriptome during aging. Nat Genet 2023; 55:268-279. [PMID: 36658433 PMCID: PMC9925383 DOI: 10.1038/s41588-022-01279-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/07/2022] [Indexed: 01/21/2023]
Abstract
Gene expression profiling has identified numerous processes altered in aging, but how these changes arise is largely unknown. Here we combined nascent RNA sequencing and RNA polymerase II chromatin immunoprecipitation followed by sequencing to elucidate the underlying mechanisms triggering gene expression changes in wild-type aged mice. We found that in 2-year-old liver, 40% of elongating RNA polymerases are stalled, lowering productive transcription and skewing transcriptional output in a gene-length-dependent fashion. We demonstrate that this transcriptional stress is caused by endogenous DNA damage and explains the majority of gene expression changes in aging in most mainly postmitotic organs, specifically affecting aging hallmark pathways such as nutrient sensing, autophagy, proteostasis, energy metabolism, immune function and cellular stress resilience. Age-related transcriptional stress is evolutionary conserved from nematodes to humans. Thus, accumulation of stochastic endogenous DNA damage during aging deteriorates basal transcription, which establishes the age-related transcriptome and causes dysfunction of key aging hallmark pathways, disclosing how DNA damage functionally underlies major aspects of normal aging.
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Affiliation(s)
- Akos Gyenis
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- University of Cologne, Faculty of Medicine, Cluster of Excellence for Aging Research, Institute for Genome Stability in Ageing and Disease, Cologne, Germany
| | - Jiang Chang
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joris J P G Demmers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Serena T Bruens
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sander Barnhoorn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Renata M C Brandt
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marjolein P Baar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marko Raseta
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kasper W J Derks
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics and School for Oncology & Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- University of Cologne, Faculty of Medicine, Cluster of Excellence for Aging Research, Institute for Genome Stability in Ageing and Disease, Cologne, Germany
- Princess Maxima Center for Pediatric Oncology, Oncode Institute, Utrecht, The Netherlands
| | - Joris Pothof
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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10
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Kuan MI, Caruso LB, Zavala AG, Rana PSJB, O'Dowd JM, Tempera I, Fortunato EA. Human Cytomegalovirus Utilizes Multiple Viral Proteins to Regulate the Basement Membrane Protein Nidogen 1. J Virol 2022;:e0133622. [PMID: 36218358 DOI: 10.1128/jvi.01336-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nidogen 1 (NID1) is an important basement membrane protein secreted by many cell types. We previously found that human cytomegalovirus (HCMV) infection rapidly induced chromosome 1 breaks and that the basement membrane protein NID1, encoded near the 1q42 break site, was downregulated. We have now determined that the specific breaks in and of themselves did not regulate NID1, rather interactions between several viral proteins and the cellular machinery and DNA regulated NID1. We screened a battery of viral proteins present by 24 hours postinfection (hpi) when regulation was induced, including components of the incoming virion and immediate early (IE) proteins. Adenovirus (Ad) delivery of the tegument proteins pp71 and UL35 and the IE protein IE1 influenced steady-state (ss) NID1 levels. IE1's mechanism of regulation was unclear, while UL35 influenced proteasomal regulation of ss NID1. Real-time quantitative PCR (RT-qPCR) experiments determined that pp71 downregulated NID1 transcription. Surprisingly, WF28-71, a fibroblast clone that expresses minute quantities of pp71, suppressed NID1 transcription as efficiently as HCMV infection, resulting in the near absence of ss NID1. Sequence analysis of the region surrounding the 1q42 break sites and NID1 promoter revealed CCCTC-binding factor (CTCF) binding sites. Chromatin immunoprecipitation experiments determined that pp71 and CTCF were both bound at these two sites during HCMV infection. Expression of pp71 alone replicated this binding. Binding was observed as early as 1 hpi, and colocalization of pp71 and CTCF occurred as quickly as 15 min postinfection (pi) in infected cell nuclei. In fibroblasts where CTCF was knocked down, Adpp71 infection did not decrease NID1 transcription nor ss NID1 protein levels. Our results emphasize another aspect of pp71 activity during infection and identify this viral protein as a key contributor to HCMV's efforts to eliminate NID1. Further, we show, for the first time, direct interaction between pp71 and the cellular genome. IMPORTANCE We have found that human cytomegalovirus (HCMV) utilizes multiple viral proteins in multiple pathways to regulate a ubiquitous cellular basement membrane protein, nidogen-1 (NID1). The extent of the resources and the redundant methods that the virus has evolved to affect this control strongly suggest that its removal provides a life cycle advantage to HCMV. Our discoveries that one of the proteins that HCMV uses to control NID1, pp71, binds directly to the cellular DNA and can exert control when present in vanishingly small quantities may have broad implications in a wide range of infection scenarios. Dysregulation of NID1 in an immunocompetent host is not known to manifest complications during infection; however, in the naive immune system of a developing fetus, disruption of this developmentally critical protein could initiate catastrophic HCMV-induced birth defects.
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11
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Dowdell AS, Cartwright IM, Kitzenberg DA, Kostelecky RE, Mahjoob O, Saeedi BJ, Welch N, Glover LE, Colgan SP. Essential role for epithelial HIF-mediated xenophagy in control of Salmonella infection and dissemination. Cell Rep 2022; 40:111409. [PMID: 36170839 PMCID: PMC9553003 DOI: 10.1016/j.celrep.2022.111409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/21/2022] [Accepted: 09/02/2022] [Indexed: 01/18/2023] Open
Abstract
The intestinal mucosa exists in a state of “physiologic hypoxia,” where oxygen tensions are markedly lower than those in other tissues. Intestinal epithelial cells (IECs) have evolved to maintain homeostasis in this austere environment through oxygen-sensitive transcription factors, including hypoxia-inducible factors (HIFs). Using an unbiased chromatin immunoprecipitation (ChIP) screen for HIF-1 targets, we identify autophagy as a major pathway induced by hypoxia in IECs. One important function of autophagy is to defend against intracellular pathogens, termed “xenophagy.” Analysis reveals that HIF is a central regulator of autophagy and that in vitro infection of IECs with Salmonella Typhimurium results in induction of HIF transcriptional activity that tracks with the clearance of intracellular Salmonella. Work in vivo demonstrates that IEC-specific deletion of HIF compromises xenophagy and exacerbates bacterial dissemination. These results reveal that the interaction between hypoxia, HIF, and xenophagy is an essential innate immune component for the control of intracellular pathogens. Dowdell et al. show that hypoxia, through stabilization of HIF-1α, activates autophagy in intestinal epithelial cells (IECs). Further, the model invasive bacterium Salmonella Typhimurium stabilizes HIF in IECs to trigger anti-bacterial autophagy (xenophagy). This mechanism demonstrates an essential mucosal innate immune response for control of invasive pathogens.
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Affiliation(s)
- Alexander S Dowdell
- Mucosal Inflammation Program and Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; Rocky Mountain Veterans Hospital, Aurora, CO, USA
| | - Ian M Cartwright
- Mucosal Inflammation Program and Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; Rocky Mountain Veterans Hospital, Aurora, CO, USA
| | - David A Kitzenberg
- Mucosal Inflammation Program and Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Rachael E Kostelecky
- Mucosal Inflammation Program and Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Omemh Mahjoob
- Mucosal Inflammation Program and Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Bejan J Saeedi
- Mucosal Inflammation Program and Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nichole Welch
- Mucosal Inflammation Program and Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Louise E Glover
- Mucosal Inflammation Program and Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Sean P Colgan
- Mucosal Inflammation Program and Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; Rocky Mountain Veterans Hospital, Aurora, CO, USA.
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12
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Chen C, Zuo J, Zhang H. Sevoflurane Post-treatment Mitigates Oxygen-glucose Deprivationinduced Pyroptosis of Hippocampal Neurons by Regulating the Mafb/DUSP14 Axis. Curr Neurovasc Res 2022; 19:245-254. [PMID: 35927915 DOI: 10.2174/1567202619666220802104426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/25/2022] [Accepted: 06/18/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Ischemic brain injury often results in irreversible pyroptosis of neurons. Sevoflurane (Sevo) post-treatment exerts an alleviative role in neuroinflammation. OBJECTIVES This work evaluated the mechanism of Sevo post-treatment in oxygen-glucose deprivation (OGD)-induced pyroptosis of rat hippocampal neurons. METHODS Rat hippocampal neuron cell line H19-7 cells were treated with OGD, followed by posttreatment of 2% Sevo. The expression patterns of Mafb ZIP Transcription Factor B (Mafb) and dual- specificity phosphatase 14 (DUSP14) were determined via quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting methods. H19-7 cell viability and the release of lactate dehydrogenase (LDH) were examined via the cell counting kit-8 and LDH assay kits. Levels of pyroptosis-related proteins and cytokines NOD-like receptor family, pyrin domain containing 3 (NLRP3), N-term cleaved Gasdermin-D (GSDMD-N), cleaved-caspase-1, interleukin (IL)-1β, and IL-18 were also examined. The binding relation between Mafb and the DUSP14 promoter was detected. Besides, the roles of Mafb/DUSP14 in OGD-induced pyroptosis of rat hippocampal neurons were investigated through functional rescue experiments. RESULTS Mafb and DUSP14 expression levels were decreased in OGD-induced hippocampal neurons. Sevo post-treatment up-regulated Mafb and DUSP14, facilitated H19-7 cell viability, inhibited LDH release, and reduced levels of NLRP3, GSDMD-N, cleaved-caspase-1, IL-1β, and IL-18. Mafb increased DUSP14 expression via binding to the DUSP14 promoter. Repressing Mafb or DUSP14 exacerbated pyroptosis of hippocampal neurons. CONCLUSION Sevo post-treatment increased Mafb and DUSP14 expressions, which repressed OGDinduced pyroptosis of hippocampal neurons.
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Affiliation(s)
- Chen Chen
- Department of Anesthesiology, Peking University Shenzhen Hospital, 1120 Lianhua Road, Shenzhen, Guangdong 518036, P.R. China
| | - Jianwei Zuo
- Department of Sports Medicine, Peking University Shenzhen Hospital, 1120 Lianhua Road, Shenzhen, Guangdong 518036, P.R. China
| | - Huimei Zhang
- Department of Clinical Laboratory, Shenzhen Traditional Chinese Medicine Hospital, No.1 Fuhua Road, Shenzhen, Guangdong 518033, P.R. China
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13
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Tang JJ, Pan YF, Chen C, Cui XL, Yan ZJ, Zhou DX, Guo LN, Cao D, Yu LX, Wang HY. Androgens drive sexual dimorphism in liver metastasis by promoting hepatic accumulation of neutrophils. Cell Rep 2022; 39:110987. [PMID: 35732131 DOI: 10.1016/j.celrep.2022.110987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 03/22/2022] [Accepted: 05/31/2022] [Indexed: 12/24/2022] Open
Abstract
The liver is one of the most-favored distant metastatic sites for solid tumors, and interactions between cancer cells and components of the hepatic microenvironment are essential for liver metastasis (LM). Although sex is one of the determinants for primary liver cancer, sexual dimorphism in LM (SDLM) and the underlying mechanisms remain unclear. We herein demonstrate a significant male-biased SDLM, which is attributed to host androgen/androgen receptor (Ar) signaling that promotes hepatic seeding of tumor cells and subsequent outgrowth in a neutrophil-dependent manner. Mechanistically, androgen/Ar signaling promotes hepatic accumulation of neutrophils by promoting proliferation and development of neutrophil precursors in the bone marrow, as well as modulating hepatic recruitment of neutrophils and their functions. Antagonizing the androgen/Ar/neutrophil axis significantly mitigates LM in males. Our data thus reveal an important role of androgen in LM and suggest that androgen/Ar modulation represents a promising target for LM therapy in men.
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Affiliation(s)
- Jiao-Jiao Tang
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China; National Center for Liver Cancer, Second Military Medical University, Shanghai 201805, China; Division of Life Sciences and Medicine, Cancer Research Center, the First Affiliated Hospital of University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yu-Fei Pan
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China; National Center for Liver Cancer, Second Military Medical University, Shanghai 201805, China
| | - Can Chen
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian 350000, China; Fujian Medical University Cancer Center, Fuzhou, Fujian 350000, China
| | - Xiu-Liang Cui
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China; National Center for Liver Cancer, Second Military Medical University, Shanghai 201805, China
| | - Zi-Jun Yan
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China; National Center for Liver Cancer, Second Military Medical University, Shanghai 201805, China
| | - Dong-Xun Zhou
- Department of Endoscopy, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Lin-Na Guo
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China; National Center for Liver Cancer, Second Military Medical University, Shanghai 201805, China
| | - Dan Cao
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China; National Center for Liver Cancer, Second Military Medical University, Shanghai 201805, China
| | - Le-Xing Yu
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China; National Center for Liver Cancer, Second Military Medical University, Shanghai 201805, China.
| | - Hong-Yang Wang
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China; National Center for Liver Cancer, Second Military Medical University, Shanghai 201805, China; Division of Life Sciences and Medicine, Cancer Research Center, the First Affiliated Hospital of University of Science and Technology of China, Hefei, Anhui 230027, China.
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14
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Abstract
Objective To explore functions of the histone H3 lysine 79 (K79) methyltransferase Dot1L in the development of pancreatic cancer and evaluate the possibility of targeting Dot1L to inhibit pancreatic cancer progression. Methods Patient samples were used to detect differences in Dot1L expression between tumor and adjacent tissues and to determine correlations between Dot1L expression in patients with different stages of pancreatic cancer. Lentiviral-mediated knockdown of Dot1L expression and flow cytometry were used to detect apoptosis in pancreatic cancer lacking Dot1L expression; chromatin immunoprecipitation and quantitative PCR were used to detect downstream target genes of Dot1L. Results We show that Dot1L is highly expressed in pancreatic cancer, and that its expression is related to pancreatic cancer stage. Knocking down Dot1L significantly promoted apoptosis in pancreatic cancer cells, while overexpressing Dot1L inhibited apoptosis. Mechanistically, Dot1L regulated apoptosis in pancreatic cancer cells by promoting NUPR1 expression. The enriched H3K79 trimethylation in the transcription initiation region of NUPR1 promoted its expression. Overexpressing NUPR1 inhibited the pancreatic cancer cell apoptosis caused by Dot1L knockdown. Conclusions Dot1L inhibits pancreatic cancer cell apoptosis by targeting NUPR1; thus, Dot1L is a promising target for pancreatic cancer treatment.
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Affiliation(s)
- Lin Shan
- Affiliated Hospital of Putian University
| | - Chen Hao
- Affiliated Hospital of Putian University
| | - Zheng Jun
- Affiliated Hospital of Putian University
| | - Cai Qinghe
- Affiliated Hospital of Putian University
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15
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Joshi S, Paul P, Hartman JM, Perry SE. AGL15 Promotion of Somatic Embryogenesis: Role and Molecular Mechanism. Front Plant Sci 2022; 13:861556. [PMID: 35419012 PMCID: PMC8996056 DOI: 10.3389/fpls.2022.861556] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Plants have amazing regenerative properties with single somatic cells, or groups of cells able to give rise to fully formed plants. One means of regeneration is somatic embryogenesis, by which an embryonic structure is formed that "converts" into a plantlet. Somatic embryogenesis has been used as a model for zygotic processes that are buried within layers of maternal tissues. Understanding mechanisms of somatic embryo induction and development are important as a more accessible model for seed development. We rely on seed development not only for most of our caloric intake, but also as a delivery system for engineered crops to meet agricultural challenges. Regeneration of transformed cells is needed for this applied work as well as basic research to understand gene function. Here we focus on a MADS-domain transcription factor, AGAMOUS-Like15 (AGL15) that shows a positive correlation between accumulation levels and capacity for somatic embryogenesis. We relate AGL15 function to other transcription factors, hormones, and epigenetic modifiers involved in somatic embryo development.
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Affiliation(s)
- Sanjay Joshi
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Priyanka Paul
- Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, United States
| | - Jeanne M. Hartman
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Sharyn E. Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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16
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Wang W, Cheng L, Sun Q. Chromatin Immunoprecipitation in Chloroplasts. Curr Protoc 2022; 2:e360. [PMID: 35077029 DOI: 10.1002/cpz1.360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Chromatin is the genetic material assembled by nucleic acids (including DNA and RNA) and proteins. The biological functions of chromatin are highly dependent on the interaction between DNA (and/or RNA) and proteins that bind to it. Chromatin immunoprecipitation (ChIP) is a powerful technique for evaluating these interactions and has been widely used to characterize the functions of nuclear proteins. However, its application in identifying plant organellar chromatin-binding proteins is lagging. This article describes the method for analyzing the association of chloroplast-localized proteins with the chloroplast genome. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Chloroplast isolation Basic Protocol 2: Crosslinking of DNA-Protein complexes Basic Protocol 3: Chromatin isolation and preparation Support Protocol: Bead-antibody complex preparation Basic Protocol 4: Immunoprecipitation and washes Basic Protocol 5: DNA preparation Basic Protocol 6: Analysis of results.
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Affiliation(s)
- Wenjie Wang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lingling Cheng
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
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17
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Mei L, Huang Y, Wu X, He H, Ye R, Ma J, He X, Shi Y, Li P. Mutations in FIGLA Associated With Premature Ovarian Insufficiency in a Chinese Population. Front Med (Lausanne) 2021; 8:714306. [PMID: 34778283 PMCID: PMC8585841 DOI: 10.3389/fmed.2021.714306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/28/2021] [Indexed: 11/25/2022] Open
Abstract
Objective: Premature ovarian insufficiency (POI) is one of the most common reproductive endocrinological causes of infertility in women of child-bearing age. The purpose of this study was to identify FIGLA gene mutations in Chinese patients with POI and to investigate the underlying mechanism. Methods: A total of 113 patients with idiopathic POI and 100 healthy controls were recruited for the analysis of FIGLA variants. Based on the identification of common mutations in the FIGLA, wild-type and mutant plasmids were constructed and transfected into HEK293 cells. Luciferase reporter genes were used to determine the effect of wild-type and mutant FIGLA genotypes on the transcriptional activity of its downstream targets, the zona pellucida glycoprotein genes ZP1, ZP2, and ZP3. Chromatin immunoprecipitation was used to determine the level of binding between wild-type and mutant FIGLA with the ZP1, ZP2, and ZP3 promoters. Results: Three different FIGLA mutations were identified in four patients with POI. Two patients carried the mutation c.11C>A (p.A4E), and the other two patients, respectively, carried the mutations c.625G>A (p.V209I) and c.84C>A (p.D28E). The luciferase reporter assay indicated that ZP1, ZP2, and ZP3 transcriptional activities were significantly reduced in individuals with FIGLA mutations. Chromatin immunoprecipitation indicated that the FIGLA mutation significantly decreased binding with the ZP1, ZP2, and ZP3 promoters. Conclusion:FIGLA mutation affects gene transcriptional regulation of its downstream target genes ZP1, ZP2, and ZP3, highlighting a new candidate genetic factor that causes POI. Our study demonstrates that FIGLA has a regulatory effect on reproduction-specific genes, thereby providing a basis for elucidating the specific regulatory mechanism of FIGLA in germ cell growth and development.
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Affiliation(s)
- Libin Mei
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Reproduction and Genetics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Yanru Huang
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Xiaoling Wu
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Reproduction and Genetics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Huang He
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Reproduction and Genetics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Ronghui Ye
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Reproduction and Genetics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Jinxiu Ma
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Reproduction and Genetics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - XueMei He
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Reproduction and Genetics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Yuhua Shi
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, China
| | - Ping Li
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Reproduction and Genetics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
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Abstract
To investigate the function of histone-lysine N-methyltransferase 2D (KMT2D) on the methylation of H3 lysine 4 (H3K4) in the progression of Ovarian cancer (OV). KMT2D, ESR1 and H3K4me expressions in surgical resected tumors and tumor adjacent tissues of OV from 198 patients were determined using immunohistochemistry (IHC). Human OV cell lines including SKOV3, HO-8910 cells and normal ovarian epithelial cell line IOSE80 were employed for in vitro experiment, and BALB/C female nude mice were used for in vivo study. qRT-PCR and Western blotting were implemented for measuring the KMT2D, ESR1, PTGS2, STAT3, VEGFR2, H3K4me and ELF3 levels. Chromatin immunoprecipitation (ChIP) analysis was used for studying the binding between ESR1 and H3K4me. Edu staining assay was executed to determine cell viability, and colony formation and cell invasion assay. The immunofluorescence method was utilized for the visualization of protein expression and distribution in cells. In this study, KMT2D, ESR1 and H3K4me were found upregulated in OV progression. Mutated H3K4me could inhibit the proliferation, colony formation and invasion ability of OV cells. Mutated H3K4me could also hinder the ESR1 in SKOV3 expressions and HO-8910 cells, which would further mediate PTGS2/STAT3/VEGF pathway. In vivo studies also demonstrated that mutated H3K4me inhibited OV progression via targeting ESR1. All the ChIP-PCR analysis indicated the moderator effect of H3K4me on ESR1. Our findings indicated that ESR1 played an important role in the OV progression. Besides, H3K4me could promote cell proliferation and inhibit apoptosis of OV cells. Meanwhile, it could also targets the ESR1 production to enhance the migration and invasion of OV cells, which was through the activation of ESR1-ELF3-PTGS2-STAT3-VEGF cascade signaling pathway.
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Affiliation(s)
- Ming Li
- Department of Pathology, the Affiliated Suzhou Municipal Hospital of Nanjing Medical University, Suzhou, China
- Co-first author
| | - Mengdie Shi
- Department of obstetrics and gynecology, the Affiliated Suzhou Municipal Hospital of Nanjing Medical University, Suzhou, China
- Co-first author
| | - Ying Xu
- Department of obstetrics and gynecology, the Affiliated Suzhou Municipal Hospital of Nanjing Medical University, Suzhou, China
| | - Jianping Qiu
- Department of obstetrics and gynecology, the Affiliated Suzhou Municipal Hospital of Nanjing Medical University, Suzhou, China
- Jianping Qiu, Department of obstetrics and gynecology, the Affiliated Suzhou Municipal Hospital of Nanjing Medical University, No.242 Guangji Road, Suzhou, 215008, China.
| | - Qing Lv
- Department of Breast Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China
- Qing Lv, Department of Breast Surgery, Affiliated Hospital of Jiangnan University, No.1000 Hefeng Road, Wuxi, 214000, China.
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19
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Singh P, Bhadada SK, Dahiya D, Saikia UN, Arya AK, Sachdeva N, Kaur J, Behera A, Brandi ML, Rao SD. GCM2 Silencing in Parathyroid Adenoma Is Associated With Promoter Hypermethylation and Gain of Methylation on Histone 3. J Clin Endocrinol Metab 2021; 106:e4084-e4096. [PMID: 34077544 PMCID: PMC8475237 DOI: 10.1210/clinem/dgab374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Indexed: 02/06/2023]
Abstract
CONTEXT Glial cells missing 2 (GCM2), a zinc finger-transcription factor, is essentially required for the development of the parathyroid glands. OBJECTIVE We sought to identify whether the epigenetic alterations in GCM2 transcription are involved in the pathogenesis of sporadic parathyroid adenoma. In addition, we examined the association between promoter methylation and histone modifications with disease indices. METHODS Messenger RNA (mRNA) and protein expression of GCM2 were analyzed by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry in 33 adenomatous and 10 control parathyroid tissues. DNA methylation and histone methylation/acetylation of the GCM2 promoter were measured by bisulfite sequencing and chromatin immunoprecipitation-qPCR. Additionally, we investigated the role of epigenetic modifications on GCM2 and DNA methyltransferase 1 (DNMT1) expression in parathyroid (PTH)-C1 cells by treating with 5-aza-2'-deoxycytidine (DAC) and BRD4770 and assessed for GCM2 mRNA and DNMT1 protein levels. RESULTS mRNA and protein expression of GCM2 were lower in sporadic adenomatous than in control parathyroid tissues. This reduction correlated with hypermethylation (P < .001) and higher H3K9me3 levels in the GCM2 promoter (P < .04) in adenomas. In PTH-C1 cells, DAC treatment resulted in increased GCM2 transcription and decreased DNMT1 protein expression, while cells treated with the BRD4770 showed reduced H3K9me3 levels but a nonsignificant change in GCM2 transcription. CONCLUSION These findings suggest the concurrent association of promoter hypermethylation and higher H3K9me3 with the repression of GCM2 expression in parathyroid adenomas. Treatment with DAC restored GCM2 expression in PTH-C1 cells. Our results showed a possible epigenetic landscape in the tumorigenesis of parathyroid adenoma and also that DAC may be a promising avenue of research for parathyroid adenoma therapeutics.
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Affiliation(s)
- Priyanka Singh
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Sanjay Kumar Bhadada
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
- Correspondence: Sanjay Kumar Bhadada, MD, DM, Department of Endocrinology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India.
| | - Divya Dahiya
- Department of General Surgery, PGIMER, Chandigarh, 160012, India
| | | | - Ashutosh Kumar Arya
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Naresh Sachdeva
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Jyotdeep Kaur
- Department of Biochemistry, PGIMER, Chandigarh, 160012, India
| | - Arunanshu Behera
- Department of General Surgery, PGIMER, Chandigarh, 160012, India
| | - Maria Luisa Brandi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50121, Italy
| | - Sudhaker Dhanwada Rao
- Bone and Mineral Research Laboratory, Henry Ford Hospital, Detroit, Michigan 48202, USA
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20
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Yuno M, Nagata S, Fujita T, Fujii H. MSCV-based retroviral plasmids expressing 3xFLAG-Sp-dCas9 for enChIP analysis. Biol Methods Protoc 2021; 6:bpab013. [PMID: 34409168 PMCID: PMC8365529 DOI: 10.1093/biomethods/bpab013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/17/2022] Open
Abstract
Engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) is a technology for purifying specific genomic regions to facilitate identification of their associated molecules, including proteins, RNAs, and other genomic regions. In enChIP, the target genomic region is tagged with engineered DNA-binding molecules, for example, a variant of the clustered regularly interspaced short palindromic repeats (CRISPR) system consisting of a guide RNA (gRNA) and a catalytically inactive form of Cas9 (dCas9). In this study, to increase the flexibility of enChIP and expand the range of target cells, we generated murine stem cell virus (MSCV)-based retroviral plasmids for expressing dCas9. We constructed MSCV-based retroviral plasmids expressing Streptococcus pyogenes dCas9 fused to a 3xFLAG-tag (3xFLAG-Sp-dCas9) and various drug resistance genes. We showed that by using these plasmids, it is feasible to purify target genomic regions with yields comparable to those reported using other systems. These systems might give enChIP users greater flexibility in choosing optimal systems for drug selection of transduced cells.
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Affiliation(s)
- Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shoko Nagata
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
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21
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Perie L, Verma N, Mueller E. The Forkhead Box Transcription Factor FoxP4 Regulates Thermogenic Programs in Adipocytes. J Lipid Res 2021;:100102. [PMID: 34384787 DOI: 10.1016/j.jlr.2021.100102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 11/23/2022] Open
Abstract
Forkhead box transcription factors have been shown to be involved in various developmental and differentiation processes. In particular, members of the FoxP family have been previously characterized in depth for their participation in the regulation of lung and neuronal cell differentiation and T-cell development and function; however, their role in adipocyte functionality has not yet been investigated. Here, we report for the first time that Forkhead box P4 (FoxP4) is expressed at high levels in subcutaneous fat depots and mature thermogenic adipocytes. Through molecular and gene expression analyses, we revealed that FoxP4 is induced in response to thermogenic stimuli, both in vivo and in isolated cells, and is regulated directly by the heat shock factor protein 1 through a heat shock response element identified in the proximal promoter region of FoxP4. Further detailed analysis involving chromatin immunoprecipitation and luciferase assays demonstrated that FoxP4 directly controls the levels of uncoupling protein 1, a key regulator of thermogenesis that uncouples fatty acid oxidation from ATP production. In addition, through our gain-of-function and loss-of-function studies, we showed that FoxP4 regulates the expression of a number of classic brown and beige fat genes and affects oxygen consumption in isolated adipocytes. Overall, our data demonstrate for the first time the novel role of FoxP4 in the regulation of thermogenic adipocyte functionality.
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22
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Lawal B, Kuo YC, Wu ATH, Huang HS. BC-N102 suppress breast cancer tumorigenesis by interfering with cell cycle regulatory proteins and hormonal signaling, and induction of time-course arrest of cell cycle at G1/G0 phase. Int J Biol Sci 2021; 17:3224-3238. [PMID: 34421361 PMCID: PMC8375223 DOI: 10.7150/ijbs.62808] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Mechanisms of breast cancer progression and invasion, often involve alteration of hormonal signaling, and upregulation and/or activation of signal transduction pathways that input to cell cycle regulation. Herein, we describe a rationally designed first-in-class novel small molecule inhibitor for targeting oncogenic and hormonal signaling in ER-positive breast cancer. BC-N102 treatment exhibits dose-dependent cytotoxic effects against ER+ breast cancer cell lines. BC-N102 exhibited time course- and dose-dependent cell cycle arrest via downregulation of the estrogen receptor (ER), progesterone receptor (PR), androgen receptor (AR), phosphatidylinositol 3-kinase (PI3K), phosphorylated (p)-extracellular signal-regulated kinase (ERK), p-Akt, CDK2, and CDK4 while increasing p38 mitogen-activated protein kinase (MAPK), and mineralocorticoid receptor (MR) signaling in breast cancer cell line. In addition, we found that BC-N102 suppressed breast cancer tumorigenesis in vivo and prolonged the survival of animals. Our results suggest that the proper application of BC-N102 may be a beneficial chemotherapeutic strategy for ER+ breast cancer patients.
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Affiliation(s)
- Bashir Lawal
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Graduate Institute for Cancer Biology & Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Yu-Cheng Kuo
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei11031, Taiwan
- School of Post-baccalaureate Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung40402, Taiwan
| | - Alexander T H Wu
- The PhD Program of Translational Medicine, College of Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 11490, Taiwan
| | - Hsu-Shan Huang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Graduate Institute for Cancer Biology & Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 11490, Taiwan
- School of Pharmacy, National Defense Medical Center, Taipei 11490, Taiwan
- PhD Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
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23
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Abstract
Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) has become one of the most popular methods to study protein-DNA interactions and can be used, for instance, to identify the binding sites of transcription factors or to determine the distributions of histones with specific post-translational modifications throughout the genome. Although standard ChIP-seq protocols work well in most experimental systems, there are exceptions, and one of these is the popular model organism Caenorhabditis elegans. Even though this system is very amenable to genetic and cytological methods, biochemical approaches are challenging. This is due to both the animals' cuticle, which impairs lysis as well as penetration by cross-linkers, and the rather low protein and chromatin content per body weight. These issues have rendered standard ChIP-seq protocols inefficient in C. elegans and raised a need for their improvement. Here, we describe improved protocols, with the most important advances being the efficient breakage of the C. elegans cuticle by freeze-grinding and the use of a very sensitive sequencing library construction procedure, optimized for the relatively low DNA content per body weight of C. elegans. The protocols should therefore improve the reproducibility, sensitivity, and uniformity across tissues of ChIP-seq in this organism. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Growth and harvesting of synchronized Caenorhabditis elegans Basic Protocol 2: Chromatin immunoprecipitation (ChIP) Basic Protocol 3: Library construction for Illumina sequencing.
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Affiliation(s)
- Ilke Sen
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Alan Kavšek
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Christian G Riedel
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
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24
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Finn MB, Ramsey KM, Dove SL, Wessels MR. Identification of Group A Streptococcus Genes Directly Regulated by CsrRS and Novel Intermediate Regulators. mBio 2021; 12:e0164221. [PMID: 34253064 DOI: 10.1128/mBio.01642-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adaptation of group A Streptococcus (GAS) to its human host is mediated by two-component systems that transduce external stimuli to regulate bacterial physiology. Among such systems, CsrRS (also known as CovRS) is the most extensively characterized for its role in regulating ∼10% of the GAS genome, including several virulence genes. Here, we show that extracellular magnesium and the human antimicrobial peptide LL-37 have opposing effects on the phosphorylation of the response regulator CsrR by the receptor kinase CsrS. Genetic inactivation of CsrS phosphatase or kinase activity, respectively, had similar but more pronounced effects on CsrR phosphorylation compared to growth in magnesium or LL-37. These changes in CsrR phosphorylation were correlated with the repression or activation of CsrR-regulated genes as assessed by NanoString analysis. Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) revealed CsrR occupancy at CsrRS-regulated promoters and lower-affinity associations at many other locations on the GAS chromosome. Because ChIP-seq did not detect CsrR occupancy at promoters associated with some CsrR-regulated genes, we investigated whether these genes might be controlled indirectly by intermediate regulators whose expression is modulated by CsrR. Transcriptional profiling of mutant strains deficient in the expression of either of two previously uncharacterized transcription regulators in the CsrR regulon indicated that one or both proteins participated in the regulation of 22 of the 42 CsrR-regulated promoters for which no CsrR association was detected by ChIP-seq. Taken together, these results illuminate CsrRS-mediated regulation of GAS gene expression through modulation of CsrR phosphorylation, CsrR association with regulated promoters, and the control of intermediate transcription regulators. IMPORTANCE Group A Streptococcus (GAS) is an important public health threat as a cause of sore throat, skin infections, life-threatening invasive infections, and the postinfectious complications of acute rheumatic fever, a leading cause of acquired heart disease. This work characterizes CsrRS, a GAS system for the detection of environmental signals that enables adaptation of the bacteria for survival in the human throat by regulating the production of products that allow the bacteria to resist clearance by the human immune system. CsrRS consists of two proteins: CsrS, which is on the bacterial surface to detect specific stimuli, and CsrR, which receives signals from CsrS and, in response, represses or activates the expression of genes coding for proteins that enhance bacterial survival. Some of the genes regulated by CsrR encode proteins that are themselves regulators of gene expression, thereby creating a regulatory cascade.
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25
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Abstract
During retrovirus infection, a histone-free DNA copy of the viral RNA genome is synthesized and rapidly loaded with nucleosomes de novo upon nuclear entry. The potential role of viral accessory proteins in histone loading onto retroviral DNAs has not been extensively investigated. The p12 protein of Moloney murine leukemia virus (MMLV) is a virion protein that is critical for tethering the incoming viral DNA to host chromatin in the early stages of infection. Infection by virions containing a mutant p12 (PM14) defective in chromatin tethering results in the formation of viral DNAs that do not accumulate in the nucleus. In this report, we show that viral DNAs of these mutants are not loaded with histones. Moreover, the DNA genomes delivered by mutant p12 show prolonged association with viral structural proteins nucleocapsid (NC) and capsid (CA). The histone-poor viral DNA genomes do not become associated with the host RNA polymerase II machinery. These findings provide insights into fundamental aspects of retroviral biology, indicating that tethering to host chromatin by p12 and retention in the nucleus are required to allow loading of histones onto the viral DNA. IMPORTANCE Incoming retroviral DNAs are rapidly loaded with nucleosomal histones upon entry into the nucleus and before integration into the host genome. The entry of murine leukemia virus DNA into the nucleus occurs only upon dissolution of the nuclear membrane in mitosis, and retention in the nucleus requires the action of a viral protein, p12, which tethers the DNA to host chromatin. Data presented here show that the tethering activity of p12 is required for the loading of histones onto the viral DNA. p12 mutants lacking tethering activity fail to acquire histones, retain capsid and nucleocapsid proteins, and are poorly transcribed. The work defines a new requirement for a viral protein to allow chromatinization of viral DNA.
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26
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Yang J, Perez EA, Hou C, Zhang P, Van Scoyk M, Winn RA, Rong L, Liu J. Identification of the SARS-CoV-2 Entry Receptor ACE2 as a Direct Target for Transcriptional Repression by Miz1. Front Immunol 2021; 12:648815. [PMID: 34305888 PMCID: PMC8292894 DOI: 10.3389/fimmu.2021.648815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/18/2021] [Indexed: 01/16/2023] Open
Abstract
Multiple lines of evidence have demonstrated that cigarette smoke or Chronic Obstructive Pulmonary Disease upregulates angiotensin-converting enzyme 2, the cellular receptor for the entry of the severe acute respiratory syndrome coronavirus 2, which predisposes individuals to develop severe Coronavirus disease 2019. The reason for this observation is unknown. We recently reported that the loss of function of Miz1 in the lung epithelium in mice leads to a spontaneous COPD-like phenotype, associated with upregulation of angiotensin-converting enzyme 2. We also reported that cigarette smoke exposure downregulates Miz1 in lung epithelial cells and in mice, and Miz1 is also downregulated in the lungs of COPD patients. Here, we provide further evidence that Miz1 directly binds to and represses the promoter of angiotensin-converting enzyme 2 in mouse and human lung epithelial cells. Our data provide a potential molecular mechanism for the upregulation of angiotensin-converting enzyme 2 observed in smokers and COPD patients, with implication in severe Coronavirus disease 2019.
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Affiliation(s)
- Jing Yang
- Department of Surgery, College of Medicine and University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Edith A Perez
- Department of Surgery, College of Medicine and University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Changchun Hou
- Department of Surgery, College of Medicine and University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Pin Zhang
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Michelle Van Scoyk
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Robert A Winn
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Jing Liu
- Department of Surgery, College of Medicine and University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, United States
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27
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Toledo EM, Yang S, Gyllborg D, van Wijk KE, Sinha I, Varas-Godoy M, Grigsby CL, Lönnerberg P, Islam S, Steffensen KR, Linnarsson S, Arenas E. Srebf1 Controls Midbrain Dopaminergic Neurogenesis. Cell Rep 2021; 31:107601. [PMID: 32375051 DOI: 10.1016/j.celrep.2020.107601] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 02/17/2020] [Accepted: 04/10/2020] [Indexed: 12/20/2022] Open
Abstract
Liver X receptors (LXRs) and their ligands are potent regulators of midbrain dopaminergic (mDA) neurogenesis and differentiation. However, the molecular mechanisms by which LXRs control these functions remain to be elucidated. Here, we perform a combined transcriptome and chromatin immunoprecipitation sequencing (ChIP-seq) analysis of midbrain cells after LXR activation, followed by bioinformatic analysis to elucidate the transcriptional networks controlling mDA neurogenesis. Our results identify the basic helix-loop-helix transcription factor sterol regulatory element binding protein 1 (SREBP1) as part of a cluster of proneural transcription factors in radial glia and as a regulator of transcription factors controlling mDA neurogenesis, such as Foxa2. Moreover, loss- and gain-of-function experiments in vitro and in vivo demonstrate that Srebf1 is both required and sufficient for mDA neurogenesis. Our data, thus, identify Srebf1 as a central player in mDA neurogenesis.
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Affiliation(s)
- Enrique M Toledo
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Shanzheng Yang
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Daniel Gyllborg
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Kim E van Wijk
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Indranil Sinha
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Manuel Varas-Godoy
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Christopher L Grigsby
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden; Division of Biomaterials, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Peter Lönnerberg
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Saiful Islam
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Knut R Steffensen
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Ernest Arenas
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden.
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28
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Monteiro FA, Miranda RM, Samina MC, Dias AF, Raposo AASF, Oliveira P, Reguenga C, Castro DS, Lima D. Tlx3 Exerts Direct Control in Specifying Excitatory Over Inhibitory Neurons in the Dorsal Spinal Cord. Front Cell Dev Biol 2021; 9:642697. [PMID: 33996801 PMCID: PMC8117147 DOI: 10.3389/fcell.2021.642697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/30/2021] [Indexed: 11/28/2022] Open
Abstract
The spinal cord dorsal horn is a major station for integration and relay of somatosensory information and comprises both excitatory and inhibitory neuronal populations. The homeobox gene Tlx3 acts as a selector gene to control the development of late-born excitatory (dILB) neurons by specifying glutamatergic transmitter fate in dorsal spinal cord. However, since Tlx3 direct transcriptional targets remain largely unknown, it remains to be uncovered how Tlx3 functions to promote excitatory cell fate. Here we combined a genomics approach based on chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) and expression profiling, with validation experiments in Tlx3 null embryos, to characterize the transcriptional program of Tlx3 in mouse embryonic dorsal spinal cord. We found most dILB neuron specific genes previously identified to be directly activated by Tlx3. Surprisingly, we found Tlx3 also directly represses many genes associated with the alternative inhibitory dILA neuronal fate. In both cases, direct targets include transcription factors and terminal differentiation genes, showing that Tlx3 directly controls cell identity at distinct levels. Our findings provide a molecular frame for the master regulatory role of Tlx3 in developing glutamatergic dILB neurons. In addition, they suggest a novel function for Tlx3 as direct repressor of GABAergic dILA identity, pointing to how generation of the two alternative cell fates being tightly coupled.
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Affiliation(s)
- Filipe A Monteiro
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Rafael M Miranda
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Marta C Samina
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Ana F Dias
- Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Alexandre A S F Raposo
- Molecular Neurobiology Group, Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Patrícia Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Diagnostics, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Carlos Reguenga
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Diogo S Castro
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Molecular Neurobiology Group, Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Stem Cells & Neurogenesis Group, Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - Deolinda Lima
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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29
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Keller CA, Wixom AQ, Heuston EF, Giardine B, Hsiung CCS, Long MR, Miller A, Anderson SM, Cockburn A, Blobel GA, Bodine DM, Hardison RC. Effects of sheared chromatin length on ChIP-seq quality and sensitivity. G3 (Bethesda) 2021; 11:6206780. [PMID: 33788948 PMCID: PMC8495733 DOI: 10.1093/g3journal/jkab101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 03/26/2021] [Indexed: 01/22/2023]
Abstract
Chromatin immunoprecipitation followed by massively parallel, high throughput sequencing (ChIP-seq) is the method of choice for genome-wide identification of DNA segments bound by specific transcription factors or in chromatin with particular histone modifications. However, the quality of ChIP-seq datasets varies widely, with a substantial fraction being of intermediate to poor quality. Thus, it is important to discern and control the factors that contribute to variation in ChIP-seq. In this study, we focused on sonication, a user-controlled variable, to produce sheared chromatin. We systematically varied the amount of shearing of fixed chromatin from a mouse erythroid cell line, carefully measuring the distribution of resultant fragment lengths prior to ChIP-seq. This systematic study was complemented with a retrospective analysis of additional experiments. We found that the level of sonication had a pronounced impact on the quality of ChIP-seq signals. Over-sonication consistently reduced quality, while the impact of under-sonication differed among transcription factors, with no impact on sites bound by CTCF but frequently leading to the loss of sites occupied by TAL1 or bound by POL2. The bound sites not observed in low quality datasets were inferred to be a mix of both direct and indirect binding. We leveraged these findings to produce a set of CTCF ChIP-seq datasets in rare, primary hematopoietic progenitor cells. Our observation that the amount of chromatin sonication is a key variable in success of ChIP-seq experiments indicates that monitoring the level of sonication can improve ChIP-seq quality and reproducibility and facilitate ChIP-seq in rare cell types.
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Affiliation(s)
- Cheryl A Keller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Alexander Q Wixom
- Mayo Clinic, Department of Gastroenterology and Hepatology , Rochester, MN 55905, USA
| | - Elisabeth F Heuston
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chris C-S Hsiung
- Department of Pathology, Stanford University School of Medicine, CA 94305, USA.,Department of Urology, University of California, CA 94158, USA
| | - Maria R Long
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Amber Miller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Stacie M Anderson
- NHGRI Flow Cytometry Core, National Institutes of Health, Bethesda, MD 20882, USA
| | - April Cockburn
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David M Bodine
- NHGRI Hematopoiesis Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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30
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Johnson TA, Paakinaho V, Kim S, Hager GL, Presman DM. Genome-wide binding potential and regulatory activity of the glucocorticoid receptor's monomeric and dimeric forms. Nat Commun 2021; 12:1987. [PMID: 33790284 DOI: 10.1038/s41467-021-22234-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/05/2021] [Indexed: 02/01/2023] Open
Abstract
A widely regarded model for glucocorticoid receptor (GR) action postulates that dimeric binding to DNA regulates unfavorable metabolic pathways while monomeric receptor binding promotes repressive gene responses related to its anti-inflammatory effects. This model has been built upon the characterization of the GRdim mutant, reported to be incapable of DNA binding and dimerization. Although quantitative live-cell imaging data shows GRdim as mostly dimeric, genomic studies based on recovery of enriched half-site response elements suggest monomeric engagement on DNA. Here, we perform genome-wide studies on GRdim and a constitutively monomeric mutant. Our results show that impairing dimerization affects binding even to open chromatin. We also find that GRdim does not exclusively bind half-response elements. Our results do not support a physiological role for monomeric GR and are consistent with a common mode of receptor binding via higher order structures that drives both the activating and repressive actions of glucocorticoids.
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31
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Kutashev KO, Franek M, Diamanti K, Komorowski J, Olšinová M, Dvořáčková M. Nucleolar rDNA folds into condensed foci with a specific combination of epigenetic marks. Plant J 2021; 105:1534-1548. [PMID: 33314374 DOI: 10.1111/tpj.15130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/30/2020] [Indexed: 05/15/2023]
Abstract
Arabidopsis thaliana 45S ribosomal genes (rDNA) are located in tandem arrays called nucleolus organizing regions on the termini of chromosomes 2 and 4 (NOR2 and NOR4) and encode rRNA, a crucial structural element of the ribosome. The current model of rDNA organization suggests that inactive rRNA genes accumulate in the condensed chromocenters in the nucleus and at the nucleolar periphery, while the nucleolus delineates active genes. We challenge the perspective that all intranucleolar rDNA is active by showing that a subset of nucleolar rDNA assembles into condensed foci marked by H3.1 and H3.3 histones that also contain the repressive H3K9me2 histone mark. By using plant lines containing a low number of rDNA copies, we further found that the condensed foci relate to the folding of rDNA, which appears to be a common mechanism of rDNA regulation inside the nucleolus. The H3K9me2 histone mark found in condensed foci represents a typical modification of bulk inactive rDNA, as we show by genome-wide approaches, similar to the H2A.W histone variant. The euchromatin histone marks H3K27me3 and H3K4me3, in contrast, do not colocalize with nucleolar foci and their overall levels in the nucleolus are very low. We further demonstrate that the rDNA promoter is an important regulatory region of the rDNA, where the distribution of histone variants and histone modifications are modulated in response to rDNA activity.
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Affiliation(s)
- Konstantin O Kutashev
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 61137, Czech Republic
| | - Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Klev Diamanti
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 751 08, Sweden
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, 012-48, Poland
| | - Marie Olšinová
- BioCEV Imaging Methods Core Facility, Průmyslová 595, Vestec, 252 50, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
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32
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von Scheidt M, Zhao Y, de Aguiar Vallim TQ, Che N, Wierer M, Seldin MM, Franzén O, Kurt Z, Pang S, Bongiovanni D, Yamamoto M, Edwards PA, Ruusalepp A, Kovacic JC, Mann M, Björkegren JLM, Lusis AJ, Yang X, Schunkert H. Transcription Factor MAFF (MAF Basic Leucine Zipper Transcription Factor F) Regulates an Atherosclerosis Relevant Network Connecting Inflammation and Cholesterol Metabolism. Circulation 2021; 143:1809-1823. [PMID: 33626882 DOI: 10.1161/circulationaha.120.050186] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Coronary artery disease (CAD) is a multifactorial condition with both genetic and exogenous causes. The contribution of tissue-specific functional networks to the development of atherosclerosis remains largely unclear. The aim of this study was to identify and characterize central regulators and networks leading to atherosclerosis. METHODS Based on several hundred genes known to affect atherosclerosis risk in mouse (as demonstrated in knockout models) and human (as shown by genome-wide association studies), liver gene regulatory networks were modeled. The hierarchical order and regulatory directions of genes within the network were based on Bayesian prediction models, as well as experimental studies including chromatin immunoprecipitation DNA-sequencing, chromatin immunoprecipitation mass spectrometry, overexpression, small interfering RNA knockdown in mouse and human liver cells, and knockout mouse experiments. Bioinformatics and correlation analyses were used to clarify associations between central genes and CAD phenotypes in both human and mouse. RESULTS The transcription factor MAFF (MAF basic leucine zipper transcription factor F) interacted as a key driver of a liver network with 3 human genes at CAD genome-wide association studies loci and 11 atherosclerotic murine genes. Most importantly, expression levels of the low-density lipoprotein receptor (LDLR) gene correlated with MAFF in 600 CAD patients undergoing bypass surgery (STARNET [Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task]) and a hybrid mouse diversity panel involving 105 different inbred mouse strains. Molecular mechanisms of MAFF were tested in noninflammatory conditions and showed positive correlation between MAFF and LDLR in vitro and in vivo. Interestingly, after lipopolysaccharide stimulation (inflammatory conditions), an inverse correlation between MAFF and LDLR in vitro and in vivo was observed. Chromatin immunoprecipitation mass spectrometry revealed that the human CAD genome-wide association studies candidate BACH1 (BTB domain and CNC homolog 1) assists MAFF in the presence of lipopolysaccharide stimulation with respective heterodimers binding at the MAF recognition element of the LDLR promoter to transcriptionally downregulate LDLR expression. CONCLUSIONS The transcription factor MAFF was identified as a novel central regulator of an atherosclerosis/CAD-relevant liver network. MAFF triggered context-specific expression of LDLR and other genes known to affect CAD risk. Our results suggest that MAFF is a missing link between inflammation, lipid and lipoprotein metabolism, and a possible treatment target.
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Affiliation(s)
- Moritz von Scheidt
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (M.v.S., S.P., H.S.).,Deutsches Zentrum für Herz- und Kreislauferkrankungen, Partner Site Munich Heart Alliance, Germany (M.v.S., D.B., H.S.)
| | | | - Thomas Q de Aguiar Vallim
- Departments of Medicine (T.Q.d.A.V., N.C., P.A.E., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Biological Chemistry (T.Q.d.A.V., P.A.E.), David Geffen School of Medicine, University of California, Los Angeles
| | - Nam Che
- Departments of Medicine (T.Q.d.A.V., N.C., P.A.E., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Microbiology, Immunology and Molecular Genetics (N.C., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Human Genetics (N.C., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany (M.W., M.M.)
| | - Marcus M Seldin
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, Irvine (M.M.S.)
| | - Oscar Franzén
- Integrated Cardio Metabolic Centre, Karolinska Institutet, Novum, Huddinge, Sweden (O.F., J.L.M.B.)
| | - Zeyneb Kurt
- Department of Computer and Information Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom (Z.K.)
| | - Shichao Pang
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (M.v.S., S.P., H.S.)
| | - Dario Bongiovanni
- Deutsches Zentrum für Herz- und Kreislauferkrankungen, Partner Site Munich Heart Alliance, Germany (M.v.S., D.B., H.S.).,Department of Internal Medicine, School of Medicine, University Hospital Rechts der Isar, Technical University of Munich, Germany (D.B.)
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan (M.Y.)
| | - Peter A Edwards
- Departments of Medicine (T.Q.d.A.V., N.C., P.A.E., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Biological Chemistry (T.Q.d.A.V., P.A.E.), David Geffen School of Medicine, University of California, Los Angeles
| | - Arno Ruusalepp
- Department of Cardiac Surgery, Tartu University Hospital, Estonia (A.R.).,Clinical Gene Networks AB, Stockholm, Sweden (A.R., J.L.M.B.)
| | - Jason C Kovacic
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York (J.C.K., J.L.M.B.)
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany (M.W., M.M.)
| | - Johan L M Björkegren
- Integrated Cardio Metabolic Centre, Karolinska Institutet, Novum, Huddinge, Sweden (O.F., J.L.M.B.).,Clinical Gene Networks AB, Stockholm, Sweden (A.R., J.L.M.B.).,Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York (J.C.K., J.L.M.B.)
| | - Aldons J Lusis
- Departments of Medicine (T.Q.d.A.V., N.C., P.A.E., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Microbiology, Immunology and Molecular Genetics (N.C., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Human Genetics (N.C., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles
| | - Xia Yang
- Department of Integrative Biology and Physiology, Institute for Quantitative and Computational Biosciences (Y.Z., X.Y.), David Geffen School of Medicine, University of California, Los Angeles
| | - Heribert Schunkert
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (M.v.S., S.P., H.S.).,Deutsches Zentrum für Herz- und Kreislauferkrankungen, Partner Site Munich Heart Alliance, Germany (M.v.S., D.B., H.S.)
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Zhong L, Liu Q, Liu Q, Zhang S, Cao Y, Yang D, Wang MW. W2476 represses TXNIP transcription via dephosphorylation of FOXO1 at Ser319. Chem Biol Drug Des 2021; 97:1089-1099. [PMID: 33560565 DOI: 10.1111/cbdd.13828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/27/2021] [Accepted: 01/31/2021] [Indexed: 12/20/2022]
Abstract
Thioredoxin-interacting protein (TXNIP) overexpression is implicated in the pathogenesis of type 2 diabetes. Previous studies have shown that a small molecule compound (W2476) was able to improve β-cell dysfunction and exert therapeutic effects in diabetic mice via repression of TXNIP signaling pathway. The impact of W2476 on TXNIP transcription was thus investigated using the chromatin immunoprecipitation method. It was found that W2476 promotes competitive binding of forkhead box O1 transcription factor (FOXO1) to the carbohydrate response element (ChoRE) sequence associated with ChoRE-binding protein (ChREBP)/Mlx interacting protein-like(Mlx) complexes. This interaction hinders the attachment of histone acetyltransferase p300 and reduces histone H4 acetylation on the TXNIP promoter, leading to decreasing TXNIP transcription.
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Affiliation(s)
- Li Zhong
- The National Center for Drug Screening, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qing Liu
- The National Center for Drug Screening, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Qiaofeng Liu
- School of Pharmacy, Fudan University, Shanghai, China
| | - Shikai Zhang
- Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yongbing Cao
- Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Dehua Yang
- The National Center for Drug Screening, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Ming-Wei Wang
- The National Center for Drug Screening, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Pharmacy, Fudan University, Shanghai, China
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34
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Slaughter MJ, Shanle EK, Khan A, Chua KF, Hong T, Boxer LD, Allis CD, Josefowicz SZ, Garcia BA, Rothbart SB, Strahl BD, Davis IJ. HDAC inhibition results in widespread alteration of the histone acetylation landscape and BRD4 targeting to gene bodies. Cell Rep 2021; 34:108638. [PMID: 33472068 DOI: 10.1016/j.celrep.2020.108638] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 09/18/2020] [Accepted: 12/21/2020] [Indexed: 12/31/2022] Open
Abstract
Histone acetylation levels are regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs) that antagonistically control the overall balance of this post-translational modification. HDAC inhibitors (HDACi) are potent agents that disrupt this balance and are used clinically to treat diseases including cancer. Despite their use, little is known about their effects on chromatin regulators, particularly those that signal through lysine acetylation. We apply quantitative genomic and proteomic approaches to demonstrate that HDACi robustly increases a low-abundance histone 4 polyacetylation state, which serves as a preferred binding substrate for several bromodomain-containing proteins, including BRD4. Increased H4 polyacetylation occurs in transcribed genes and correlates with the targeting of BRD4. Collectively, these results suggest that HDAC inhibition functions, at least in part, through expansion of a rare histone acetylation state, which then retargets lysine-acetyl readers associated with changes in gene expression, partially mimicking the effect of bromodomain inhibition.
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35
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Whongsiri P, Goering W, Lautwein T, Hader C, Niegisch G, Köhrer K, Hoffmann MJ, Schulz WA. Many Different LINE-1 Retroelements Are Activated in Bladder Cancer. Int J Mol Sci 2020; 21:E9433. [PMID: 33322422 DOI: 10.3390/ijms21249433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 11/17/2022] Open
Abstract
Human genomes contain about 100,000 LINE-1 (L1) retroelements, of which more than 100 are intact. L1s are normally tightly controlled by epigenetic mechanisms, which often fail in cancer. In bladder urothelial carcinoma (UC), particularly, L1s become DNA-hypomethylated, expressed and contribute to genomic instability and tumor growth. It is, however, unknown which individual L1s are activated. Following RNA-immunoprecipitation with a L1-specific antibody, third generation nanopore sequencing detected transcripts of 90 individual elements in the VM-Cub-1 UC line with high overall L1 expression. In total, 10 L1s accounted for >60% of the reads. Analysis of five specific L1s by RT-qPCR revealed generally increased expression in UC tissues and cell lines over normal controls, but variable expression among tumor cell lines from bladder, prostate and testicular cancer. Chromatin immunoprecipitation demonstrated active histone marks at L1 sequences with increased expression in VM-Cub-1, but not in a different UC cell line with low L1 expression. We conclude that many L1 elements are epigenetically activated in bladder cancer in a varied pattern. Our findings indicate that expression of individual L1s is highly heterogeneous between and among cancer types.
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36
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Ruspita I, Das P, Xia Y, Kelangi S, Miyoshi K, Noma T, Snead ML, D'Souza RN, Bei M. An Msx2- Sp6-Follistatin Pathway Operates During Late Stages of Tooth Development to Control Amelogenesis. Front Physiol 2020; 11:582610. [PMID: 33192593 PMCID: PMC7649293 DOI: 10.3389/fphys.2020.582610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
Background Ameloblasts are epithelially derived cells responsible for enamel formation through a process known as amelogenesis. Amongst the several transcription factors that are expressed during amelogenesis, both Msx2 and Sp6 transcription factors play important role. Msx2 and Sp6 mouse mutants, exhibit similar amelogenesis defects, namely enamel hypoplasia, while humans with amelogenesis imperfecta (AI) carry mutations in the human homologues of MSX2 or SP6 genes. These across species similarities in function indicate that these two transcription factors may reside in the same developmental pathway. In this paper, we test whether they work in a coordinated manner to exert their effect during amelogenesis. Methods Two different dental epithelial cell lines, the mouse LS8 and the rat G5 were used for either overexpression or silencing of Msx2 or Sp6 or both. Msx2 mutant mouse embryos or pups were used for in vivo studies. In situ hybridization, semi-quantitative and quantitative real time PCR were employed to study gene expression pattern. MatInspector was used to identify several potential putative Msx2 binding sites upstream of the murine Sp6 promoter region. Chromatin Immunoprecipitation (chIP) was used to confirm the binding of Msx2 to Sp6 promoter at the putative sites. Results Using the above methods we identified that (i) Msx2 and Sp6 exhibit overlapping expression in secretory ameloblasts, (ii) Sp6 expression is reduced in the Msx2 mouse mutant secretoty ameloblasts, and (iii) that Msx2, like Sp6 inhibits follistatin expression. Specifically, our loss-of function studies by silencing Msx2 and/or Sp6 in mouse dental epithelial (LS8) cells showed significant downregulation of Sp6 but upregulation of Fst expression. Transient transfection of Msx2 overexpression plasmid, up-regulated Sp6 and downregulated Fst expression. Additionally, using MatInspector, we identified several potential putative Msx2 binding sites, 3.5 kb upstream of the murine Sp6 promoter region. By chIP, we confirmed the binding of Msx2 to Sp6 promoter at these sites, thus suggesting that Sp6 is a direct target of Msx2. Conclusion Collectively, these results show that Sp6 and Msx2 work in a concerted manner to form part of a network of transcription factors that operate during later stages of tooth development controlling ameloblast life cycle and amelogenesis.
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Affiliation(s)
- Intan Ruspita
- Center for Regenerative and Developmental Biology, The Forsyth Institute, Cambridge, MA, United States.,Department of Prosthodontics, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Pragnya Das
- Center for Regenerative and Developmental Biology, The Forsyth Institute, Cambridge, MA, United States.,Division of Neonatology, Cooper University Hospital, Camden, NJ, United States
| | - Yan Xia
- Center for Regenerative and Developmental Biology, The Forsyth Institute, Cambridge, MA, United States
| | - Sarah Kelangi
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.,Shriners Hospital for Children, Boston, MA, United States
| | - Keiko Miyoshi
- Department of Molecular Biology, Institute of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Takafumi Noma
- Faculty of Human Life Studies, Hiroshima Jogakuin University, Hiroshima, Japan
| | - Malcolm L Snead
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA, United States
| | | | - Marianna Bei
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.,Shriners Hospital for Children, Boston, MA, United States
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37
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Tian H, Yang Z, Xu X, Liu L. [Three-dimensional chromosome conformation capture and its derived technologies]. Sheng Wu Gong Cheng Xue Bao 2020; 36:2040-2050. [PMID: 33169569 DOI: 10.13345/j.cjb.200112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Linear chromatin is compacted into eukaryotic nucleus through a complex and multi-layered architecture. Consequently, chromatin conformation in a local or long-distance manner is strongly correlated with gene expression. Chromosome conformation capture (3C) technology, together with its variants like 4C/5C/Hi-C, has been well developed to study chromatin looping and whole genome structure. In this review, we introduce new technologies including chromosome capture combined with immunoprecipitation, nuclei acid-based hybridization, single cell and genome sequencing, as well as their application.
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Affiliation(s)
- Hao Tian
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Zijian Yang
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xingwen Xu
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Liangyu Liu
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing 100048, China
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38
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Duan H, He H, Hu Q, Lin Y, Cao S, Lan X, Li L, Pang D. Comparison of regulatory networks of E74-like factor 1 and cold-shock domain-containing E1 in breast cancer cell lines using ChIP datasets. Exp Ther Med 2020; 20:245. [PMID: 33178343 PMCID: PMC7651883 DOI: 10.3892/etm.2020.9375] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 05/01/2020] [Indexed: 12/25/2022] Open
Abstract
In the present study, differences in the expression of target genes between chromatin immunoprecipitation sequencing (ChIP-seq) datasets of breast cancer MCF-7 cells treated with antibodies to E74-like factor 1 (ELF1) and cold-shock domain-containing E1 (CSDE1) were analyzed and gene regulatory networks were established. The datasets were downloaded from the Gene Expression Omnibus (GEO) database. ELF1-associated target genes and CSDE1-associated target genes were analyzed for functional prediction and protein-protein interaction (PPI) networks. The ELF1 ChIP-seq dataset contained 95 ELF1-associated target genes, while the CSDE1 ChIP-seq dataset contained 826 CSDE1-associated target genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the ELF1- and CSDE1-associated target genes had different potential functions and signaling pathways. The ELF1-associated target genes were mainly enriched in the GO terms of molecular transducer activity, catalytic activity, cellular processes and response to sensitivity, and in the KEGG pathways of olfactory transduction, the chemokine signaling pathway, carbohydrate digestion and absorption, and starch and sucrose metabolism. The CSDE1-associated target genes were mainly enriched in the GO terms of binding, transcription regulator activity, cellular processes and metabolic processes, and in the KEGG pathways of ribosome, metabolic pathways, endocytosis, oxidative phosphorylation and transcriptional misregulation in cancer. PPI network analysis revealed that the ELF1 regulatory network primarily regulated chemokine-mediated malignant tumor cells, while the CSDE1 regulatory network mainly regulated ribosomes, metabolic pathways and oxidative phosphorylation. Reverse transcription-quantitative PCR indicated that ELF1 overexpression led to significant downregulation of C-X-C motif chemokine-8 and -6 expression levels in MCF-7 cells, while overexpression of CSDE1 significantly induced the mRNA expression of CSDE1-associated target genes, which included mitochondrial ribosomal protein L4, NADH: ubiquinone oxidoreductase subunit B7, small nuclear ribonucleoprotein polypeptide E, ribosomal protein S26 (RPS26), RPS11 and RPS6, in the MCF-7 cells. In breast cancer MCF-7 cells, the target genes and regulatory pathways of ELF1 and CSDE1 were different. Understanding these regulatory pathways may help to develop strategies for personalized breast cancer treatment.
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Affiliation(s)
- Haibo Duan
- Department of Breast Cancer Medicine, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
| | - Huafang He
- Department of Radiotherapy, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
| | - Qian Hu
- Department of Breast Cancer Medicine, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
| | - Yingxin Lin
- Department of Breast Cancer Medicine, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
| | - Shuo Cao
- Department of Breast Cancer Medicine, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
| | - Xiaoshan Lan
- Department of Breast Cancer Medicine, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
| | - Litao Li
- Department of Breast Cancer Medicine, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
| | - Danmei Pang
- Department of Breast Cancer Medicine, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
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Wang X, Wei L, Yang J, Wang Y, Chen S, Yang K, Meng X, Zhang L. DNA methylation determines the regulation of pregnane X receptor on CYP3A4 expression. Clin Exp Pharmacol Physiol 2020; 48:250-259. [PMID: 33048369 DOI: 10.1111/1440-1681.13420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/22/2020] [Accepted: 10/07/2020] [Indexed: 11/30/2022]
Abstract
The expression and activity of CYP3A4 vary among individuals. With the development of epigenetics, it is now possible to elucidate interindividual differences in drug-metabolizing enzymes. Here, we aimed to explore the potential relationship between DNA methylation and CYP3A4 expression. We analyzed the effect of a DNA methylation inhibitor, 5-aza-2-deoxycytidine, on pregnane X receptor (PXR) and CYP3A4 expression in HepG2 cells. In addition, pCpGL-CYP3A4-promoter and pCpGL-CYP3A4-enhancer plus promoter plasmids were constructed, methylated, and transfected. We found that treatment with 5-aza-2-deoxycytidine significantly increased the expression of PXR and CYP3A4 in a concentration- and time-dependent manner. In addition, CYP3A4 expression was significantly enhanced by overexpressing PXR via transfection of pSG5-PXR plasmids. Methylation of CYP3A4 enhancer inhibited CYP3A4 transcriptional activity mediated through PXR and inhibited the binding of PXR and CYP3A4 promoter. We also observed that when the promoter and enhancer of CYP3A4 were methylated, CYP3A4 expression did not increase after treatment with rifampicin. In conclusion, the investigation demonstrates that DNA methylation of CYP3A4 enhancer significantly inhibits CYP3A4 expression, mediated through PXR, which is not influenced by rifampicin.
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Affiliation(s)
- Xiaofei Wang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Luman Wei
- Department of Pharmacy, Zhengzhou People's Hospital, Zhengzhou, China
| | - Jingke Yang
- Laboratory of Cardiovascular Disease and Drug Research, The 7th People's Hospital of Zhengzhou, Zhengzhou, China
| | - Yiting Wang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Shitong Chen
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Kun Yang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Xiangguang Meng
- Laboratory of Cardiovascular Disease and Drug Research, The 7th People's Hospital of Zhengzhou, Zhengzhou, China
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
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40
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Douse CH, Tchasovnikarova IA, Timms RT, Protasio AV, Seczynska M, Prigozhin DM, Albecka A, Wagstaff J, Williamson JC, Freund SMV, Lehner PJ, Modis Y. TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control. Nat Commun 2020; 11:4940. [PMID: 33009411 PMCID: PMC7532188 DOI: 10.1038/s41467-020-18761-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022] Open
Abstract
The HUSH complex represses retroviruses, transposons and genes to maintain the integrity of vertebrate genomes. HUSH regulates deposition of the epigenetic mark H3K9me3, but how its three core subunits - TASOR, MPP8 and Periphilin - contribute to assembly and targeting of the complex remains unknown. Here, we define the biochemical basis of HUSH assembly and find that its modular architecture resembles the yeast RNA-induced transcriptional silencing complex. TASOR, the central HUSH subunit, associates with RNA processing components. TASOR is required for H3K9me3 deposition over LINE-1 repeats and repetitive exons in transcribed genes. In the context of previous studies, this suggests that an RNA intermediate is important for HUSH activity. We dissect the TASOR and MPP8 domains necessary for transgene repression. Structure-function analyses reveal TASOR bears a catalytically-inactive PARP domain necessary for targeted H3K9me3 deposition. We conclude that TASOR is a multifunctional pseudo-PARP that directs HUSH assembly and epigenetic regulation of repetitive genomic targets.
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Affiliation(s)
- Christopher H Douse
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Iva A Tchasovnikarova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
- The Gurdon Institute, Cambridge, UK
| | - Richard T Timms
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
| | - Anna V Protasio
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Marta Seczynska
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
| | - Daniil M Prigozhin
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anna Albecka
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jane Wagstaff
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - James C Williamson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
| | - Stefan M V Freund
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Paul J Lehner
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK.
| | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK.
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Montagnani V, Maresca L, Apollo A, Pepe S, Carr RM, Fernandez-Zapico ME, Stecca B. E3 ubiquitin ligase PARK2, an inhibitor of melanoma cell growth, is repressed by the oncogenic ERK1/2-ELK1 transcriptional axis. J Biol Chem 2020; 295:16058-16071. [PMID: 32938713 DOI: 10.1074/jbc.ra120.014615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/09/2020] [Indexed: 12/26/2022] Open
Abstract
Malignant melanoma, the most aggressive form of skin cancer, is characterized by high prevalence of BRAF/NRAS mutations and hyperactivation of extracellular signal-regulated kinase 1 and 2 (ERK1/2), mitogen-activated protein kinases (MAPK), leading to uncontrolled melanoma growth. Efficacy of current targeted therapies against mutant BRAF or MEK1/2 have been hindered by existence of innate or development of acquired resistance. Therefore, a better understanding of the mechanisms controlled by MAPK pathway driving melanogenesis will help develop new treatment approaches targeting this oncogenic cascade. Here, we identify E3 ubiquitin ligase PARK2 as a direct target of ELK1, a known transcriptional effector of MAPK signaling in melanoma cells. We show that pharmacological inhibition of BRAF-V600E or ERK1/2 in melanoma cells increases PARK2 expression. PARK2 overexpression reduces melanoma cell growth in vitro and in vivo and induces apoptosis. Conversely, its genetic silencing increases melanoma cell proliferation and reduces cell death. Further, we demonstrate that ELK1 is required by the BRAF-ERK1/2 pathway to repress PARK2 expression and promoter activity in melanoma cells. Clinically, PARK2 is highly expressed in WT BRAF and NRAS melanomas, but it is expressed at low levels in melanomas carrying BRAF/NRAS mutations. Overall, our data provide new insights into the tumor suppressive role of PARK2 in malignant melanoma and uncover a novel mechanism for the negative regulation of PARK2 via the ERK1/2-ELK1 axis. These findings suggest that reactivation of PARK2 may be a promising therapeutic approach to counteract melanoma growth.
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Affiliation(s)
- Valentina Montagnani
- Core Research Laboratory, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy
| | - Luisa Maresca
- Core Research Laboratory, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy
| | - Alessandro Apollo
- Core Research Laboratory, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy
| | - Sara Pepe
- Core Research Laboratory, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy; Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Ryan M Carr
- Division of Oncology Research, Department of Oncology, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota USA
| | - Martin E Fernandez-Zapico
- Division of Oncology Research, Department of Oncology, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota USA
| | - Barbara Stecca
- Core Research Laboratory, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy.
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42
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Li M, Tong H, Wang S, Ye W, Li Z, Omar MAA, Ao Y, Ding S, Li Z, Wang Y, Yin C, Zhao X, He K, Liu F, Chen X, Mei Y, Walters JR, Jiang M, Li F. A chromosome-level genome assembly provides new insights into paternal genome elimination in the cotton mealybug Phenacoccus solenopsis. Mol Ecol Resour 2020; 20:1733-1747. [PMID: 33460249 DOI: 10.1111/1755-0998.13232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 11/30/2022]
Abstract
Mealybugs (Hemiptera: Pseudococcidae) are economically important agricultural pests with several compelling biological phenomena including paternal genome elimination (PGE). However, limited high-quality genome assemblies of mealybugs hinder a full understanding of this striking and unusual biological phenomenon. Here, we generated a chromosome-level genome assembly of cotton mealybug, Phenacoccus solenopsis, by combining Illumina short reads, PacBio long reads and Hi-C scaffolding. The assembled genome was 292.54 Mb with a contig N50 of 489.8 kb and a scaffold N50 of 49.0 Mb. Hi-C scaffolding assigned 84.42% of the bases to five chromosomes. A total of 110.75 Mb (37.9%) repeat sequences and 11,880 protein-coding genes were predicted. The completeness of the genome assembly was estimated to be 95.5% based on BUSCO genes. In addition, 27,086 (95.3%) full-length PacBio transcripts were uniquely mapped to the assembled scaffolds, suggesting the high quality of the genome assembly. We showed that cotton mealybugs lack differentiated sex chromosomes by analysing genome resequencing data of males and females. DAPI staining confirmed that one chromosome set in males becomes heterochromatin at an early embryo stage. Chromatin immunoprecipitation assays with sequencing analysis demonstrated that the epigenetic modifications H3K9me3 and H3K27me3 are distributed across the whole genome in males, suggesting that these two modifications might be involved in maintaining heterochromatin status. Both markers were more likely to be distributed in repeat regions, while H3K27me3 had higher overall enrichment. Our results provide a valuable genomic resource and shed new light on the genomic and epigenetic basis of PGE in cotton mealybugs.
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Affiliation(s)
- Meizhen Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haojie Tong
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuping Wang
- Technical Centre for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai, China
| | - Wanyi Ye
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zicheng Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mohamed A A Omar
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.,Department of Plant Protection, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Yan Ao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Simin Ding
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zihao Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ying Wang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chuanlin Yin
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xianxin Zhao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Feiling Liu
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xi Chen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yang Mei
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - James R Walters
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - Mingxing Jiang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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43
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Grubert F, Srivas R, Spacek DV, Kasowski M, Ruiz-Velasco M, Sinnott-Armstrong N, Greenside P, Narasimha A, Liu Q, Geller B, Sanghi A, Kulik M, Sa S, Rabinovitch M, Kundaje A, Dalton S, Zaugg JB, Snyder M. Landscape of cohesin-mediated chromatin loops in the human genome. Nature 2020; 583:737-743. [PMID: 32728247 PMCID: PMC7410831 DOI: 10.1038/s41586-020-2151-x] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/11/2019] [Indexed: 01/14/2023]
Abstract
Physical interactions between distal regulatory elements have a key role in regulating gene expression, but the extent to which these interactions vary between cell types and contribute to cell-type-specific gene expression remains unclear. Here, to address these questions as part of phase III of the Encyclopedia of DNA Elements (ENCODE), we mapped cohesin-mediated chromatin loops, using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), and analysed gene expression in 24 diverse human cell types, including core ENCODE cell lines. Twenty-eight per cent of all chromatin loops vary across cell types; these variations modestly correlate with changes in gene expression and are effective at grouping cell types according to their tissue of origin. The connectivity of genes corresponds to different functional classes, with housekeeping genes having few contacts, and dosage-sensitive genes being more connected to enhancer elements. This atlas of chromatin loops complements the diverse maps of regulatory architecture that comprise the ENCODE Encyclopedia, and will help to support emerging analyses of genome structure and function.
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Affiliation(s)
- Fabian Grubert
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Rohith Srivas
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Damek V Spacek
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Maya Kasowski
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Mariana Ruiz-Velasco
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Peyton Greenside
- Biomedical Informatics Graduate Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Anil Narasimha
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Qing Liu
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Benjamin Geller
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Akshay Sanghi
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Michael Kulik
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Silin Sa
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Palo Alto, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Marlene Rabinovitch
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Palo Alto, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Stephen Dalton
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Judith B Zaugg
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA.
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Tunjić Cvitanić M, Vojvoda Zeljko T, Pasantes JJ, García-Souto D, Gržan T, Despot-Slade E, Plohl M, Šatović E. Sequence Composition Underlying Centromeric and Heterochromatic Genome Compartments of the Pacific Oyster Crassostrea gigas. Genes (Basel) 2020; 11:genes11060695. [PMID: 32599860 PMCID: PMC7348941 DOI: 10.3390/genes11060695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/10/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023] Open
Abstract
Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere is a crucial region of eukaryotic chromosomes responsible for the accurate segregation of genetic material. The typical landmark of centromere chromatin is the rapidly-evolving variant of the histone H3, CenH3, while DNA sequences packed in constitutive heterochromatin are associated with H3K9me3-modified histones. In the Pacific oyster Crassostrea gigas we identified its centromere histone variant, Cg-CenH3, that shows stage-specific distribution in gonadal cells. In order to investigate the DNA composition of genomic regions associated with the two specific chromatin types, we employed chromatin immunoprecipitation followed by high-throughput next-generation sequencing of the Cg-CenH3- and H3K9me3-associated sequences. CenH3-associated sequences were assigned to six groups of repetitive elements, while H3K9me3-associated-ones were assigned only to three. Those associated with CenH3 indicate the lack of uniformity in the chromosomal distribution of sequences building the centromeres, being also in the same time dispersed throughout the genome. The heterochromatin of C. gigas exhibited general paucity and limited chromosomal localization as predicted, with H3K9me3-associated sequences being predominantly constituted of DNA transposons.
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Affiliation(s)
- Monika Tunjić Cvitanić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
| | - Tanja Vojvoda Zeljko
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
| | - Juan J. Pasantes
- Departamento de Bioquímica, Xenética e Inmunoloxía, Centro de Investigación Mariña (CIM), Universidade de Vigo, 36310 Vigo, Spain; (J.J.P.); (D.G.-S.)
| | - Daniel García-Souto
- Departamento de Bioquímica, Xenética e Inmunoloxía, Centro de Investigación Mariña (CIM), Universidade de Vigo, 36310 Vigo, Spain; (J.J.P.); (D.G.-S.)
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Praza do Obradoiro, 0, 15705 Santiago de Compostela, Spain
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Tena Gržan
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
| | - Evelin Despot-Slade
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
| | - Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
- Correspondence: (M.P.); (E.Š.)
| | - Eva Šatović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
- Correspondence: (M.P.); (E.Š.)
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45
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Goethe E, Laarmann K, Lührs J, Jarek M, Meens J, Lewin A, Goethe R. Critical Role of Zur and SmtB in Zinc Homeostasis of Mycobacterium smegmatis. mSystems 2020; 5:e00880-19. [PMID: 32317393 DOI: 10.1128/mSystems.00880-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Zinc homeostasis is crucial for bacterial cells, since imbalances affect viability. However, in mycobacteria, knowledge of zinc metabolism is incomplete. Mycobacterium smegmatis (MSMEG) is an environmental, nonpathogenic Mycobacterium that is widely used as a model organism to study mycobacterial metabolism and pathogenicity. How MSMEG maintains zinc homeostasis is largely unknown. SmtB and Zur are important regulators of bacterial zinc metabolism. In mycobacteria, these regulators are encoded by an operon, whereas in other bacterial species, SmtB and Zur are encoded on separate loci. Here, we show that the smtB-zur operon is consistently present within the genus Mycobacterium but otherwise found only in Nocardia, Saccharothrix, and Corynebacterium diphtheriae By RNA deep sequencing, we determined the Zur and SmtB regulons of MSMEG and compared them with transcriptional responses after zinc starvation or excess. We found an exceptional genomic clustering of genes whose expression was strongly induced by zur deletion and zinc starvation. These genes encoded zinc importers such as ZnuABC and three additional putative zinc transporters, including the porin MspD, as well as alternative ribosomal proteins. In contrast, only a few genes were affected by deletion of smtB and zinc excess. The zinc exporter ZitA was most prominently regulated by SmtB. Moreover, transcriptional analyses in combination with promoter and chromatin immunoprecipitation assays revealed a special regulation of the smtB-zur operon itself: an apparently zinc-independent, constitutive expression of smtB-zur resulted from sensitive coregulation by both SmtB and Zur. Overall, our data revealed yet unknown peculiarities of mycobacterial zinc homeostasis.IMPORTANCE Zinc is crucial for many biological processes, as it is an essential cofactor of enzymes and a structural component of regulatory and DNA binding proteins. Hence, all living cells require zinc to maintain constant intracellular levels. However, in excess, zinc is toxic. Therefore, cellular zinc homeostasis needs to be tightly controlled. In bacteria, this is achieved by transcriptional regulators whose activity is mediated via zinc-dependent conformational changes promoting or preventing their binding to DNA. SmtB and Zur are important antagonistically acting bacterial regulators in mycobacteria. They sense changes in zinc concentrations in the femtomolar range and regulate transcription of genes for zinc acquisition, storage, and export. Here, we analyzed the role of SmtB and Zur in zinc homeostasis in Mycobacterium smegmatis Our results revealed novel insights into the transcriptional processes of zinc homeostasis in mycobacteria and their regulation.
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Park JH, Park KS. SMAD3 promotes ELK3 expression following transforming growth factor β-mediated stimulation of MDA-MB231 cells. Oncol Lett 2020; 19:2749-2754. [PMID: 32218827 PMCID: PMC7068580 DOI: 10.3892/ol.2020.11375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/19/2019] [Indexed: 12/05/2022] Open
Abstract
Transforming growth factor-β (TGFβ) is a secreted cytokine whose aberrant spatiotemporal expression is related to cancer progression and metastasis. While TGFβ acts as a tumor suppressor in normal and premalignant stages, TGFβ functions as a tumor promoter during the malignant phases of tumor progression by prompting cancer cells to undergo epithelial-mesenchymal transition (EMT), which enhances tumor cell invasion and ultimately promotes metastasis to other organs. Extensive studies have been performed to uncover the molecular and cellular mechanisms underlying TGFβ inducing EMT in cancer cells. Here, we suggested that ELK3, which encodes a protein that orchestrates invasion and metastasis of triple negative breast cancer cells, is a downstream target of TGFβ-SMAD3 in MDA-MB231 cells. ELK3 expression was increased in a time-dependent manner upon TGFβ treatment. Chemical and molecular inhibition of the TGFβ receptor blocked the ability of TGFβ to induce ELK3 expression. Small interfering RNA-mediated suppression analysis revealed that SMAD3 induces TGFβ signaling to express ELK3. Moreover, the results of the luciferase reporter assay and chromatin immunoprecipitation analysis showed that SMAD3 directly binds to the SMAD-binding element on the promoter of ELK3 to activate gene expression following TGFβ stimulation. We concluded that ELK3 is a novel downstream target of TGFβ-SMAD3 signaling in aggressive breast cancer cells.
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Affiliation(s)
- Ji-Hoon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do 463-400, Republic of Korea
| | - Kyung-Soon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do 463-400, Republic of Korea
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Crespo-Salvador Ó, Sánchez-Giménez L, López-Galiano MJ, Fernández-Crespo E, Schalschi L, García-Robles I, Rausell C, Real MD, González-Bosch C. The Histone Marks Signature in Exonic and Intronic Regions Is Relevant in Early Response of Tomato Genes to Botrytis cinerea and in miRNA Regulation. Plants (Basel) 2020; 9:plants9030300. [PMID: 32121544 PMCID: PMC7154849 DOI: 10.3390/plants9030300] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 12/31/2022]
Abstract
Research into the relationship between epigenetic regulation and resistance to biotic stresses provides alternatives for plant protection and crop improvement. To unravel the mechanisms underlying tomato responses to Botrytis cinerea, we performed a chromatin immunoprecipitation (ChIP) analysis showing the increase in H3K9ac mark along the early induced genes SlyDES, SlyDOX1, and SlyLoxD encoding oxylipin-pathway enzymes, and SlyWRKY75 coding for a transcriptional regulator of hormonal signaling. This histone mark showed a more distinct distribution than the previously studied H3K4me3. The RNAPol-ChIP analysis reflected the actual gene transcription associated with increased histone modifications. A different pattern of marks in the oxylipin-related genes against P. syringae supported a pathogen-specific profile, while no significant differences occurred in SlyWRKY75. The epigenetic regulation of SlyWRKY75 by the intron-binding miR1127-3p was supported by the presence of SlyWRKY75 pre-mRNA in control plants. Interestingly, mRNA was found to be accumulated in response to B. cinerea and P. syringae, while reduction in miRNA only occurred against B. cinerea. The intronic region presented a similar pattern of marks than the rest of the gene in both pathosystems, except for H3K4me3 in the miRNA binding site upon B. cinerea. We located the gene encoding Sly-miR1127-3p, which presented reduced H3K4me3 on its promoter against B. cinerea.
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Affiliation(s)
- Óscar Crespo-Salvador
- Department of Biochemistry and Molecular Biology, University of Valencia, Agrochemical and Food Technology Institute (CSIC), 46980 Paterna, Valencia, Spain; (Ó.C.-S.); (L.S.-G.)
| | - Lorena Sánchez-Giménez
- Department of Biochemistry and Molecular Biology, University of Valencia, Agrochemical and Food Technology Institute (CSIC), 46980 Paterna, Valencia, Spain; (Ó.C.-S.); (L.S.-G.)
| | - Mª José López-Galiano
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (M.J.L.-G.); (I.G.-R.); (C.R.); (M.D.R.)
| | - Emma Fernández-Crespo
- Plant Physiology Area, Biochemistry and Biotechnology Group, Department CAMN, University Jaume I, 12071 Castellón, Spain; (E.F.-C.); (L.S.)
| | - Loredana Schalschi
- Plant Physiology Area, Biochemistry and Biotechnology Group, Department CAMN, University Jaume I, 12071 Castellón, Spain; (E.F.-C.); (L.S.)
| | - Inmaculada García-Robles
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (M.J.L.-G.); (I.G.-R.); (C.R.); (M.D.R.)
| | - Carolina Rausell
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (M.J.L.-G.); (I.G.-R.); (C.R.); (M.D.R.)
| | - M Dolores Real
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (M.J.L.-G.); (I.G.-R.); (C.R.); (M.D.R.)
| | - Carmen González-Bosch
- Department of Biochemistry and Molecular Biology, University of Valencia, Agrochemical and Food Technology Institute (CSIC), 46980 Paterna, Valencia, Spain; (Ó.C.-S.); (L.S.-G.)
- Correspondence: ; Tel.: +34-963900022
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Kim KD, Tanizawa H, De Leo A, Vladimirova O, Kossenkov A, Lu F, Showe LC, Noma KI, Lieberman PM. Epigenetic specifications of host chromosome docking sites for latent Epstein-Barr virus. Nat Commun 2020; 11:877. [PMID: 32054837 PMCID: PMC7018943 DOI: 10.1038/s41467-019-14152-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 12/07/2019] [Indexed: 12/12/2022] Open
Abstract
Epstein-Barr virus (EBV) genomes persist in latently infected cells as extrachromosomal episomes that attach to host chromosomes through the tethering functions of EBNA1, a viral encoded sequence-specific DNA binding protein. Here we employ circular chromosome conformation capture (4C) analysis to identify genome-wide associations between EBV episomes and host chromosomes. We find that EBV episomes in Burkitt's lymphoma cells preferentially associate with cellular genomic sites containing EBNA1 binding sites enriched with B-cell factors EBF1 and RBP-jK, the repressive histone mark H3K9me3, and AT-rich flanking sequence. These attachment sites correspond to transcriptionally silenced genes with GO enrichment for neuronal function and protein kinase A pathways. Depletion of EBNA1 leads to a transcriptional de-repression of silenced genes and reduction in H3K9me3. EBV attachment sites in lymphoblastoid cells with different latency type show different correlations, suggesting that host chromosome attachment sites are functionally linked to latency type gene expression programs.
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MESH Headings
- Attachment Sites, Microbiological/genetics
- Attachment Sites, Microbiological/physiology
- Burkitt Lymphoma/genetics
- Burkitt Lymphoma/virology
- Cell Line, Tumor
- Chromosomes, Human/genetics
- Chromosomes, Human/virology
- Epigenesis, Genetic
- Epstein-Barr Virus Nuclear Antigens/physiology
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/pathogenicity
- Herpesvirus 4, Human/physiology
- Host Microbial Interactions/genetics
- Host Microbial Interactions/physiology
- Humans
- Models, Biological
- Plasmids/genetics
- Virus Latency/genetics
- Virus Latency/physiology
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Affiliation(s)
- Kyoung-Dong Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Korea
| | - Hideki Tanizawa
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | - Alessandra De Leo
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19146, USA
| | - Olga Vladimirova
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19146, USA
| | - Andrew Kossenkov
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19146, USA
| | - Fang Lu
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19146, USA
| | - Louise C Showe
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19146, USA
| | - Ken-Ichi Noma
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | - Paul M Lieberman
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19146, USA.
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49
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Ma T, Ye Z, Wang L. Genome Wide Approaches to Identify Protein-DNA Interactions. Curr Med Chem 2020; 26:7641-7654. [PMID: 29848263 DOI: 10.2174/0929867325666180530115711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 02/27/2018] [Accepted: 05/11/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Transcription factors are DNA-binding proteins that play key roles in many fundamental biological processes. Unraveling their interactions with DNA is essential to identify their target genes and understand the regulatory network. Genome-wide identification of their binding sites became feasible thanks to recent progress in experimental and computational approaches. ChIP-chip, ChIP-seq, and ChIP-exo are three widely used techniques to demarcate genome-wide transcription factor binding sites. OBJECTIVE This review aims to provide an overview of these three techniques including their experiment procedures, computational approaches, and popular analytic tools. CONCLUSION ChIP-chip, ChIP-seq, and ChIP-exo have been the major techniques to study genome- wide in vivo protein-DNA interaction. Due to the rapid development of next-generation sequencing technology, array-based ChIP-chip is deprecated and ChIP-seq has become the most widely used technique to identify transcription factor binding sites in genome-wide. The newly developed ChIP-exo further improves the spatial resolution to single nucleotide. Numerous tools have been developed to analyze ChIP-chip, ChIP-seq and ChIP-exo data. However, different programs may employ different mechanisms or underlying algorithms thus each will inherently include its own set of statistical assumption and bias. So choosing the most appropriate analytic program for a given experiment needs careful considerations. Moreover, most programs only have command line interface so their installation and usage will require basic computation expertise in Unix/Linux.
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Affiliation(s)
- Tao Ma
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, United States
| | - Zhenqing Ye
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, United States
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, United States
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50
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Cheedipudi SM, Matkovich SJ, Coarfa C, Hu X, Robertson MJ, Sweet M, Taylor M, Mestroni L, Cleveland J, Willerson JT, Gurha P, Marian AJ. Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes Is Associated With Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy. Circ Res 2020; 124:1198-1213. [PMID: 30739589 DOI: 10.1161/circresaha.118.314177] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RATIONALE LMNA (Lamin A/C), a nuclear membrane protein, interacts with genome through lamin-associated domains (LADs) and regulates gene expression. Mutations in the LMNA gene cause a diverse array of diseases, including dilated cardiomyopathy (DCM). DCM is the leading cause of death in laminopathies. OBJECTIVE To identify LADs and characterize their associations with CpG methylation and gene expression in human cardiac myocytes in DCM. METHODS AND RESULTS LMNA chromatin immunoprecipitation-sequencing, reduced representative bisulfite sequencing, and RNA-sequencing were performed in 5 control and 5 LMNA-associated DCM hearts. LADs were identified using enriched domain detector program. Genome-wide 331±77 LADs with an average size of 2.1±1.5 Mbp were identified in control human cardiac myocytes. LADs encompassed ≈20% of the genome and were predominantly located in the heterochromatin and less so in the promoter and actively transcribed regions. LADs were redistributed in DCM as evidenced by a gain of 520 and loss of 149 genomic regions. Approximately, 4500 coding genes and 800 long noncoding RNAs, whose levels correlated with the transcript levels of coding genes in cis, were differentially expressed in DCM. TP53 (tumor protein 53) was the most prominent among the dysregulated pathways. CpG sites were predominantly hypomethylated genome-wide in controls and DCM hearts, but overall CpG methylation was increased in DCM. LADs were associated with increased CpG methylation and suppressed gene expression. Integrated analysis identified genes whose expressions were regulated by LADs or CpG methylation, or by both, the latter pertained to genes involved in cell death, cell cycle, and metabolic regulation. CONCLUSIONS LADs encompass ≈20% of the genome in human cardiac myocytes comprised several hundred coding and noncoding genes. LADs are redistributed in LMNA-associated DCM in association with markedly altered CpG methylation and gene expression. Thus, LADs through genomic alterations contribute to the pathogenesis of DCM in laminopathies.
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Affiliation(s)
- Sirisha M Cheedipudi
- From the Center for Cardiovascular Genetics, Department of Medicine, Institute of Molecular Medicine, Texas Heart Institute, University of Texas Health Sciences Center at Houston (S.M.C., P.G., A.J.M.)
| | - Scot J Matkovich
- Center for Cardiovascular Research, Washington University, School of Medicine, St Louis, MO (S.J.M.)
| | | | - Xin Hu
- MD Anderson Cancer Center, Houston, TX (X.H.)
| | | | - Mary Sweet
- Division of Cardiology (M.S., M.T., L.M.), University of Colorado, Denver
| | - Matthew Taylor
- Division of Cardiology (M.S., M.T., L.M.), University of Colorado, Denver
| | - Luisa Mestroni
- Division of Cardiology (M.S., M.T., L.M.), University of Colorado, Denver
| | - Joseph Cleveland
- Division of Cardiothoracic Surgery (J.C.), University of Colorado, Denver
| | | | - Priyatansh Gurha
- From the Center for Cardiovascular Genetics, Department of Medicine, Institute of Molecular Medicine, Texas Heart Institute, University of Texas Health Sciences Center at Houston (S.M.C., P.G., A.J.M.)
| | - Ali J Marian
- From the Center for Cardiovascular Genetics, Department of Medicine, Institute of Molecular Medicine, Texas Heart Institute, University of Texas Health Sciences Center at Houston (S.M.C., P.G., A.J.M.)
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