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Abstract
Background The introduction of novel CTCF binding sites in gene regulatory regions in the rodent lineage is partly the effect of transposable element expansion, particularly in the murine lineage. The exact mechanism and functional impact of evolutionarily novel CTCF binding sites are not yet fully understood. We investigated the impact of novel subspecies-specific CTCF binding sites in two Mus genus subspecies, Mus musculus domesticus and Mus musculus castaneus, that diverged 0.5 million years ago. Results CTCF binding site evolution is influenced by the action of the B2-B4 family of transposable elements independently in both lineages, leading to the proliferation of novel CTCF binding sites. A subset of evolutionarily young sites may harbour transcriptional functionality as evidenced by the stability of their binding across multiple tissues in M. musculus domesticus (BL6), while overall the distance of subspecies-specific CTCF binding to the nearest transcription start sites and/or topologically associated domains (TADs) is largely similar to musculus-common CTCF sites. Remarkably, we discovered a recurrent regulatory architecture consisting of a CTCF binding site and an interferon gene that appears to have been tandemly duplicated to create a 15-gene cluster on chromosome 4, thus forming a novel BL6 specific immune locus in which CTCF may play a regulatory role. Conclusions Our results demonstrate that thousands of CTCF binding sites show multiple functional signatures rapidly after incorporation into the genome.
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Affiliation(s)
- Dhoyazan Azazi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.,German Cancer Research Center (DKFZ), Division Regulatory Genomics and Cancer Evolution, 69120, Heidelberg, Germany
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. .,University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK. .,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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Mead S, Uphill J, Beck J, Poulter M, Campbell T, Lowe J, Adamson G, Hummerich H, Klopp N, Rückert IM, Wichmann HE, Azazi D, Plagnol V, Pako WH, Whitfield J, Alpers MP, Whittaker J, Balding DJ, Zerr I, Kretzschmar H, Collinge J. Genome-wide association study in multiple human prion diseases suggests genetic risk factors additional to PRNP. Hum Mol Genet 2012; 21:1897-906. [PMID: 22210626 PMCID: PMC3313791 DOI: 10.1093/hmg/ddr607] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 12/04/2011] [Accepted: 12/16/2011] [Indexed: 11/14/2022] Open
Abstract
Prion diseases are fatal neurodegenerative diseases of humans and animals caused by the misfolding and aggregation of prion protein (PrP). Mammalian prion diseases are under strong genetic control but few risk factors are known aside from the PrP gene locus (PRNP). No genome-wide association study (GWAS) has been done aside from a small sample of variant Creutzfeldt-Jakob disease (CJD). We conducted GWAS of sporadic CJD (sCJD), variant CJD (vCJD), iatrogenic CJD, inherited prion disease, kuru and resistance to kuru despite attendance at mortuary feasts. After quality control, we analysed 2000 samples and 6015 control individuals (provided by the Wellcome Trust Case Control Consortium and KORA-gen) for 491032-511862 SNPs in the European study. Association studies were done in each geographical and aetiological group followed by several combined analyses. The PRNP locus was highly associated with risk in all geographical and aetiological groups. This association was driven by the known coding variation at rs1799990 (PRNP codon 129). No non-PRNP loci achieved genome-wide significance in the meta-analysis of all human prion disease. SNPs at the ZBTB38-RASA2 locus were associated with CJD in the UK (rs295301, P = 3.13 × 10(-8); OR, 0.70) but these SNPs showed no replication evidence of association in German sCJD or in Papua New Guinea-based tests. A SNP in the CHN2 gene was associated with vCJD [P = 1.5 × 10(-7); odds ratio (OR), 2.36], but not in UK sCJD (P = 0.049; OR, 1.24), in German sCJD or in PNG groups. In the overall meta-analysis of CJD, 14 SNPs were associated (P < 10(-5); two at PRNP, three at ZBTB38-RASA2, nine at nine other independent non-PRNP loci), more than would be expected by chance. None of the loci recently identified as genome-wide significant in studies of other neurodegenerative diseases showed any clear evidence of association in prion diseases. Concerning common genetic variation, it is likely that the PRNP locus contains the only strong risk factors that act universally across human prion diseases. Our data are most consistent with several other risk loci of modest overall effects which will require further genetic association studies to provide definitive evidence.
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Affiliation(s)
- Simon Mead
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, LondonWC1N 3BG, UK
| | - James Uphill
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, LondonWC1N 3BG, UK
| | - John Beck
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, LondonWC1N 3BG, UK
| | - Mark Poulter
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, LondonWC1N 3BG, UK
| | - Tracy Campbell
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, LondonWC1N 3BG, UK
| | - Jessica Lowe
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, LondonWC1N 3BG, UK
| | - Gary Adamson
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, LondonWC1N 3BG, UK
| | - Holger Hummerich
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, LondonWC1N 3BG, UK
| | - Norman Klopp
- KORA-gen, Helmholtz-Zentrum München, Institute for Epidemiology, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Ina-Maria Rückert
- KORA-gen, Helmholtz-Zentrum München, Institute for Epidemiology, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - H-Erich Wichmann
- KORA-gen, Helmholtz-Zentrum München, Institute for Epidemiology, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Dhoyazan Azazi
- Department of Statistics, Institute of Genetics, University College London, Darwin Building Gower Street, London WC1E 6BT, UK
| | - Vincent Plagnol
- Department of Statistics, Institute of Genetics, University College London, Darwin Building Gower Street, London WC1E 6BT, UK
| | - Wandagi H. Pako
- Papua New Guinea (PNG) Institute of Medical Research, Goroka, EHP, Papua New Guinea
| | - Jerome Whitfield
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, LondonWC1N 3BG, UK
- Centre for International Health, Curtin University, Perth, Australia
| | - Michael P. Alpers
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, LondonWC1N 3BG, UK
- Papua New Guinea (PNG) Institute of Medical Research, Goroka, EHP, Papua New Guinea
- Centre for International Health, Curtin University, Perth, Australia
| | - John Whittaker
- London School of Hygiene and Tropical Medicine, LondonWC1E 7HT, UK
| | - David J. Balding
- Department of Statistics, Institute of Genetics, University College London, Darwin Building Gower Street, London WC1E 6BT, UK
| | - Inga Zerr
- Department of Neurology, Georg-August University Göttingen, Göttingen, Germany and
| | - Hans Kretzschmar
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 23, D-81377 Munich, Germany
| | - John Collinge
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, LondonWC1N 3BG, UK
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