1
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Graham MK, Xu B, Davis C, Meeker AK, Heaphy CM, Yegnasubramanian S, Dyer MA, Zeineldin M. The TERT Promoter is Polycomb-Repressed in Neuroblastoma Cells with Long Telomeres. CANCER RESEARCH COMMUNICATIONS 2024; 4:1533-1547. [PMID: 38837897 PMCID: PMC11188873 DOI: 10.1158/2767-9764.crc-22-0287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 05/04/2023] [Accepted: 05/22/2024] [Indexed: 06/07/2024]
Abstract
Acquiring a telomere maintenance mechanism is a hallmark of high-risk neuroblastoma and commonly occurs by expressing telomerase (TERT). Telomerase-negative neuroblastoma has long telomeres and utilizes the telomerase-independent alternative lengthening of telomeres (ALT) mechanism. Conversely, no discernable telomere maintenance mechanism is detected in a fraction of neuroblastoma with long telomeres. Here, we show, unlike most cancers, DNA of the TERT promoter is broadly hypomethylated in neuroblastoma. In telomerase-positive neuroblastoma cells, the hypomethylated DNA promoter is approximately 1.5 kb. The TERT locus shows active chromatin marks with low enrichment for the repressive mark, H3K27me3. MYCN, a commonly amplified oncogene in neuroblstoma, binds to the promoter and induces TERT expression. Strikingly, in neuroblastoma with long telomeres, the hypomethylated region spans the entire TERT locus, including multiple nearby genes with enrichment for the repressive H3K27me3 chromatin mark. Furthermore, subtelomeric regions showed enrichment of repressive chromatin marks in neuroblastomas with long telomeres relative to those with short telomeres. These repressive marks were even more evident at the genic loci, suggesting a telomere position effect (TPE). Inhibiting H3K27 methylation by three different EZH2 inhibitors induced the expression of TERT in cell lines with long telomeres and H3K27me3 marks in the promoter region. EZH2 inhibition facilitated MYCN binding to the TERT promoter in neuroblastoma cells with long telomeres. Taken together, these data suggest that epigenetic regulation of TERT expression differs in neuroblastoma depending on the telomere maintenance status, and H3K27 methylation is important in repressing TERT expression in neuroblastoma with long telomeres. SIGNIFICANCE The epigenetic landscape of the TERT locus is unique in neuroblastoma. The DNA at the TERT locus, unlike other cancer cells and similar to normal cells, are hypomethylated in telomerase-positive neuroblastoma cells. The TERT locus is repressed by polycomb repressive complex-2 complex in neuroblastoma cells that have long telomeres and do not express TERT. Long telomeres in neuroblastoma cells are also associated with repressive chromatin states at the chromosomal termini, suggesting TPE.
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Affiliation(s)
- Mindy K. Graham
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Christine Davis
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alan K. Meeker
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher M. Heaphy
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Srinivasan Yegnasubramanian
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michael A. Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Maged Zeineldin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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2
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Schoelz JM, Riddle NC. Functions of HP1 proteins in transcriptional regulation. Epigenetics Chromatin 2022; 15:14. [PMID: 35526078 PMCID: PMC9078007 DOI: 10.1186/s13072-022-00453-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/18/2022] [Indexed: 01/24/2023] Open
Abstract
In eukaryotes, DNA is packaged into chromatin, which presents significant barriers to transcription. Non-histone chromatin proteins such as the Heterochromatin Protein 1 (HP1) proteins are critical regulators of transcription, contributing to gene regulation through a variety of molecular mechanisms. HP1 proteins are highly conserved, and many eukaryotic genomes contain multiple HP1 genes. Given the presence of multiple HP1 family members within a genome, HP1 proteins can have unique as well as shared functions. Here, we review the mechanisms by which HP1 proteins contribute to the regulation of transcription. Focusing on the Drosophila melanogaster HP1 proteins, we examine the role of these proteins in regulating the transcription of genes, transposable elements, and piRNA clusters. In D. melanogaster, as in other species, HP1 proteins can act as transcriptional repressors and activators. The available data reveal that the precise impact of HP1 proteins on gene expression is highly context dependent, on the specific HP1 protein involved, on its protein partners present, and on the specific chromatin context the interaction occurs in. As a group, HP1 proteins utilize a variety of mechanisms to contribute to transcriptional regulation, including both transcriptional (i.e. chromatin-based) and post-transcriptional (i.e. RNA-based) processes. Despite extensive studies of this important protein family, open questions regarding their functions in gene regulation remain, specifically regarding the role of hetero- versus homodimerization and post-translational modifications of HP1 proteins.
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Affiliation(s)
- John M Schoelz
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicole C Riddle
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
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3
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El-Sappah AH, Yan K, Huang Q, Islam MM, Li Q, Wang Y, Khan MS, Zhao X, Mir RR, Li J, El-Tarabily KA, Abbas M. Comprehensive Mechanism of Gene Silencing and Its Role in Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2021; 12:705249. [PMID: 34589097 PMCID: PMC8475493 DOI: 10.3389/fpls.2021.705249] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/10/2021] [Indexed: 05/19/2023]
Abstract
Gene silencing is a negative feedback mechanism that regulates gene expression to define cell fate and also regulates metabolism and gene expression throughout the life of an organism. In plants, gene silencing occurs via transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS). TGS obscures transcription via the methylation of 5' untranslated region (5'UTR), whereas PTGS causes the methylation of a coding region to result in transcript degradation. In this review, we summarized the history and molecular mechanisms of gene silencing and underlined its specific role in plant growth and crop production.
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Affiliation(s)
- Ahmed H. El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Kuan Yan
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Qiulan Huang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
- College of Tea Science, Yibin University, Yibin, China
| | | | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yu Wang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Muhammad Sarwar Khan
- Center of Agriculture Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Xianming Zhao
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST–K), Sopore, India
| | - Jia Li
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Khaled A. El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
- Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
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4
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Modulation of telomerase expression and function by miRNAs: Anti-cancer potential. Life Sci 2020; 259:118387. [PMID: 32890603 DOI: 10.1016/j.lfs.2020.118387] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 08/24/2020] [Accepted: 08/30/2020] [Indexed: 12/11/2022]
Abstract
Telomerase is a nucleoprotein reverse transcriptase that maintains the telomere, a protective structure at the ends of the chromosome, and is active in cancer cells, stem cells, and fetal cells. Telomerase immortalizes cancer cells and induces unlimited cell division by preventing telomere shortening. Immortalized cancer cells have unlimited proliferative potential due to telomerase activity that causes tumorigenesis and malignancy. Therefore, telomerase can be a lucrative anti-cancer target. The regulation of catalytic subunit of telomerase (TERT) determines the extent of telomerase activity. miRNAs, as an endogenous regulator of gene expression, can control telomerase activity by targeting TERT mRNA. miRNAs that have a decreasing effect on TERT translation mediate modulation of telomerase activity in cancer cells by binding to TERT mRNA and regulating TERT translation. In this review, we provide an update on miRNAs that influence telomerase activity by regulation of TERT translation.
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5
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Mir SM, Samavarchi Tehrani S, Goodarzi G, Jamalpoor Z, Asadi J, Khelghati N, Qujeq D, Maniati M. Shelterin Complex at Telomeres: Implications in Ageing. Clin Interv Aging 2020; 15:827-839. [PMID: 32581523 PMCID: PMC7276337 DOI: 10.2147/cia.s256425] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/18/2020] [Indexed: 12/16/2022] Open
Abstract
Different factors influence the development and control of ageing. It is well known that progressive telomere shorting is one of the molecular mechanisms underlying ageing. The shelterin complex consists of six telomere-specific proteins which are involved in the protection of chromosome ends. More particularly, this vital complex protects the telomeres from degradation, prevents from activation of unwanted repair systems, regulates the activity of telomerase, and has a crucial role in cellular senescent and ageing-related pathologies. This review explores the organization and function of telomeric DNA along with the mechanism of telomeres during ageing, followed by a discussion of the critical role of shelterin components and their changes during ageing.
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Affiliation(s)
- Seyed Mostafa Mir
- Trauma Research Center, AJA University of Medical Sciences, Tehran, Iran.,Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Sadra Samavarchi Tehrani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Golnaz Goodarzi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Jamalpoor
- Trauma Research Center, AJA University of Medical Sciences, Tehran, Iran
| | - Jahanbakhsh Asadi
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Nafiseh Khelghati
- Department of Clinical Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Durdi Qujeq
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mahmood Maniati
- School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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6
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Lodens S, Roelants SLKW, Luyten G, Geys R, Coussement P, De Maeseneire SL, Soetaert W. Unraveling the regulation of sophorolipid biosynthesis in Starmerella bombicola. FEMS Yeast Res 2020; 20:5824630. [DOI: 10.1093/femsyr/foaa021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/22/2020] [Indexed: 01/18/2023] Open
Abstract
ABSTRACTStarmerella bombicola very efficiently produces the secondary metabolites sophorolipids (SLs). Their biosynthesis is not-growth associated and highly upregulated in the stationary phase. Despite high industrial and academic interest, the underlying regulation of SL biosynthesis remains unknown. In this paper, potential regulation of SL biosynthesis through the telomere positioning effect (TPE) was investigated, as the SL gene cluster is located adjacent to a telomere. An additional copy of this gene cluster was introduced elsewhere in the genome to investigate if this results in a decoy of regulation. Indeed, for the new strain, the onset of SL production was shifted to the exponential phase. This result was confirmed by RT-qPCR analysis. The TPE effect was further investigated by developing and applying a suitable reporter system for this non-conventional yeast, enabling non-biased comparison of gene expression between the subtelomeric CYP52M1- and the URA3 locus. This was done with a constitutive endogenous promotor (pGAPD) and one of the endogenous promotors of the SL biosynthetic gene cluster (pCYP52M1). A clear positioning effect was observed for both promotors with significantly higher GFP expression levels at the URA3 locus. No clear GFP upregulation was observed in the stationary phase for any of the new strains.
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Affiliation(s)
- Sofie Lodens
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Sophie L K W Roelants
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Goedele Luyten
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Robin Geys
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Pieter Coussement
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Sofie L De Maeseneire
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Wim Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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7
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Saravanan K, Kumar H, Chhotaray S, Preethi AL, Talokar AJ, Natarajan A, Parida S, Bhushan B, Panigrahi M. Drosophila melanogaster: a promising model system for epigenetic research. BIOL RHYTHM RES 2019. [DOI: 10.1080/09291016.2019.1685216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- K.A. Saravanan
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Supriya Chhotaray
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - A. Latha Preethi
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Amol J. Talokar
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - A. Natarajan
- Division of Animal Nutrition, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Subhashree Parida
- Division of Pharmacology and Toxicology, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
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8
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Schwartz C, Cheng JF, Evans R, Schwartz CA, Wagner JM, Anglin S, Beitz A, Pan W, Lonardi S, Blenner M, Alper HS, Yoshikuni Y, Wheeldon I. Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica. Metab Eng 2019; 55:102-110. [PMID: 31216436 DOI: 10.1016/j.ymben.2019.06.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/06/2019] [Accepted: 06/14/2019] [Indexed: 12/26/2022]
Abstract
Genome-wide mutational screens are central to understanding the genetic underpinnings of evolved and engineered phenotypes. The widespread adoption of CRISPR-Cas9 genome editing has enabled such screens in many organisms, but identifying functional sgRNAs still remains a challenge. Here, we developed a methodology to quantify the cutting efficiency of each sgRNA in a genome-scale library, and in doing so improve screens in the biotechnologically important yeast Yarrowia lipolytica. Screening in the presence and absence of native DNA repair enabled high-throughput quantification of sgRNA function leading to the identification of high efficiency sgRNAs that cover 94% of genes. Library validation enhanced the classification of essential genes by identifying inactive guides that create false negatives and mask the effects of successful disruptions. Quantification of guide effectiveness also creates a dataset from which determinants of CRISPR-Cas9 can be identified. Finally, application of the library identified novel mutations for metabolic engineering of high lipid accumulation.
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Affiliation(s)
- Cory Schwartz
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Robert Evans
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Christopher A Schwartz
- Department of Civil and Mechanical Engineering, United States Military Academy, West Point, NY, 10996, USA
| | - James M Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
| | - Scott Anglin
- Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, 29634, USA
| | - Adam Beitz
- Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, 29634, USA
| | - Weihua Pan
- Computer Science and Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Computer Science and Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Mark Blenner
- Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, 29634, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, 78712, USA
| | - Yasuo Yoshikuni
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA.
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9
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Brunner E, Yagi R, Debrunner M, Beck-Schneider D, Burger A, Escher E, Mosimann C, Hausmann G, Basler K. CRISPR-induced double-strand breaks trigger recombination between homologous chromosome arms. Life Sci Alliance 2019; 2:e201800267. [PMID: 31196871 PMCID: PMC6587125 DOI: 10.26508/lsa.201800267] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 12/27/2022] Open
Abstract
CRISPR-Cas9-based genome editing has transformed the life sciences, enabling virtually unlimited genetic manipulation of genomes: The RNA-guided Cas9 endonuclease cuts DNA at a specific target sequence and the resulting double-strand breaks are mended by one of the intrinsic cellular repair pathways. Imprecise double-strand repair will introduce random mutations such as indels or point mutations, whereas precise editing will restore or specifically edit the locus as mandated by an endogenous or exogenously provided template. Recent studies indicate that CRISPR-induced DNA cuts may also result in the exchange of genetic information between homologous chromosome arms. However, conclusive data of such recombination events in higher eukaryotes are lacking. Here, we show that in Drosophila, the detected Cas9-mediated editing events frequently resulted in germline-transmitted exchange of chromosome arms-often without indels. These findings demonstrate the feasibility of using the system for generating recombinants and also highlight an unforeseen risk of using CRISPR-Cas9 for therapeutic intervention.
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Affiliation(s)
- Erich Brunner
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ryohei Yagi
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland
| | - Marc Debrunner
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Alexa Burger
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Eliane Escher
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - George Hausmann
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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10
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Kordyukova MY, Kalmykova AI. Nature and Functions of Telomeric Transcripts. BIOCHEMISTRY (MOSCOW) 2019; 84:137-146. [DOI: 10.1134/s0006297919020044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Mills BB, Thomas AD, Riddle NC. HP1B is a euchromatic Drosophila HP1 homolog with links to metabolism. PLoS One 2018; 13:e0205867. [PMID: 30346969 PMCID: PMC6197686 DOI: 10.1371/journal.pone.0205867] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/02/2018] [Indexed: 11/30/2022] Open
Abstract
Heterochromatin Protein 1 (HP1) proteins are an important family of chromosomal proteins conserved among all major eukaryotic lineages. While HP1 proteins are best known for their role in heterochromatin, many HP1 proteins function in euchromatin as well. As a group, HP1 proteins carry out diverse functions, playing roles in the regulation of gene expression, genome stability, chromatin structure, and DNA repair. While the heterochromatic HP1 proteins are well studied, our knowledge of HP1 proteins with euchromatic distribution is lagging behind. We have created the first mutations in HP1B, a Drosophila HP1 protein with euchromatic function, and the Drosophila homolog most closely related to mammalian HP1α, HP1β, and HP1γ. We find that HP1B is a non-essential protein in Drosophila, with mutations affecting fertility and animal activity levels. In addition, animals lacking HP1B show altered food intake and higher body fat levels. Gene expression analysis of animals lacking HP1B demonstrates that genes with functions in various metabolic processes are affected primarily by HP1B loss. Our findings suggest that there is a link between the chromatin protein HP1B and the regulation of metabolism.
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Affiliation(s)
- Benjamin B. Mills
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Andrew D. Thomas
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Nicole C. Riddle
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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12
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Jamieson K, McNaught KJ, Ormsby T, Leggett NA, Honda S, Selker EU. Telomere repeats induce domains of H3K27 methylation in Neurospora. eLife 2018; 7:31216. [PMID: 29297465 PMCID: PMC5752202 DOI: 10.7554/elife.31216] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 12/18/2017] [Indexed: 12/31/2022] Open
Abstract
Development in higher organisms requires selective gene silencing, directed in part by di-/trimethylation of lysine 27 on histone H3 (H3K27me2/3). Knowledge of the cues that control formation of such repressive Polycomb domains is extremely limited. We exploited natural and engineered chromosomal rearrangements in the fungus Neurospora crassa to elucidate the control of H3K27me2/3. Analyses of H3K27me2/3 in strains bearing chromosomal rearrangements revealed both position-dependent and position-independent facultative heterochromatin. We found that proximity to chromosome ends is necessary to maintain, and sufficient to induce, transcriptionally repressive, subtelomeric H3K27me2/3. We ascertained that such telomere-proximal facultative heterochromatin requires native telomere repeats and found that a short array of ectopic telomere repeats, (TTAGGG)17, can induce a large domain (~225 kb) of H3K27me2/3. This provides an example of a cis-acting sequence that directs H3K27 methylation. Our findings provide new insight into the relationship between genome organization and control of heterochromatin formation.
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Affiliation(s)
- Kirsty Jamieson
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Kevin J McNaught
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Tereza Ormsby
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Neena A Leggett
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Shinji Honda
- Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, United States
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13
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Swenson JM, Colmenares SU, Strom AR, Costes SV, Karpen GH. The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic. eLife 2016; 5:e16096. [PMID: 27514026 PMCID: PMC4981497 DOI: 10.7554/elife.16096] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
Heterochromatin is enriched for specific epigenetic factors including Heterochromatin Protein 1a (HP1a), and is essential for many organismal functions. To elucidate heterochromatin organization and regulation, we purified Drosophila melanogaster HP1a interactors, and performed a genome-wide RNAi screen to identify genes that impact HP1a levels or localization. The majority of the over four hundred putative HP1a interactors and regulators identified were previously unknown. We found that 13 of 16 tested candidates (83%) are required for gene silencing, providing a substantial increase in the number of identified components that impact heterochromatin properties. Surprisingly, image analysis revealed that although some HP1a interactors and regulators are broadly distributed within the heterochromatin domain, most localize to discrete subdomains that display dynamic localization patterns during the cell cycle. We conclude that heterochromatin composition and architecture is more spatially complex and dynamic than previously suggested, and propose that a network of subdomains regulates diverse heterochromatin functions.
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Affiliation(s)
- Joel M Swenson
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Serafin U Colmenares
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Amy R Strom
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Sylvain V Costes
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Gary H Karpen
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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14
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Targeting of P-Element Reporters to Heterochromatic Domains by Transposable Element 1360 in Drosophila melanogaster. Genetics 2015; 202:565-82. [PMID: 26680659 DOI: 10.1534/genetics.115.183228] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/10/2015] [Indexed: 11/18/2022] Open
Abstract
Heterochromatin is a common DNA packaging form employed by eukaryotes to constitutively silence transposable elements. Determining which sequences to package as heterochromatin is vital for an organism. Here, we use Drosophila melanogaster to study heterochromatin formation, exploiting position-effect variegation, a process whereby a transgene is silenced stochastically if inserted in proximity to heterochromatin, leading to a variegating phenotype. Previous studies identified the transposable element 1360 as a target for heterochromatin formation. We use transgene reporters with either one or four copies of 1360 to determine if increasing local repeat density can alter the fraction of the genome supporting heterochromatin formation. We find that including 1360 in the reporter increases the frequency with which variegating phenotypes are observed. This increase is due to a greater recovery of insertions at the telomere-associated sequences (∼50% of variegating inserts). In contrast to variegating insertions elsewhere, the phenotype of telomere-associated sequence insertions is largely independent of the presence of 1360 in the reporter. We find that variegating and fully expressed transgenes are located in different types of chromatin and that variegating reporters in the telomere-associated sequences differ from those in pericentric heterochromatin. Indeed, chromatin marks at the transgene insertion site can be used to predict the eye phenotype. Our analysis reveals that increasing the local repeat density (via the transgene reporter) does not enlarge the fraction of the genome supporting heterochromatin formation. Rather, additional copies of 1360 appear to target the reporter to the telomere-associated sequences with greater efficiency, thus leading to an increased recovery of variegating insertions.
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15
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Habibi L, Pedram M, AmirPhirozy A, Bonyadi K. Mobile DNA Elements: The Seeds of Organic Complexity on Earth. DNA Cell Biol 2015. [DOI: 10.1089/dna.2015.2938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Laleh Habibi
- Department of Pharmaceutics, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Nutrition Department, School of Nutritional Science and Dietetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Pedram
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Akbar AmirPhirozy
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Bonyadi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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16
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Tritto P, Palumbo V, Micale L, Marzulli M, Bozzetti MP, Specchia V, Palumbo G, Pimpinelli S, Berloco M. Loss of Pol32 in Drosophila melanogaster causes chromosome instability and suppresses variegation. PLoS One 2015; 10:e0120859. [PMID: 25826374 PMCID: PMC4380491 DOI: 10.1371/journal.pone.0120859] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/27/2015] [Indexed: 11/29/2022] Open
Abstract
Pol32 is an accessory subunit of the replicative DNA Polymerase δ and of the translesion Polymerase ζ. Pol32 is involved in DNA replication, recombination and repair. Pol32’s participation in high- and low-fidelity processes, together with the phenotypes arising from its disruption, imply multiple roles for this subunit within eukaryotic cells, not all of which have been fully elucidated. Using pol32 null mutants and two partial loss-of-function alleles pol32rd1 and pol32rds in Drosophila melanogaster, we show that Pol32 plays an essential role in promoting genome stability. Pol32 is essential to ensure DNA replication in early embryogenesis and it participates in the repair of mitotic chromosome breakage. In addition we found that pol32 mutantssuppress position effect variegation, suggesting a role for Pol32 in chromatin architecture.
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Affiliation(s)
- Patrizia Tritto
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy
| | - Valeria Palumbo
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Università degli Studi di Roma “La Sapienza”, 00185 Roma, Italy
| | - Lucia Micale
- IRCCS Casa Sollievo Della Sofferenza Hospital, 71013 San Giovanni Rotondo, Italy
| | - Marco Marzulli
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, United States of America
| | - Maria Pia Bozzetti
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, 73100 Lecce, Italy
| | - Valeria Specchia
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, 73100 Lecce, Italy
| | - Gioacchino Palumbo
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy
| | - Sergio Pimpinelli
- Istituto Pasteur—Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie “C. Darwin”, Università degli Studi di Roma “La Sapienza”, 00185 Roma, Italy
| | - Maria Berloco
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy
- * E-mail:
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17
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Robin JD, Ludlow AT, Batten K, Magdinier F, Stadler G, Wagner KR, Shay JW, Wright WE. Telomere position effect: regulation of gene expression with progressive telomere shortening over long distances. Genes Dev 2015; 28:2464-76. [PMID: 25403178 PMCID: PMC4233240 DOI: 10.1101/gad.251041.114] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
While global chromatin conformation studies are emerging, very little is known about the chromatin conformation of human telomeres. Most studies have focused on the role of telomeres as a tumor suppressor mechanism. Here we describe how telomere length regulates gene expression long before telomeres become short enough to produce a DNA damage response (senescence). We directly mapped the interactions adjacent to specific telomere ends using a Hi-C (chromosome capture followed by high-throughput sequencing) technique modified to enrich for specific genomic regions. We demonstrate that chromosome looping brings the telomere close to genes up to 10 Mb away from the telomere when telomeres are long and that the same loci become separated when telomeres are short. Furthermore, expression array analysis reveals that many loci, including noncoding RNAs, may be regulated by telomere length. We report three genes (ISG15 [interferon-stimulated gene 15 kd], DSP [Desmoplakin], and C1S [complement component 1s subcomplement]) located at three different subtelomeric ends (1p, 6p, and 12p) whose expressions are altered with telomere length. Additionally, we confirmed by in situ analysis (3D-FISH [three-dimensional fluorescence in situ hybridization]) that chromosomal looping occurs between the loci of those genes and their respective telomere ends. We term this process TPE-OLD for "telomere position effect over long distances." Our results suggest a potential novel mechanism for how telomere shortening could contribute to aging and disease initiation/progression in human cells long before the induction of a critical DNA damage response.
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Affiliation(s)
- Jérôme D Robin
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Andrew T Ludlow
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Kimberly Batten
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | | | - Guido Stadler
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Kathyrin R Wagner
- Center for Genetic Muscle Disorders, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; Department of Neurology, Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Center for Excellence in Genomics Medicine Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Woodring E Wright
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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18
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Anderson MZ, Gerstein AC, Wigen L, Baller JA, Berman J. Silencing is noisy: population and cell level noise in telomere-adjacent genes is dependent on telomere position and sir2. PLoS Genet 2014; 10:e1004436. [PMID: 25057900 PMCID: PMC4109849 DOI: 10.1371/journal.pgen.1004436] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/27/2014] [Indexed: 11/18/2022] Open
Abstract
Cell-to-cell gene expression noise is thought to be an important mechanism for generating phenotypic diversity. Furthermore, telomeric regions are major sites for gene amplification, which is thought to drive genetic diversity. Here we found that individual subtelomeric TLO genes exhibit increased variation in transcript and protein levels at both the cell-to-cell level as well as at the population-level. The cell-to-cell variation, termed Telomere-Adjacent Gene Expression Noise (TAGEN) was largely intrinsic noise and was dependent upon genome position: noise was reduced when a TLO gene was expressed at an ectopic internal locus and noise was elevated when a non-telomeric gene was expressed at a telomere-adjacent locus. This position-dependent TAGEN also was dependent on Sir2p, an NAD+-dependent histone deacetylase. Finally, we found that telomere silencing and TAGEN are tightly linked and regulated in cis: selection for either silencing or activation of a TLO-adjacent URA3 gene resulted in reduced noise at the neighboring TLO but not at other TLO genes. This provides experimental support to computational predictions that the ability to shift between silent and active chromatin states has a major effect on cell-to-cell noise. Furthermore, it demonstrates that these shifts affect the degree of expression variation at each telomere individually.
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Affiliation(s)
- Matthew Z. Anderson
- Department of Genetics, Cell Biology and Development, University of Minnesota – Twin Cities, Minneapolis, Minnesota, United States of America
| | - Aleeza C. Gerstein
- Department of Genetics, Cell Biology and Development, University of Minnesota – Twin Cities, Minneapolis, Minnesota, United States of America
- Department of Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Lauren Wigen
- Department of Genetics, Cell Biology and Development, University of Minnesota – Twin Cities, Minneapolis, Minnesota, United States of America
| | - Joshua A. Baller
- Department of Genetics, Cell Biology and Development, University of Minnesota – Twin Cities, Minneapolis, Minnesota, United States of America
| | - Judith Berman
- Department of Genetics, Cell Biology and Development, University of Minnesota – Twin Cities, Minneapolis, Minnesota, United States of America
- Department of Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
- * E-mail:
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19
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TCTP directly regulates ATM activity to control genome stability and organ development in Drosophila melanogaster. Nat Commun 2014; 4:2986. [PMID: 24352200 DOI: 10.1038/ncomms3986] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 11/21/2013] [Indexed: 02/03/2023] Open
Abstract
Translationally controlled tumour protein (TCTP) is implicated in growth regulation and cancer. Recently, human TCTP has been suggested to play a role in the DNA damage response by forming a complex with ataxia telangiectasia-mutated (ATM) kinase . However, the exact nature of this interaction and its roles in vivo remained unclear. Here, we utilize Drosophila as an animal model to study the nuclear function of Drosophila TCTP (dTCTP). dTCTP mutants show increased radiation sensitivity during development as well as strong genetic interaction with dATM mutations, resulting in severe defects in developmental timing, organ size and chromosome stability. We identify Drosophila ATM (dATM) as a direct binding partner of dTCTP and describe a mechanistic basis for dATM activation by dTCTP. Altogether, this study provides the first in vivo evidence for direct modulation of dATM activity by dTCTP in the control of genome stability and organ development.
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20
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Sentmanat M, Wang SH, Elgin SCR. Targeting heterochromatin formation to transposable elements in Drosophila: potential roles of the piRNA system. BIOCHEMISTRY (MOSCOW) 2014; 78:562-71. [PMID: 23980883 DOI: 10.1134/s0006297913060023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Successful heterochromatin formation is critical for genome stability in eukaryotes, both to maintain structures needed for mitosis and meiosis and to silence potentially harmful transposable elements. Conversely, inappropriate heterochromatin assembly can lead to inappropriate silencing and other deleterious effects. Hence targeting heterochromatin assembly to appropriate regions of the genome is of utmost importance. Here we focus on heterochromatin assembly in Drosophila melanogaster, the model organism in which variegation, or cell-to-cell variable gene expression resulting from heterochromatin formation, was first described. In particular, we review the potential role of transposable elements as genetic determinants of the chromatin state and examine how small RNA pathways may participate in the process of targeted heterochromatin formation.
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Affiliation(s)
- M Sentmanat
- Department of Biology, Washington University, St. Louis, MO 63130-4899, USA
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21
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Wang SH, Nan R, Accardo MC, Sentmanat M, Dimitri P, Elgin SCR. A distinct type of heterochromatin at the telomeric region of the Drosophila melanogaster Y chromosome. PLoS One 2014; 9:e86451. [PMID: 24475122 PMCID: PMC3901700 DOI: 10.1371/journal.pone.0086451] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 12/16/2013] [Indexed: 11/24/2022] Open
Abstract
Heterochromatin assembly and its associated phenotype, position effect variegation (PEV), provide an informative system to study chromatin structure and genome packaging. In the fruit fly Drosophila melanogaster, the Y chromosome is entirely heterochromatic in all cell types except the male germline; as such, Y chromosome dosage is a potent modifier of PEV. However, neither Y heterochromatin composition, nor its assembly, has been carefully studied. Here, we report the mapping and characterization of eight reporter lines that show male-specific PEV. In all eight cases, the reporter insertion sites lie in the telomeric transposon array (HeT-A and TART-B2 homologous repeats) of the Y chromosome short arm (Ys). Investigations of the impact on the PEV phenotype of mutations in known heterochromatin proteins (i.e., modifiers of PEV) show that this Ys telomeric region is a unique heterochromatin domain: it displays sensitivity to mutations in HP1a, EGG and SU(VAR)3-9, but no sensitivity to Su(z)2 mutations. It appears that the endo-siRNA pathway plays a major targeting role for this domain. Interestingly, an ectopic copy of 1360 is sufficient to induce a piRNA targeting mechanism to further enhance silencing of a reporter cytologically localized to the Ys telomere. These results demonstrate the diversity of heterochromatin domains, and the corresponding variation in potential targeting mechanisms.
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Affiliation(s)
- Sidney H. Wang
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Ruth Nan
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Maria C. Accardo
- Dipartimento di Biologia e Biotecnologie “Charles Darwin” and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, Roma, Italy
| | - Monica Sentmanat
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Patrizio Dimitri
- Dipartimento di Biologia e Biotecnologie “Charles Darwin” and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, Roma, Italy
| | - Sarah C. R. Elgin
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
- * E-mail:
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22
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Wyse BA, Oshidari R, Jeffery DC, Yankulov KY. Parasite epigenetics and immune evasion: lessons from budding yeast. Epigenetics Chromatin 2013; 6:40. [PMID: 24252437 PMCID: PMC3843538 DOI: 10.1186/1756-8935-6-40] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/11/2013] [Indexed: 11/23/2022] Open
Abstract
The remarkable ability of many parasites to evade host immunity is the key to their success and pervasiveness. The immune evasion is directly linked to the silencing of the members of extended families of genes that encode for major parasite antigens. At any time only one of these genes is active. Infrequent switches to other members of the gene family help the parasites elude the immune system and cause prolonged maladies. For most pathogens, the detailed mechanisms of gene silencing and switching are poorly understood. On the other hand, studies in the budding yeast Saccharomyces cerevisiae have revealed similar mechanisms of gene repression and switching and have provided significant insights into the molecular basis of these phenomena. This information is becoming increasingly relevant to the genetics of the parasites. Here we summarize recent advances in parasite epigenetics and emphasize the similarities between S. cerevisiae and pathogens such as Plasmodium, Trypanosoma, Candida, and Pneumocystis. We also outline current challenges in the control and the treatment of the diseases caused by these parasites and link them to epigenetics and the wealth of knowledge acquired from budding yeast.
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Affiliation(s)
| | | | | | - Krassimir Y Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2 W1, Canada.
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23
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Vasanthi D, Nagabhushan A, Matharu NK, Mishra RK. A functionally conserved Polycomb response element from mouse HoxD complex responds to heterochromatin factors. Sci Rep 2013; 3:3011. [PMID: 24145990 PMCID: PMC3804862 DOI: 10.1038/srep03011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 10/04/2013] [Indexed: 12/14/2022] Open
Abstract
Anterior-posterior body axis in all bilaterians is determined by the Hox gene clusters that are activated in a spatio-temporal order. This expression pattern of Hox genes is established and maintained by regulatory mechanisms that involve higher order chromatin structure and Polycomb group (PcG) and trithorax group (trxG) proteins. We identified earlier a Polycomb response element (PRE) in the mouse HoxD complex that is functionally conserved in flies. We analyzed the molecular and genetic interactions of mouse PRE using Drosophilamelanogaster and vertebrate cell culture as the model systems. We demonstrate that the repressive activity of this PRE depends on PcG/trxG genes as well as the heterochromatin components. Our findings indicate that a wide range of factors interact with the HoxD PRE that can contribute to establishing the expression pattern of homeotic genes in the complex early during development and maintain that pattern at subsequent stages.
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Affiliation(s)
- Dasari Vasanthi
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial research, Uppal Road, Hyderabad 500007, India
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24
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Cipressa F, Cenci G. Effete, an E2 ubiquitin-conjugating enzyme with multiple roles in Drosophila development and chromatin organization. Fly (Austin) 2013; 7:256-62. [PMID: 24088712 DOI: 10.4161/fly.26567] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Drosophila effete gene encodes an extremely conserved class I E2 ubiquitin-conjugating enzyme. Growing evidence indicates that Eff is involved in many cellular processes including eye development, maintenance of female germline stem cells, and regulation of apoptosis. Eff is also a major component of Drosophila chromatin and it is particularly enriched in chromatin with repressive properties. In addition, Eff is required for telomere protection and to prevent telomere fusion. Consistent with its multiple roles in chromatin maintenance, Eff is also one of the rare factors that modulate both telomere-induced and heterochromatin-induced position effect variegation.
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Affiliation(s)
- Francesca Cipressa
- Dipartimento di Biologia e Biotecnologie "C. Darwin"; SAPIENZA Università di Roma; Roma, Italy
| | - Giovanni Cenci
- Dipartimento di Biologia e Biotecnologie "C. Darwin"; SAPIENZA Università di Roma; Roma, Italy
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25
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Jeffery DCB, Wyse BA, Rehman MA, Brown GW, You Z, Oshidari R, Masai H, Yankulov KY. Analysis of epigenetic stability and conversions in Saccharomyces cerevisiae reveals a novel role of CAF-I in position-effect variegation. Nucleic Acids Res 2013; 41:8475-88. [PMID: 23863839 PMCID: PMC3794585 DOI: 10.1093/nar/gkt623] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Position-effect variegation (PEV) phenotypes are characterized by the robust multigenerational repression of a gene located at a certain locus (often called gene silencing) and occasional conversions to fully active state. Consequently, the active state then persists with occasional conversions to the repressed state. These effects are mediated by the establishment and maintenance of heterochromatin or euchromatin structures, respectively. In this study, we have addressed an important but often neglected aspect of PEV: the frequency of conversions at such loci. We have developed a model and have projected various PEV scenarios based on various rates of conversions. We have also enhanced two existing assays for gene silencing in Saccharomyces cerevisiae to measure the rate of switches from repressed to active state and vice versa. We tested the validity of our methodology in Δsir1 cells and in several mutants with defects in gene silencing. The assays have revealed that the histone chaperone Chromatin Assembly Factor I is involved in the control of epigenetic conversions. Together, our model and assays provide a comprehensive methodology for further investigation of epigenetic stability and position effects.
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Affiliation(s)
- Daniel C B Jeffery
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada, Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada and Department of Genome Medicine, Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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26
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Effete, a Drosophila chromatin-associated ubiquitin-conjugating enzyme that affects telomeric and heterochromatic position effect variegation. Genetics 2013; 195:147-58. [PMID: 23821599 DOI: 10.1534/genetics.113.153320] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Drosophila telomeres are elongated by the transposition of telomere-specific retrotransposons rather than telomerase activity. Proximal to the terminal transposon array, Drosophila chromosomes contain several kilobases of a complex satellite DNA termed telomere-associated sequences (TASs). Reporter genes inserted into or next to the TAS are silenced through a mechanism called telomere position effect (TPE). TPE is reminiscent of the position effect variegation (PEV) induced by Drosophila constitutive heterochromatin. However, most genes that modulate PEV have no effect on TPE, and systematic searches for TPE modifiers have so far identified only a few dominant suppressors. Surprisingly, only a few of the genes required to prevent telomere fusion have been tested for their effect on TPE. Here, we show that with the exception of the effete (eff; also called UbcD1) mutant alleles, none of the tested mutations at the other telomere fusion genes affects TPE. We also found that mutations in eff, which encodes a class I ubiquitin-conjugating enzyme, act as suppressors of PEV. Thus, eff is one of the rare genes that can modulate both TPE and PEV. Immunolocalization experiments showed that Eff is a major constituent of polytene chromosomes. Eff is enriched at several euchromatic bands and interbands, the TAS regions, and the chromocenter. Our results suggest that Eff associates with different types of chromatin affecting their abilities to regulate gene expression.
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27
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Maqsood MI, Matin MM, Bahrami AR, Ghasroldasht MM. Immortality of cell lines: challenges and advantages of establishment. Cell Biol Int 2013; 37:1038-45. [PMID: 23723166 DOI: 10.1002/cbin.10137] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 05/02/2013] [Indexed: 12/29/2022]
Abstract
Cellular immortality happens upon impairment of cell-cycle checkpoint pathways (p53/p16/pRb), reactivation or up-regulation of telomerase enzyme, or upregulation of some oncogenes or oncoproteins leading to a higher rate of cell division.There are also some other factors and mechanisms involved in immortalisation, which need to be discovered. Immortalisation of cells derived from different sources and establishment of immortal cell lines has proven useful in understanding the molecular pathways governing cell developmental cascades in eukaryotic, especially human, cells. After the breakthrough of achieving the immortal cells and understanding their critical importance in the field of molecular biology, intense efforts have been dedicated to establish cell lines useful for elucidating the functions of telomerase, developmental lineage of progenitors, self-renewal potency, cellular transformation, differentiation patterns and some bioprocesses, like odontogenesis. Meanwhile, discovering the exact mechanisms of immortality, a major challenge for science yet, is believed to open new gateways toward understanding and treatment of cancer in the long term. This review summarises the methods involved in establishing immortality, its advantages and the challenges still being faced in this field.
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Affiliation(s)
- Muhammad Irfan Maqsood
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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28
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Levine MT, McCoy C, Vermaak D, Lee YCG, Hiatt MA, Matsen FA, Malik HS. Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1) gene family. PLoS Genet 2012; 8:e1002729. [PMID: 22737079 PMCID: PMC3380853 DOI: 10.1371/journal.pgen.1002729] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 04/10/2012] [Indexed: 01/12/2023] Open
Abstract
Heterochromatin is the gene-poor, satellite-rich eukaryotic genome compartment that supports many essential cellular processes. The functional diversity of proteins that bind and often epigenetically define heterochromatic DNA sequence reflects the diverse functions supported by this enigmatic genome compartment. Moreover, heterogeneous signatures of selection at chromosomal proteins often mirror the heterogeneity of evolutionary forces that act on heterochromatic DNA. To identify new such surrogates for dissecting heterochromatin function and evolution, we conducted a comprehensive phylogenomic analysis of the Heterochromatin Protein 1 gene family across 40 million years of Drosophila evolution. Our study expands this gene family from 5 genes to at least 26 genes, including several uncharacterized genes in Drosophila melanogaster. The 21 newly defined HP1s introduce unprecedented structural diversity, lineage-restriction, and germline-biased expression patterns into the HP1 family. We find little evidence of positive selection at these HP1 genes in both population genetic and molecular evolution analyses. Instead, we find that dynamic evolution occurs via prolific gene gains and losses. Despite this dynamic gene turnover, the number of HP1 genes is relatively constant across species. We propose that karyotype evolution drives at least some HP1 gene turnover. For example, the loss of the male germline-restricted HP1E in the obscura group coincides with one episode of dramatic karyotypic evolution, including the gain of a neo-Y in this lineage. This expanded compendium of ovary- and testis-restricted HP1 genes revealed by our study, together with correlated gain/loss dynamics and chromosome fission/fusion events, will guide functional analyses of novel roles supported by germline chromatin. Our genome is comprised of two compartments. The euchromatin harbors abundant genes and regulatory information, while heterochromatin harbors few genes and abundant repetitive DNA. These characteristic features of heterochromatin challenge traditional methods of sequence assembly and molecular dissection. The analysis, instead, of proteins that localize to and often functionally define heterochromatic sequence has illuminated numerous heterochromatin-dependent, essential cellular processes, including chromosome segregation, telomere stability, and gene regulation. With the aim of increasing our sample of heterochromatin-localizing proteins, we performed a comprehensive search for new members of Heterochromatin Protein 1 gene family over 40 million years of Drosophila evolution. Our report expands this family from a modest five genes to 26 genes. Unlike the founding family members, the HP1s we describe are structurally diverse, largely restricted to male reproductive tissue, and highly dynamic over evolutionary time. Despite recurrent HP1 gene birth and death, gene numbers per species are relatively constant. These gene “replacements” likely support a dynamic biological process. We propose, and present evidence for, the hypothesis that recurrent chromosomal rearrangements drive at least some HP1 gene family dynamics observed. We anticipate that these HP1 genes will help define new heterochromatin-dependent processes in the male germline.
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Affiliation(s)
- Mia T Levine
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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29
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Protein landscape at Drosophila melanogaster telomere-associated sequence repeats. Mol Cell Biol 2012; 32:2170-82. [PMID: 22493064 DOI: 10.1128/mcb.00010-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The specific set of proteins bound at each genomic locus contributes decisively to regulatory processes and to the identity of a cell. Understanding of the function of a particular locus requires the knowledge of what factors interact with that locus and how the protein composition changes in different cell types or during the response to internal and external signals. Proteomic analysis of isolated chromatin segments (PICh) was developed as a tool to target, purify, and identify proteins associated with a defined locus and was shown to allow the purification of human telomeric chromatin. Here we have developed this method to identify proteins that interact with the Drosophila telomere-associated sequence (TAS) repeats. Several of the purified factors were validated as novel TAS-bound proteins by chromatin immunoprecipitation, and the Brahma complex was confirmed as a dominant modifier of telomeric position effect through the use of a genetic test. These results offer information on the efficacy of applying the PICh protocol to loci with sequence more complex than that found at human telomeres and identify proteins that bind to the TAS repeats, which might contribute to TAS biology and chromatin silencing.
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Lobetti-Bodoni C, Bernocco E, Genuardi E, Boccadoro M, Ladetto M. Telomeres and telomerase in normal and malignant B-cells. Hematol Oncol 2011; 28:157-67. [PMID: 20213664 DOI: 10.1002/hon.937] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The telomeric checkpoint is emerging as a critical sensor of cellular damage, playing a major role in human aging and cancer development. In the meantime, telomere biology is rapidly evolving from a basic discipline to a translational branch, capable of providing major hints for biomarker development, risk assessment and targeted treatment of cancer. These advances have a number of implications in the biology of lymphoid tumours. Moreover, there is considerable interest in the potential role of telomeric dysfunction in the wide array of immunological abnormalities, grouped under the definition of 'immunosenescence'. This review will summarize the impact of recent advances in telomere biology on the physiology and pathology of the B lymphocyte, with special interest in immunosenescence and lymphomagenesis.
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Affiliation(s)
- Chiara Lobetti-Bodoni
- Department of Experimental Oncology, Division of Hematology, University of Torino, Italy
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Wang QP, Kawahara T, Horn D. Histone deacetylases play distinct roles in telomeric VSG expression site silencing in African trypanosomes. Mol Microbiol 2010; 77:1237-45. [PMID: 20624217 PMCID: PMC2941730 DOI: 10.1111/j.1365-2958.2010.07284.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2010] [Indexed: 01/10/2023]
Abstract
African trypanosomes evade the host immune response through antigenic variation, which is achieved by periodically expressing different variant surface glycoproteins (VSGs). VSG expression is monoallelic such that only one of approximately 15 telomeric VSG expression sites (ESs) is transcribed at a time. Epigenetic regulation is involved in VSG control but our understanding of the mechanisms involved remains incomplete. Histone deacetylases are potential drug targets for diseases caused by protozoan parasites. Here, using recombinant expression we show that the essential Trypanosoma brucei deacetylases, DAC1 (class I) and DAC3 (class II) display histone deacetylase activity. Both DAC1 and DAC3 are nuclear proteins in the bloodstream stage parasite, while only DAC3 remains concentrated in the nucleus in insect-stage cells. Consistent with developmentally regulated localization, DAC1 antagonizes SIR2rp1-dependent telomeric silencing only in the bloodstream form, indicating a conserved role in the control of silent chromatin domains. In contrast, DAC3 is specifically required for silencing at VSG ES promoters in both bloodstream and insect-stage cells. We conclude that DAC1 and DAC3 play distinct roles in subtelomeric gene silencing and that DAC3 represents the first readily druggable target linked to VSG ES control in the African trypanosome.
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Affiliation(s)
- Qiao-Ping Wang
- London School of Hygiene and Tropical MedicineKeppel Street, London WC1E 7HT, UK
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, Key Laboratory of Tropical Diseases Control, Ministry of Education, Zhongshan Medical College, Sun Yat-Sen UniversityGuangzhou 510275, China
| | - Taemi Kawahara
- London School of Hygiene and Tropical MedicineKeppel Street, London WC1E 7HT, UK
| | - David Horn
- London School of Hygiene and Tropical MedicineKeppel Street, London WC1E 7HT, UK
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Palmer JM, Keller NP. Secondary metabolism in fungi: does chromosomal location matter? Curr Opin Microbiol 2010; 13:431-6. [PMID: 20627806 DOI: 10.1016/j.mib.2010.04.008] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 04/22/2010] [Accepted: 04/27/2010] [Indexed: 10/19/2022]
Abstract
Filamentous fungi produce a vast array of small molecules called secondary metabolites, which include toxins as well as antibiotics. Coregulated gene clusters are the hallmark of fungal secondary metabolism, and there is a growing body of evidence that suggests regulation is at least, in part, epigenetic. Chromatin-level control is involved in several silencing phenomena observed in fungi including mating type switching, telomere position effect (TPE), silencing of ribosomal DNA, regulation of genes involved in nutrient acquisition, and as presented here, secondary metabolite cluster expression. These phenomena are tied together by the underlying theme of chromosomal location, often near centromeres and telomeres, where facultative heterochromatin plays a role in transcription. Secondary metabolite gene clusters are often located subtelomerically and recently it has been shown that proteins involved in chromatin remodeling, such as LaeA, ClrD, CclA, and HepA mediate cluster regulation.
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Affiliation(s)
- Jonathan M Palmer
- Plant Pathology Department, University of Wisconsin, Madison, WI 53706, USA
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A 'higher order' of telomere regulation: telomere heterochromatin and telomeric RNAs. EMBO J 2009; 28:2323-36. [PMID: 19629032 PMCID: PMC2722253 DOI: 10.1038/emboj.2009.197] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 06/24/2009] [Indexed: 01/20/2023] Open
Abstract
Protection of chromosome ends from DNA repair and degradation activities is mediated by specialized protein complexes bound to telomere repeats. Recently, it has become apparent that epigenetic regulation of the telomric chromatin template critically impacts on telomere function and telomere-length homeostasis from yeast to man. Across all species, telomeric repeats as well as the adjacent subtelomeric regions carry features of repressive chromatin. Disruption of this silent chromatin environment results in loss of telomere-length control and increased telomere recombination. In turn, progressive telomere loss reduces chromatin compaction at telomeric and subtelomeric domains. The recent discoveries of telomere chromatin regulation during early mammalian development, as well as during nuclear reprogramming, further highlights a central role of telomere chromatin changes in ontogenesis. In addition, telomeres were recently shown to generate long, non-coding RNAs that remain associated to telomeric chromatin and will provide new insights into the regulation of telomere length and telomere chromatin. In this review, we will discuss the epigenetic regulation of telomeres across species, with special emphasis on mammalian telomeres. We will also discuss the links between epigenetic alterations at mammalian telomeres and telomere-associated diseases.
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