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Unni R, Liang J, Jelaidan I, Harnett D, Boodhwani M, Glineur D, Burwash I, Chan KL, Coutinho T, Prosperi-Porta G, Fu A, Willner N, Messika-Zeitoun D, Beauchesne L. Mechanistic classification and outcomes of isolated aortic regurgitation in a contemporary cohort of patients. Archives of Cardiovascular Diseases Supplements 2023. [DOI: 10.1016/j.acvdsp.2022.10.232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Ringel AR, Szabo Q, Chiariello AM, Chudzik K, Schöpflin R, Rothe P, Mattei AL, Zehnder T, Harnett D, Laupert V, Bianco S, Hetzel S, Glaser J, Phan MHQ, Schindler M, Ibrahim DM, Paliou C, Esposito A, Prada-Medina CA, Haas SA, Giere P, Vingron M, Wittler L, Meissner A, Nicodemi M, Cavalli G, Bantignies F, Mundlos S, Robson MI. Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes. Cell 2022; 185:3689-3704.e21. [PMID: 36179666 PMCID: PMC9567273 DOI: 10.1016/j.cell.2022.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/03/2022] [Accepted: 08/30/2022] [Indexed: 01/26/2023]
Abstract
Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.
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Affiliation(s)
- Alessa R Ringel
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Quentin Szabo
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Andrea M Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Konrad Chudzik
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Patricia Rothe
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandra L Mattei
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Tobias Zehnder
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Dermot Harnett
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Verena Laupert
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Simona Bianco
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Sara Hetzel
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Juliane Glaser
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Mai H Q Phan
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Magdalena Schindler
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Daniel M Ibrahim
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Christina Paliou
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Cesar A Prada-Medina
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Stefan A Haas
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Peter Giere
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexander Meissner
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Giacomo Cavalli
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Frédéric Bantignies
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany.
| | - Michael I Robson
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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Chong C, Müller M, Pak H, Harnett D, Huber F, Grun D, Leleu M, Auger A, Arnaud M, Stevenson BJ, Michaux J, Bilic I, Hirsekorn A, Calviello L, Simó-Riudalbas L, Planet E, Lubiński J, Bryśkiewicz M, Wiznerowicz M, Xenarios I, Zhang L, Trono D, Harari A, Ohler U, Coukos G, Bassani-Sternberg M. Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes. Nat Commun 2020; 11:1293. [PMID: 32157095 PMCID: PMC7064602 DOI: 10.1038/s41467-020-14968-9] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 02/12/2020] [Indexed: 12/20/2022] Open
Abstract
Efforts to precisely identify tumor human leukocyte antigen (HLA) bound peptides capable of mediating T cell-based tumor rejection still face important challenges. Recent studies suggest that non-canonical tumor-specific HLA peptides derived from annotated non-coding regions could elicit anti-tumor immune responses. However, sensitive and accurate mass spectrometry (MS)-based proteogenomics approaches are required to robustly identify these non-canonical peptides. We present an MS-based analytical approach that characterizes the non-canonical tumor HLA peptide repertoire, by incorporating whole exome sequencing, bulk and single-cell transcriptomics, ribosome profiling, and two MS/MS search tools in combination. This approach results in the accurate identification of hundreds of shared and tumor-specific non-canonical HLA peptides, including an immunogenic peptide derived from an open reading frame downstream of the melanoma stem cell marker gene ABCB5. These findings hold great promise for the discovery of previously unknown tumor antigens for cancer immunotherapy.
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Affiliation(s)
- Chloe Chong
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Markus Müller
- Vital IT, Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, 1015, Lausanne, Switzerland
| | - HuiSong Pak
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Dermot Harnett
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany
| | - Florian Huber
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Delphine Grun
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland
| | - Marion Leleu
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, 1015, Lausanne, Switzerland
| | - Aymeric Auger
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Marion Arnaud
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Brian J Stevenson
- Vital IT, Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, 1015, Lausanne, Switzerland
| | - Justine Michaux
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Ilija Bilic
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany
| | - Antje Hirsekorn
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany
| | - Lorenzo Calviello
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany
| | - Laia Simó-Riudalbas
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, ul. Rybacka 1, 70-204, Szczecin, Poland
- International Institute for Molecular Oncology, Jakuba Krauthofera 23, 60-203, Poznań, Poland
| | - Marta Bryśkiewicz
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, ul. Rybacka 1, 70-204, Szczecin, Poland
- International Institute for Molecular Oncology, Jakuba Krauthofera 23, 60-203, Poznań, Poland
| | - Maciej Wiznerowicz
- International Institute for Molecular Oncology, Jakuba Krauthofera 23, 60-203, Poznań, Poland
- Poznan University of Medical Sciences, Fredry 10, 61-701, Poznań, Poland
| | - Ioannis Xenarios
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Genome Center Health 2030, Chemin de Mines 9, 1202, Genève, Switzerland
- Department of Training and Research, CHUV/UNIL Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
| | - Lin Zhang
- Center for Research on Reproduction and Women's Health, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA, 19104, USA
- Department of Obstetrics and Gynecology, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Uwe Ohler
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany
- Departments of Biology and Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland.
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Foddis M, Winek K, Bentele K, Mueller S, Blumenau S, Reichhart N N, Crespo-Garcia S, Harnett D, Ivanov A, Meisel A, Joussen A, Strauss O, Beule D, Dirnagl U, Sassi C. An exploratory investigation of brain collateral circulation plasticity after cerebral ischemia in two experimental C57BL/6 mouse models. J Cereb Blood Flow Metab 2020; 40:276-287. [PMID: 31549895 PMCID: PMC7370619 DOI: 10.1177/0271678x19827251] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Brain collateral circulation is an essential compensatory mechanism in response to acute brain ischemia. To study the temporal evolution of brain macro and microcollateral recruitment and their reciprocal interactions in response to different ischemic conditions, we applied a combination of complementary techniques (T2-weighted magnetic resonance imaging [MRI], time of flight [TOF] angiography [MRA], cerebral blood flow [CBF] imaging and histology) in two different mouse models. Hypoperfusion was either induced by permanent bilateral common carotid artery stenosis (BCCAS) or 60-min transient unilateral middle cerebral artery occlusion (MCAO). In both models, collateralization is a very dynamic phenomenon with a global effect affecting both hemispheres. Patency of ipsilateral posterior communicating artery (PcomA) represents the main variable survival mechanism and the main determinant of stroke lesion volume and recovery in MCAO, whereas the promptness of external carotid artery retrograde flow recruitment together with PcomA patency, critically influence survival, brain ischemic lesion volume and retinopathy in BCCAS mice. Finally, different ischemic gradients shape microcollateral density and size.
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Affiliation(s)
- Marco Foddis
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Katarzyna Winek
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Kajetan Bentele
- Berlin Institute of Health, BIH, Unit Bioinformatics, Berlin, Germany
| | - Susanne Mueller
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Charité - Universitätsmedizin Berlin, NeuroCure Cluster of Excellence and Charité Core Facility 7T Experimental MRIs, Berlin, Germany
| | - Sonja Blumenau
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nadine Reichhart N
- Department of Ophthalmology, Experimental Ophthalmology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Sergio Crespo-Garcia
- Department of Ophthalmology, Experimental Ophthalmology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Dermot Harnett
- Berlin Institute of Health, BIH, Unit Bioinformatics, Berlin, Germany
| | - Andranik Ivanov
- Berlin Institute of Health, BIH, Unit Bioinformatics, Berlin, Germany
| | - Andreas Meisel
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Antonia Joussen
- Department of Ophthalmology, Experimental Ophthalmology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Olaf Strauss
- Department of Ophthalmology, Experimental Ophthalmology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health, BIH, Unit Bioinformatics, Berlin, Germany
| | - Ulrich Dirnagl
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,QUEST Center for Transforming Biomedical Research, Berlin Institute of Health (BIH), Berlin, Germany
| | - Celeste Sassi
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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Ainslie M, Potluri R, Harnett D, Golian M, J Marbach, Ramirez D. DO AF SYMPTOMS MATTER. Can J Cardiol 2019. [DOI: 10.1016/j.cjca.2019.07.580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Mikhaylichenko O, Bondarenko V, Harnett D, Schor IE, Males M, Viales RR, Furlong EEM. The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription. Genes Dev 2018; 32:42-57. [PMID: 29378788 PMCID: PMC5828394 DOI: 10.1101/gad.308619.117] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/21/2017] [Indexed: 12/03/2022]
Abstract
Here, Mikhaylichenko et al. investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. The authors demonstrate that while the timing of enhancer transcription is correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers and conclude that this is likely an inherent sequence property of the elements themselves. Gene expression is regulated by promoters, which initiate transcription, and enhancers, which control their temporal and spatial activity. However, the discovery that mammalian enhancers also initiate transcription questions the inherent differences between enhancers and promoters. Here, we investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. We show that while the timing of enhancer transcription is generally correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers. To assess how this impacts function, we developed a dual transgenic assay to simultaneously measure enhancer and promoter activities from a single element in the same embryo. Extensive transgenic analysis revealed a relationship between the direction of endogenous transcription and the ability to function as an enhancer or promoter in vivo, although enhancer RNA (eRNA) production and activity are not always strictly coupled. Some enhancers (mainly bidirectional) can act as weak promoters, producing overlapping spatio–temporal expression. Conversely, bidirectional promoters often act as strong enhancers, while unidirectional promoters generally cannot. The balance between enhancer and promoter activity is generally reflected in the levels and directionality of eRNA transcription and is likely an inherent sequence property of the elements themselves.
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Affiliation(s)
- Olga Mikhaylichenko
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Vladyslav Bondarenko
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Dermot Harnett
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Ignacio E Schor
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Matilda Males
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Rebecca R Viales
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Eileen E M Furlong
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
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Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EEM. Promoter shape varies across populations and affects promoter evolution and expression noise. Nat Genet 2017; 49:550-558. [PMID: 28191888 DOI: 10.1038/ng.3791] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/20/2017] [Indexed: 12/29/2022]
Abstract
Animal promoters initiate transcription either at precise positions (narrow promoters) or dispersed regions (broad promoters), a distinction referred to as promoter shape. Although highly conserved, the functional properties of promoters with different shapes and the genetic basis of their evolution remain unclear. Here we used natural genetic variation across a panel of 81 Drosophila lines to measure changes in transcriptional start site (TSS) usage, identifying thousands of genetic variants affecting transcript levels (strength) or the distribution of TSSs within a promoter (shape). Our results identify promoter shape as a molecular trait that can evolve independently of promoter strength. Broad promoters typically harbor shape-associated variants, with signatures of adaptive selection. Single-cell measurements demonstrate that variants modulating promoter shape often increase expression noise, whereas heteroallelic interactions with other promoter variants alleviate these effects. These results uncover new functional properties of natural promoters and suggest the minimization of expression noise as an important factor in promoter evolution.
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Affiliation(s)
- Ignacio E Schor
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Jacob F Degner
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Dermot Harnett
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Enrico Cannavò
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Francesco P Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Heejung Shim
- Department of Statistics, Purdue University, West Lafayette, Indiana, USA
| | - David A Garfield
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
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Schröder MS, Harnett D, Minke BA, Nair PS. Organizing a PhD symposium—an inside view. EMBO Rep 2013; 14:856-60. [DOI: 10.1038/embor.2013.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Markus S Schröder
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin Ireland
| | - Dermot Harnett
- European Molecular Biology Laboratory, Heidelberg Germany
| | | | - Preethy Sasidharan Nair
- Institute of Biomedical Technology, University of Tampere, Finland and the Department of Medical Genetics, University of Helsinki Finland
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Warden G, Harnett D, Green J, Wish T, Woods MO, Green R, Dicks E, Rahman P, Zhai G, Parfrey P. A population-based study of hereditary non-polyposis colorectal cancer: evidence of pathologic and genetic heterogeneity. Clin Genet 2013; 84:522-30. [PMID: 23278430 DOI: 10.1111/cge.12080] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/13/2012] [Accepted: 12/13/2012] [Indexed: 01/30/2023]
Abstract
Hereditary non-polyposis colorectal cancer (HNPCC) may be the result of Lynch syndrome (LS) caused by mutations in mismatch repair (MMR) genes, a syndrome of unknown etiology called familial colorectal cancer type-X (FCCTX), or familial serrated neoplasia associated with the colorectal cancer (CRC) somatic BRAF mutation. To determine the cause of HNPCC in the founder population of the island of Newfoundland, we studied 37 families with LS and 29 families without LS who fulfilled the Amsterdam I criteria. In non-LS, four index CRCs were BRAF mutation positive, one of which was microsatellite instable. Geographic clustering of LS families caused by three different founder mutations in MSH2 was observed. Nine unique MMR mutations in four MMR genes were identified in single families distributed in different geographic isolates. The geographic distribution of non-LS was similar to LS. The coefficient of relatedness using genotype data was significantly higher for non-LS than for all CRC. Extensive genealogic investigation failed to connect non-LS families and in some clusters pathologic CRC heterogeneity was observed. We conclude that non-LS HNPCC may be a heterogeneous disorder with different pathogenic pathways, and that the geographic distribution is consistent with multiple different mutations in unknown CRC susceptibility gene(s).
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