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Gilroy KL, Terry A, Naseer A, de Ridder J, Allahyar A, Wang W, Carpenter E, Mason A, Wong GKS, Cameron ER, Kilbey A, Neil JC. Gamma-Retrovirus Integration Marks Cell Type-Specific Cancer Genes: A Novel Profiling Tool in Cancer Genomics. PLoS One 2016; 11:e0154070. [PMID: 27097319 PMCID: PMC4838236 DOI: 10.1371/journal.pone.0154070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/10/2016] [Indexed: 01/09/2023] Open
Abstract
Retroviruses have been foundational in cancer research since early studies identified proto-oncogenes as targets for insertional mutagenesis. Integration of murine gamma-retroviruses into the host genome favours promoters and enhancers and entails interaction of viral integrase with host BET/bromodomain factors. We report that this integration pattern is conserved in feline leukaemia virus (FeLV), a gamma-retrovirus that infects many human cell types. Analysis of FeLV insertion sites in the MCF-7 mammary carcinoma cell line revealed strong bias towards active chromatin marks with no evidence of significant post-integration growth selection. The most prominent FeLV integration targets had little overlap with the most abundantly expressed transcripts, but were strongly enriched for annotated cancer genes. A meta-analysis based on several gamma-retrovirus integration profiling (GRIP) studies in human cells (CD34+, K562, HepG2) revealed a similar cancer gene bias but also remarkable cell-type specificity, with prominent exceptions including a universal integration hotspot at the long non-coding RNA MALAT1. Comparison of GRIP targets with databases of super-enhancers from the same cell lines showed that these have only limited overlap and that GRIP provides unique insights into the upstream drivers of cell growth. These observations elucidate the oncogenic potency of the gamma-retroviruses and support the wider application of GRIP to identify the genes and growth regulatory circuits that drive distinct cancer types.
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Affiliation(s)
- Kathryn L. Gilroy
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail: (JCN); (KLG)
| | - Anne Terry
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Asif Naseer
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jeroen de Ridder
- Delft Bioinformatics Lab, Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Amin Allahyar
- Delft Bioinformatics Lab, Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Weiwei Wang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Eric Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Andrew Mason
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada
| | - Gane K-S. Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Ewan R. Cameron
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Anna Kilbey
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - James C. Neil
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail: (JCN); (KLG)
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102
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Wang Y, Jiang R, Wong WH. Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data. Natl Sci Rev 2016; 3:240-251. [PMID: 28690910 DOI: 10.1093/nsr/nww025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cell packs a lot of genetic and regulatory information through a structure known as chromatin, i.e. DNA is wrapped around histone proteins and is tightly packed in a remarkable way. To express a gene in a specific coding region, the chromatin would open up and DNA loop may be formed by interacting enhancers and promoters. Furthermore, the mediator and cohesion complexes, sequence-specific transcription factors, and RNA polymerase II are recruited and work together to elaborately regulate the expression level. It is in pressing need to understand how the information, about when, where, and to what degree genes should be expressed, is embedded into chromatin structure and gene regulatory elements. Thanks to large consortia such as Encyclopedia of DNA Elements (ENCODE) and Roadmap Epigenomic projects, extensive data on chromatin accessibility and transcript abundance are available across many tissues and cell types. This rich data offer an exciting opportunity to model the causal regulatory relationship. Here, we will review the current experimental approaches, foundational data, computational problems, interpretive frameworks, and integrative models that will enable the accurate interpretation of regulatory landscape. Particularly, we will discuss the efforts to organize, analyze, model, and integrate the DNA accessibility data, transcriptional data, and functional genomic regions together. We believe that these efforts will eventually help us understand the information flow within the cell and will influence research directions across many fields.
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Affiliation(s)
- Yong Wang
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA 94305, USA.,Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing 100080, China
| | - Rui Jiang
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA 94305, USA.,MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Wing Hung Wong
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA 94305, USA
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103
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Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility. G3-GENES GENOMES GENETICS 2016; 6:805-17. [PMID: 26818075 PMCID: PMC4825651 DOI: 10.1534/g3.115.026849] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
DNA transposons and retroviruses are important transgenic tools for genome engineering. An important consideration affecting the choice of transgenic vector is their insertion site preferences. Previous large-scale analyses of Ds transposon integration sites in plants were done on the basis of reporter gene expression or germ-line transmission, making it difficult to discern vertebrate integration preferences. Here, we compare over 1300 Ds transposon integration sites in zebrafish with Tol2 transposon and retroviral integration sites. Genome-wide analysis shows that Ds integration sites in the presence or absence of marker selection are remarkably similar and distributed throughout the genome. No strict motif was found, but a preference for structural features in the target DNA associated with DNA flexibility (Twist, Tilt, Rise, Roll, Shift, and Slide) was observed. Remarkably, this feature is also found in transposon and retroviral integrations in maize and mouse cells. Our findings show that structural features influence the integration of heterologous DNA in genomes, and have implications for targeted genome engineering.
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104
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Assay for transposase-accessible chromatin and circularized chromosome conformation capture, two methods to explore the regulatory landscapes of genes in zebrafish. Methods Cell Biol 2016; 135:413-30. [PMID: 27443938 DOI: 10.1016/bs.mcb.2016.02.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Accurate transcriptional control of genes is fundamental for the correct functioning of organs and developmental processes. This control depends on the interplay between the promoter of genes and other noncoding sequences, whose interaction is mediated by 3D chromatin arrangements. Thus, the detailed description of transcriptional regulatory landscapes is essential to understand the mechanisms of transcriptional regulation. However, to achieve that, two important challenges have to be faced: (1) the identification of the noncoding sequences that contribute to gene transcription and (2) the association of these sequences to the respective genes they control. In this chapter, we describe two protocols that allow overcoming these important challenges: the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and circularized chromosome conformation capture (4C-seq). ATAC-seq is a very efficient technique that, using a very low number of cells as starting material, allows the identification of active chromatin regions genome wide, whereas 4C-seq detects the subset of sequences that interact specifically with the promoter of a given gene. When combined, both techniques provide a comprehensive snapshot of the regulatory landscapes of developmental genes. The protocols we present here have been optimized for teleost fish samples, zebrafish and medaka, allowing the in-depth study of transcriptional regulation in these two emerging animal models. Given the amenability and easy genetic manipulation of these two experimental systems, we anticipate that they will be important in revealing general principles of the vertebrate regulatory genome.
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105
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Hardy K, Wu F, Tu W, Zafar A, Boulding T, McCuaig R, Sutton CR, Theodoratos A, Rao S. Identification of chromatin accessibility domains in human breast cancer stem cells. Nucleus 2016; 7:50-67. [PMID: 26962893 PMCID: PMC4916893 DOI: 10.1080/19491034.2016.1150392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) is physiological in embryogenesis and wound healing but also associated with the formation of cancer stem cells (CSCs). Many EMT signaling pathways are implicated in CSC formation, but the precise underlying mechanisms of CSC formation remain elusive. We have previously demonstrated that PKC is critical for EMT induction and CSC formation in inducible breast EMT/CSC models. Here, we used formaldehyde-assisted isolation of regulatory elements-sequencing (FAIRE-seq) to investigate DNA accessibility changes after PKC activation and determine how they influence EMT and CSC formation. During EMT, DNA accessibility principally increased in regions distant from transcription start sites, low in CpG content, and enriched with chromatin enhancer marks. ChIP-sequencing revealed that a subset of these regions changed from poised to active enhancers upon stimulation, with some even more acteylated in CSCs. While regions with increased accessibility were enriched for FOX, AP-1, TEAD, and TFAP2 motifs, those containing FOX and AP-1 motif were associated with increased expression of CSC-associated genes, while those with TFAP2 were associated with genes with increased expression in non-CSCs. Silencing of 2 members of the FOX family, FOXN2 and FOXQ1, repressed CSCs and the mesenchymal phenotype and inhibited the CSC gene signature. These novel, PKC-induced DNA accessibility regions help explain how the epigenomic plasticity of cells undergoing EMT leads to CSC gene activation.
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Affiliation(s)
- K Hardy
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - F Wu
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - W Tu
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - A Zafar
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - T Boulding
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - R McCuaig
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - C R Sutton
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
| | - A Theodoratos
- b JCSMR, Australian National University , Canberra, Australia
| | - S Rao
- a HRI, Faculty of ESTeM, University of Canberra , Bruce , Australia
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106
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La Fortezza M, Schenk M, Cosolo A, Kolybaba A, Grass I, Classen AK. JAK/STAT signalling mediates cell survival in response to tissue stress. Development 2016; 143:2907-19. [DOI: 10.1242/dev.132340] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 06/23/2016] [Indexed: 12/31/2022]
Abstract
Tissue homeostasis relies on the ability of tissues to respond to stress. Tissue regeneration and tumour models in Drosophila have shown that JNK is a prominent stress-response pathway promoting injury-induced apoptosis and compensatory proliferation. A central question remaining unanswered is how both responses are balanced by activation of a single pathway. JAK/STAT signalling, a potential JNK target, is implicated in promoting compensatory proliferation. While we observe JAK/STAT activation in imaginal discs upon damage, our data demonstrates that JAK/STAT and its downstream effector Zfh2 promote survival of JNK-signalling cells instead. The JNK component fos and the pro-apoptotic gene hid are regulated in a JAK/STAT-dependent manner. This molecular pathway restrains JNK-induced apoptosis and spatial propagation of JNK-signalling, thereby limiting the extent of tissue damage, as well as facilitating systemic and proliferative responses to injury. We find that the pro-survival function of JAK/STAT also drives tumour growth under conditions of chronic stress. Our study defines JAK/STAT function in tissue stress and illustrates how crosstalk between conserved signalling pathways establishes an intricate equilibrium between proliferation, apoptosis and survival to restore tissue homeostasis.
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Affiliation(s)
- Marco La Fortezza
- Ludwig-Maximilians-University Munich, Faculty of Biology, Grosshaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany
| | - Madlin Schenk
- Ludwig-Maximilians-University Munich, Faculty of Biology, Grosshaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany
| | - Andrea Cosolo
- Ludwig-Maximilians-University Munich, Faculty of Biology, Grosshaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany
| | - Addie Kolybaba
- Ludwig-Maximilians-University Munich, Faculty of Biology, Grosshaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany
| | - Isabelle Grass
- Ludwig-Maximilians-University Munich, Faculty of Biology, Grosshaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany
| | - Anne-Kathrin Classen
- Ludwig-Maximilians-University Munich, Faculty of Biology, Grosshaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany
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107
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Nevedomskaya E, Stelloo S, van der Poel HG, de Jong J, Wessels LFA, Bergman AM, Zwart W. Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer. GENOMICS DATA 2015; 7:124-6. [PMID: 26981385 PMCID: PMC4778643 DOI: 10.1016/j.gdata.2015.12.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 12/23/2015] [Indexed: 11/09/2022]
Abstract
Prostate cancer (PCa) is the second most common cancer in men. The Androgen Receptor (AR) is the major driver of PCa and the main target of therapy in the advanced setting. AR is a nuclear receptor that binds the chromatin and regulates transcription of genes involved in cancer cell proliferation and survival. In a study by Stelloo et al. (1) we explored prostate cancer on the level of transcriptional regulation by means of Formaldehyde-Assisted Isolation of Regulatory Elements and Chromatin Immunoprecipitation coupled with massive parallel sequencing (FAIRE-seq and ChIP-seq, respectively). We employed these data for the assessment of differences in transcriptional regulation at distinct stages of PCa progression and to construct a prognostic gene expression classifier. Genomics data includes FAIRE-seq data from normal prostate tissue as well as primary, hormone therapy resistant and metastatic PCa. Furthermore, ChIP-seq data from primary and resistant PCa were generated, along with multiple input controls. The data are publicly available through NCBI GEO database with accession number GSE65478. Here we describe the genomics and clinical data in detail and provide comparative analysis of FAIRE-seq and ChIP-seq data.
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Affiliation(s)
- Ekaterina Nevedomskaya
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Suzan Stelloo
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Henk G van der Poel
- Division of Urology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Jeroen de Jong
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Division of Urology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Andries M Bergman
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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108
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Bonifer C, Cockerill PN. Chromatin Structure Profiling Identifies Crucial Regulators of Tumor Maintenance. Trends Cancer 2015; 1:157-160. [PMID: 28741472 DOI: 10.1016/j.trecan.2015.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 12/25/2022]
Abstract
Cancer is primarily caused by mutations in genes encoding transcriptional regulators and signaling molecules. These mutations cooperate to deregulate the tight control over gene expression that is otherwise seen in normal cells. One consequence of this process is deregulated transcription factor (TF) activity. This forum article highlights novel strategies that use genome-wide chromatin structure profiling to identify the deregulated factors on which cancer cells depend, with the ultimate aim of targeting them.
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Affiliation(s)
- Constanze Bonifer
- Institute of Cancer and Genomic Medicine, Institute for Biomedical Research, University of Birmingham, Birmingham B15 2TT, UK.
| | - Peter N Cockerill
- Institute of Cancer and Genomic Medicine, Institute for Biomedical Research, University of Birmingham, Birmingham B15 2TT, UK.
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109
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Schick S, Fournier D, Thakurela S, Sahu SK, Garding A, Tiwari VK. Dynamics of chromatin accessibility and epigenetic state in response to UV damage. J Cell Sci 2015; 128:4380-94. [PMID: 26446258 DOI: 10.1242/jcs.173633] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/29/2015] [Indexed: 12/27/2022] Open
Abstract
Epigenetic mechanisms determine the access of regulatory factors to DNA during events such as transcription and the DNA damage response. However, the global response of histone modifications and chromatin accessibility to UV exposure remains poorly understood. Here, we report that UV exposure results in a genome-wide reduction in chromatin accessibility, while the distribution of the active regulatory mark H3K27ac undergoes massive reorganization. Genomic loci subjected to epigenetic reprogramming upon UV exposure represent target sites for sequence-specific transcription factors. Most of these are distal regulatory regions, highlighting their importance in the cellular response to UV exposure. Furthermore, UV exposure results in an extensive reorganization of super-enhancers, accompanied by expression changes of associated genes, which may in part contribute to the stress response. Taken together, our study provides the first comprehensive resource for genome-wide chromatin changes upon UV irradiation in relation to gene expression and elucidates new aspects of this relationship.
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Affiliation(s)
- Sandra Schick
- Institute of Molecular Biology (IMB), Mainz, Germany
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110
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Sun J, Rockowitz S, Chauss D, Wang P, Kantorow M, Zheng D, Cvekl A. Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators. Mol Vis 2015; 21:955-73. [PMID: 26330747 PMCID: PMC4551281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/26/2015] [Indexed: 10/26/2022] Open
Abstract
PURPOSE Gene expression correlates with local chromatin structure. Our studies have mapped histone post-translational modifications, RNA polymerase II (pol II), and transcription factor Pax6 in lens chromatin. These data represent the first genome-wide insights into the relationship between lens chromatin structure and lens transcriptomes and serve as an excellent source for additional data analysis and refinement. The principal lens proteins, the crystallins, are encoded by predominantly expressed mRNAs; however, the regulatory mechanisms underlying their high expression in the lens remain poorly understood. METHODS The formaldehyde-assisted identification of regulatory regions (FAIRE-Seq) was employed to analyze newborn lens chromatin. ChIP-seq and RNA-seq data published earlier (GSE66961) have been used to assist in FAIRE-seq data interpretation. RNA transcriptomes from murine lens epithelium, lens fibers, erythrocytes, forebrain, liver, neurons, and pancreas were compared to establish the gene expression levels of the most abundant mRNAs versus median gene expression across other differentiated cells. RESULTS Normalized RNA expression data from multiple tissues show that crystallins rank among the most highly expressed genes in mammalian cells. These findings correlate with the extremely high abundance of pol II all across the crystallin loci, including crystallin genes clustered on chromosomes 1 and 5, as well as within regions of "open" chromatin, as identified by FAIRE-seq. The expression levels of mRNAs encoding DNA-binding transcription factors (e.g., Foxe3, Hsf4, Maf, Pax6, Prox1, Sox1, and Tfap2a) revealed that their transcripts form "clusters" of abundant mRNAs in either lens fibers or lens epithelium. The expression of three autophagy regulatory mRNAs, encoding Tfeb, FoxO1, and Hif1α, was found within a group of lens preferentially expressed transcription factors compared to the E12.5 forebrain. CONCLUSIONS This study reveals novel features of lens chromatin, including the remarkably high abundance of pol II at the crystallin loci that exhibit features of "open" chromatin. Hsf4 ranks among the most abundant fiber cell-preferred DNA-binding transcription factors. Notable transcripts, including Atf4, Ctcf, E2F4, Hey1, Hmgb1, Mycn, RXRβ, Smad4, Sp1, and Taf1 (transcription factors) and Ctsd, Gabarapl1, and Park7 (autophagy regulators) have been identified with high levels of expression in lens fibers, which suggests specific roles in lens fiber cell terminal differentiation.
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Affiliation(s)
- Jian Sun
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY,Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
| | - Shira Rockowitz
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
| | - Daniel Chauss
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL
| | - Ping Wang
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY
| | - Marc Kantorow
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY,Department of Neurology, Albert Einstein College of Medicine, Bronx, NY,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY
| | - Ales Cvekl
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY,Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
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111
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Külshammer E, Mundorf J, Kilinc M, Frommolt P, Wagle P, Uhlirova M. Interplay among Drosophila transcription factors Ets21c, Fos and Ftz-F1 drives JNK-mediated tumor malignancy. Dis Model Mech 2015; 8:1279-93. [PMID: 26398940 PMCID: PMC4610234 DOI: 10.1242/dmm.020719] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 07/28/2015] [Indexed: 12/16/2022] Open
Abstract
Cancer initiation and maintenance of the transformed cell state depend on altered cellular signaling and aberrant activities of transcription factors (TFs) that drive pathological gene expression in response to cooperating genetic lesions. Deciphering the roles of interacting TFs is therefore central to understanding carcinogenesis and for designing cancer therapies. Here, we use an unbiased genomic approach to define a TF network that triggers an abnormal gene expression program promoting malignancy of clonal tumors, generated in Drosophila imaginal disc epithelium by gain of oncogenic Ras (RasV12) and loss of the tumor suppressor Scribble (scrib1). We show that malignant transformation of the rasV12scrib1 tumors requires TFs of distinct families, namely the bZIP protein Fos, the ETS-domain factor Ets21c and the nuclear receptor Ftz-F1, all acting downstream of Jun-N-terminal kinase (JNK). Depleting any of the three TFs improves viability of tumor-bearing larvae, and this positive effect can be enhanced further by their combined removal. Although both Fos and Ftz-F1 synergistically contribute to rasV12scrib1 tumor invasiveness, only Fos is required for JNK-induced differentiation defects and Matrix metalloprotease (MMP1) upregulation. In contrast, the Fos-dimerizing partner Jun is dispensable for JNK to exert its effects in rasV12scrib1 tumors. Interestingly, Ets21c and Ftz-F1 are transcriptionally induced in these tumors in a JNK- and Fos-dependent manner, thereby demonstrating a hierarchy within the tripartite TF network, with Fos acting as the most upstream JNK effector. Of the three TFs, only Ets21c can efficiently substitute for loss of polarity and cooperate with RasV12 in inducing malignant clones that, like rasV12scrib1 tumors, invade other tissues and overexpress MMP1 and the Drosophila insulin-like peptide 8 (Dilp8). While rasV12ets21c tumors require JNK for invasiveness, the JNK activity is dispensable for their growth. In conclusion, our study delineates both unique and overlapping functions of distinct TFs that cooperatively promote aberrant expression of target genes, leading to malignant tumor phenotypes. Summary: This study provides genetic evidence that malignancy driven by oncogenic Ras and loss of polarity requires transcription factors of three distinct protein families, acting in synergy downstream of JNK signaling.
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Affiliation(s)
- Eva Külshammer
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Juliane Mundorf
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Merve Kilinc
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Peter Frommolt
- Bioinformatics Facility, CECAD Research Center, University of Cologne, 50931 Cologne, Germany
| | - Prerana Wagle
- Bioinformatics Facility, CECAD Research Center, University of Cologne, 50931 Cologne, Germany
| | - Mirka Uhlirova
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
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112
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Doggett K, Turkel N, Willoughby LF, Ellul J, Murray MJ, Richardson HE, Brumby AM. BTB-Zinc Finger Oncogenes Are Required for Ras and Notch-Driven Tumorigenesis in Drosophila. PLoS One 2015. [PMID: 26207831 PMCID: PMC4514741 DOI: 10.1371/journal.pone.0132987] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
During tumorigenesis, pathways that promote the epithelial-to-mesenchymal transition (EMT) can both facilitate metastasis and endow tumor cells with cancer stem cell properties. To gain a greater understanding of how these properties are interlinked in cancers we used Drosophila epithelial tumor models, which are driven by orthologues of human oncogenes (activated alleles of Ras and Notch) in cooperation with the loss of the cell polarity regulator, scribbled (scrib). Within these tumors, both invasive, mesenchymal-like cell morphology and continual tumor overgrowth, are dependent upon Jun N-terminal kinase (JNK) activity. To identify JNK-dependent changes within the tumors we used a comparative microarray analysis to define a JNK gene signature common to both Ras and Notch-driven tumors. Amongst the JNK-dependent changes was a significant enrichment for BTB-Zinc Finger (ZF) domain genes, including chronologically inappropriate morphogenesis (chinmo). chinmo was upregulated by JNK within the tumors, and overexpression of chinmo with either RasV12 or Nintra was sufficient to promote JNK-independent epithelial tumor formation in the eye/antennal disc, and, in cooperation with RasV12, promote tumor formation in the adult midgut epithelium. Chinmo primes cells for oncogene-mediated transformation through blocking differentiation in the eye disc, and promoting an escargot-expressing stem or enteroblast cell state in the adult midgut. BTB-ZF genes are also required for Ras and Notch-driven overgrowth of scrib mutant tissue, since, although loss of chinmo alone did not significantly impede tumor development, when loss of chinmo was combined with loss of a functionally related BTB-ZF gene, abrupt, tumor overgrowth was significantly reduced. abrupt is not a JNK-induced gene, however, Abrupt is present in JNK-positive tumor cells, consistent with a JNK-associated oncogenic role. As some mammalian BTB-ZF proteins are also highly oncogenic, our work suggests that EMT-promoting signals in human cancers could similarly utilize networks of these proteins to promote cancer stem cell states.
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Affiliation(s)
- Karen Doggett
- Cell Cycle and Development Laboratory, Research Division, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
- * E-mail:
| | - Nezaket Turkel
- Cell Cycle and Development Laboratory, Research Division, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
| | - Lee F. Willoughby
- Cell Cycle and Development Laboratory, Research Division, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
| | - Jason Ellul
- Bioinformatics Core Facility, Research Division, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
| | - Michael J. Murray
- School of Biosciences, University of Melbourne, 1–100 Grattan Street, Parkville, Melbourne, Victoria, Australia
| | - Helena E. Richardson
- Cell Cycle and Development Laboratory, Research Division, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, 1–100 Grattan Street, Parkville, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, 1–100 Grattan Street, Parkville, Melbourne, Victoria, Australia
- School of Molecular Sciences, La Trobe University, Victoria, Australia
| | - Anthony M. Brumby
- Cell Cycle and Development Laboratory, Research Division, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
- School of Biosciences, University of Melbourne, 1–100 Grattan Street, Parkville, Melbourne, Victoria, Australia
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