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Razzaghian HR, Forsberg LA, Prakash KR, Przerada S, Paprocka H, Zywicka A, Westerman MP, Pedersen NL, O'Hanlon TP, Rider LG, Miller FW, Srutek E, Jankowski M, Zegarski W, Piotrowski A, Absher D, Dumanski JP. Post-zygotic and inter-individual structural genetic variation in a presumptive enhancer element of the locus between the IL10Rβ and IFNAR1 genes. PLoS One 2013; 8:e67752. [PMID: 24023707 PMCID: PMC3762855 DOI: 10.1371/journal.pone.0067752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/21/2013] [Indexed: 12/26/2022] Open
Abstract
Although historically considered as junk-DNA, tandemly repeated sequence motifs can affect human phenotype. For example, variable number tandem repeats (VNTR) with embedded enhancers have been shown to regulate gene transcription. The post-zygotic variation is the presence of genetically distinct populations of cells in an individual derived from a single zygote, and this is an understudied aspect of genome biology. We report somatically variable VNTR with sequence properties of an enhancer, located upstream of IFNAR1. Initially, SNP genotyping of 63 monozygotic twin pairs and multiple tissues from 21 breast cancer patients suggested a frequent post-zygotic mosaicism. The VNTR displayed a repeated 32 bp core motif in the center of the repeat, which was flanked by similar variable motifs. A total of 14 alleles were characterized based on combinations of segments, which showed post-zygotic and inter-individual variation, with up to 6 alleles in a single subject. Somatic variation occurred in ∼24% of cases. In this hypervariable region, we found a clustering of transcription factor binding sites with strongest sequence similarity to mouse Foxg1 transcription factor binding motif. This study describes a VNTR with sequence properties of an enhancer that displays post-zygotic and inter-individual genetic variation. This element is within a locus containing four related cytokine receptors: IFNAR2, IL10Rβ, IFNAR1 and IFNGR2, and we hypothesize that it might function in transcriptional regulation of several genes in this cluster. Our findings add another level of complexity to the variation among VNTR-based enhancers. Further work may unveil the normal function of this VNTR in transcriptional control and its possible involvement in diseases connected with these receptors, such as autoimmune conditions and cancer.
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Affiliation(s)
- Hamid Reza Razzaghian
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lars A. Forsberg
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Szymon Przerada
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Hanna Paprocka
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anna Zywicka
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Maxwell P. Westerman
- Hematology Research, Mount Sinai Hospital Medical Center, Chicago, Illinois, United States of America
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Terrance P. O'Hanlon
- Environmental Autoimmunity Group, National Institute of Environmental Health Sciences, National Institutes of Health Clinical Research Center, Bethesda, Maryland, United States of America
| | - Lisa G. Rider
- Environmental Autoimmunity Group, National Institute of Environmental Health Sciences, National Institutes of Health Clinical Research Center, Bethesda, Maryland, United States of America
| | - Frederick W. Miller
- Environmental Autoimmunity Group, National Institute of Environmental Health Sciences, National Institutes of Health Clinical Research Center, Bethesda, Maryland, United States of America
| | - Ewa Srutek
- Surgical Oncology Clinic, Collegium Medicum, Oncology Center, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Michal Jankowski
- Surgical Oncology Clinic, Collegium Medicum, Oncology Center, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Wojciech Zegarski
- Surgical Oncology Clinic, Collegium Medicum, Oncology Center, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Arkadiusz Piotrowski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Jan P. Dumanski
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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