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Dang D, Zhang L, Gao L, Peng L, Chen J, Yang L. Analysis of genomic copy number variations through whole-genome scan in Yunling cattle. Front Vet Sci 2024; 11:1413504. [PMID: 39104544 PMCID: PMC11298805 DOI: 10.3389/fvets.2024.1413504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024] Open
Abstract
Yunling cattle is a new breed of beef cattle bred in Yunnan Province, China, which has the advantages of fast growth, excellent meat quality, improved tolerance ability, and important landscape value. Copy number variation (CNV) is a significant source of gene structural variation and plays a crucial role in evolution and phenotypic diversity. Based on the latest reference genome ARS-UCD2.0, this study analyzed the genome-wide distribution of CNVs in Yunling cattle using short-read whole-genome sequencing data (n = 129) and single-molecule long-read sequencing data (n = 1), and a total of 16,507 CNVs were detected. After merging CNVs with overlapping genomic positions, 3,728 CNV regions (CNVRs) were obtained, accounting for 0.61% of the reference genome. The functional analysis indicated significant enrichment of CNVRs in 96 GO terms and 57 KEGG pathways, primarily related to cell adhesion, signal transduction, neuromodulation, and nutritional metabolism. Additionally, 111 CNVRs overlapped with 76 quantitative trait loci (QTLs), including Subcutaneous fat thickness QTL, Longissimus muscle area QTL, and Marbling score QTL. Several CNVR-overlapping genes, including BZW1, AOX1, and LOC100138449, overlap with regions associated with meat color and quality QTLs. Furthermore, Vst analysis showed that PSMB4, ERICH1, SMC2, and PPP4R3A were highly divergent between Yunling and Brahman cattle. In summary, we have constructed the genomic CNV map of Yunling cattle for the first time using whole-genome resequencing. This provides valuable genetic variation resources for the study of the Yunling cattle genome and contributes to the study of economic traits in Yunling cattle.
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Affiliation(s)
- Dong Dang
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
| | - Lilian Zhang
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
| | - Lutao Gao
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
| | - Lin Peng
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
| | - Jian Chen
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
| | - Linnan Yang
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
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2
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Kim J, Sohn WM, Bae YA. Prostaglandin synthase activity of sigma- and mu-class glutathione transferases in a parasitic trematode, Clonorchis sinensis. PARASITES, HOSTS AND DISEASES 2024; 62:205-216. [PMID: 38835261 PMCID: PMC11150925 DOI: 10.3347/phd.24004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/21/2024] [Indexed: 06/06/2024]
Abstract
Sigma-class glutathione transferase (GST) proteins with dual GST and prostaglandin synthase (PGS) activities play a crucial role in the establishment of Clonorchis sinensis infection. Herein, we analyzed the structural and enzymatic properties of sigma-class GST (CsGST-σ) proteins to obtain insight into their antioxidant and immunomodulatory functions in comparison with mu-class GST (CsGST-μ) proteins. CsGST-σ proteins conserved characteristic structures, which had been described in mammalian hematopoietic prostaglandin D2 synthases. Recombinant forms of these CsGST-σ and CsGST-μ proteins expressed in Escherichia coli exhibited considerable degrees of GST and PGS activities with substantially different specific activities. All recombinant proteins displayed higher affinities toward prostaglandin H2 (PGS substrate; average Km of 30.7 and 3.0 μm for prostaglandin D2 [PGDS] and E2 synthase [PGES], respectively) than those toward CDNB (GST substrate; average Km of 1,205.1 μm). Furthermore, the catalytic efficiency (Kcat/Km) of the PGDS/PGES activity was higher than that of GST activity (average Kcat/Km of 3.1, 0.7, and 7.0×10-3 s-1μm-1 for PGDS, PGES, and GST, respectively). Our data strongly suggest that the C. sinensis sigma- and mu-class GST proteins are deeply involved in regulating host immune responses by generating PGD2 and PGE2 in addition to their roles in general detoxification.
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Affiliation(s)
- Jiyoung Kim
- Department of Microbiology, Gachon University College of Medicine, Incheon 21999,
Korea
| | - Woon-Mok Sohn
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727,
Korea
| | - Young-An Bae
- Department of Microbiology, Gachon University College of Medicine, Incheon 21999,
Korea
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University College of Medicine, Incheon 21999,
Korea
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Macholán M, Daniszová K, Hiadlovská Z. The Expansion of House Mouse Major Urinary Protein Genes Likely Did Not Facilitate Commensalism with Humans. Genes (Basel) 2023; 14:2090. [PMID: 38003032 PMCID: PMC10671799 DOI: 10.3390/genes14112090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
Mouse wild-derived strains (WDSs) combine the advantages of classical laboratory stocks and wild animals, and thus appear to be promising tools for diverse biomedical and evolutionary studies. We employed 18 WDSs representing three non-synanthropic species (Mus spretus, Mus spicilegus, and M. macedonicus) and three house mouse subspecies (Mus musculus musculus, M. m. domesticus, M. m. castaneus), which are all important human commensals to explore whether the number of major urinary protein (MUP) genes and their final protein levels in urine are correlated with the level of commensalism. Contrary to expectations, the MUP copy number (CN) and protein excretion in the strains derived from M. m. castaneus, which is supposed to be the strongest commensal, were not significantly different from the non-commensal species. Regardless of an overall tendency for higher MUP amounts in taxa with a higher CN, there was no significant correlation at the strain level. Our study thus suggests that expansion of the Mup cluster, which appeared before the house mouse diversification, is unlikely to facilitate commensalism with humans in three house mouse subspecies. Finally, we found considerable variation among con(sub)specific WDSs, warning against generalisations of results based on a few strains.
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Affiliation(s)
- Miloš Macholán
- Institute of Animal Physiology and Genetics, Laboratory of Mammalian Evolutionary Genetics, Czech Academy of Sciences, 602 00 Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 601 77 Brno, Czech Republic
| | - Kristina Daniszová
- Institute of Animal Physiology and Genetics, Laboratory of Mammalian Evolutionary Genetics, Czech Academy of Sciences, 602 00 Brno, Czech Republic
| | - Zuzana Hiadlovská
- Institute of Animal Physiology and Genetics, Laboratory of Mammalian Evolutionary Genetics, Czech Academy of Sciences, 602 00 Brno, Czech Republic
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4
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Qian R, Xie F, Zhang W, Kong J, Zhou X, Wang C, Li X. Genome-wide detection of CNV regions between Anqing six-end-white and Duroc pigs. Mol Cytogenet 2023; 16:12. [PMID: 37400846 PMCID: PMC10316616 DOI: 10.1186/s13039-023-00646-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/19/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Anqing six-end-white pig is a native breed in Anhui Province. The pigs have the disadvantages of a slow growth rate, low proportion of lean meat, and thick back fat, but feature the advantages of strong stress resistance and excellent meat quality. Duroc pig is an introduced pig breed with a fast growth rate and high proportion of lean meat. With the latter breed featuring superior growth characteristics but inferior meat quality traits, the underlying molecular mechanism that causes these phenotypic differences between Chinese and foreign pigs is still unclear. RESULTS In this study, copy number variation (CNV) detection was performed using the re-sequencing data of Anqing Six-end-white pigs and Duroc pigs, A total of 65,701 CNVs were obtained. After merging the CNVs with overlapping genomic positions, 881 CNV regions (CNVRs) were obtained. Based on the obtained CNVR information combined with their positions on the 18 chromosomes, a whole-genome map of the pig CNVs was drawn. GO analysis of the genes in the CNVRs showed that they were primarily involved in the cellular processes of proliferation, differentiation, and adhesion, and primarily involved in the biological processes of fat metabolism, reproductive traits, and immune processes. CONCLUSION The difference analysis of the CNVs between the Chinese and foreign pig breeds showed that the CNV of the Anqing six-end-white pig genome was higher than that of the introduced pig breed Duroc. Six genes related to fat metabolism, reproductive performance, and stress resistance were found in genome-wide CNVRs (DPF3, LEPR, MAP2K6, PPARA, TRAF6, NLRP4).
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Affiliation(s)
- Rong Qian
- Institue of Agricultural Economics and Information, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Fei Xie
- College of Animal Science, Anhui Science and Technology University, Fengyang County, 233100, Anhui Province, China
| | - Wei Zhang
- Institue of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - JuanJuan Kong
- Institue of Agricultural Economics and Information, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Xueli Zhou
- Institue of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Chonglong Wang
- Institue of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China.
| | - Xiaojin Li
- College of Animal Science, Anhui Science and Technology University, Fengyang County, 233100, Anhui Province, China.
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5
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Ruohan W, Yuwei Z, Mengbo W, Xikang F, Jianping W, Shuai Cheng L. Resolving single-cell copy number profiling for large datasets. Brief Bioinform 2022; 23:6633647. [PMID: 35801503 DOI: 10.1093/bib/bbac264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/29/2022] [Accepted: 06/06/2022] [Indexed: 11/14/2022] Open
Abstract
The advances of single-cell DNA sequencing (scDNA-seq) enable us to characterize the genetic heterogeneity of cancer cells. However, the high noise and low coverage of scDNA-seq impede the estimation of copy number variations (CNVs). In addition, existing tools suffer from intensive execution time and often fail on large datasets. Here, we propose SeCNV, an efficient method that leverages structural entropy, to profile the copy numbers. SeCNV adopts a local Gaussian kernel to construct a matrix, depth congruent map (DCM), capturing the similarities between any two bins along the genome. Then, SeCNV partitions the genome into segments by minimizing the structural entropy from the DCM. With the partition, SeCNV estimates the copy numbers within each segment for cells. We simulate nine datasets with various breakpoint distributions and amplitudes of noise to benchmark SeCNV. SeCNV achieves a robust performance, i.e. the F1-scores are higher than 0.95 for breakpoint detections, significantly outperforming state-of-the-art methods. SeCNV successfully processes large datasets (>50 000 cells) within 4 min, while other tools fail to finish within the time limit, i.e. 120 h. We apply SeCNV to single-nucleus sequencing datasets from two breast cancer patients and acoustic cell tagmentation sequencing datasets from eight breast cancer patients. SeCNV successfully reproduces the distinct subclones and infers tumor heterogeneity. SeCNV is available at https://github.com/deepomicslab/SeCNV.
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Affiliation(s)
- Wang Ruohan
- Department of Computer Science at City University of Hong Kong
| | - Zhang Yuwei
- Department of Computer Science at City University of Hong Kong
| | - Wang Mengbo
- Department of Computer Science at City University of Hong Kong
| | - Feng Xikang
- School of Software, Northwestern Polytechnical University
| | - Wang Jianping
- Department of Computer Science at City University of Hong Kong
| | - Li Shuai Cheng
- Department of Computer Science at City University of Hong Kong
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Prunier J, Carrier A, Gilbert I, Poisson W, Albert V, Taillon J, Bourret V, Côté SD, Droit A, Robert C. CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly. Life Sci Alliance 2021; 5:5/3/e202101207. [PMID: 34911809 PMCID: PMC8711850 DOI: 10.26508/lsa.202101207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 01/13/2023] Open
Abstract
Rangifer tarandus has experienced recent drastic population size reductions throughout its circumpolar distribution and preserving the species implies genetic diversity conservation. To facilitate genomic studies of the species populations, we improved the genome assembly by combining long read and linked read and obtained a new highly accurate and contiguous genome assembly made of 13,994 scaffolds (L90 = 131 scaffolds). Using de novo transcriptome assembly of RNA-sequencing reads and similarity with annotated human gene sequences, 17,394 robust gene models were identified. As copy number variations (CNVs) likely play a role in adaptation, we additionally investigated these variations among 20 genomes representing three caribou ecotypes (migratory, boreal and mountain). A total of 1,698 large CNVs (length > 1 kb) showing a genome distribution including hotspots were identified. 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions likely related to the expected adaptations. This work includes the first publicly available annotation of the caribou genome and the first assembly allowing genome architecture analyses, including the likely adaptive CNVs reported here.
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Affiliation(s)
- Julien Prunier
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Quebec City, Canada
| | - Alexandra Carrier
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
| | - Isabelle Gilbert
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
| | - William Poisson
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
| | - Vicky Albert
- Ministère des Forêts, de la Faune et des Parcs du Québec, Quebec City, Canada
| | - Joëlle Taillon
- Ministère des Forêts, de la Faune et des Parcs du Québec, Quebec City, Canada
| | - Vincent Bourret
- Ministère des Forêts, de la Faune et des Parcs du Québec, Quebec City, Canada
| | - Steeve D Côté
- Caribou Ungava, département de biologie, Faculté des Sciences et de Génie, Université Laval, Quebec City, Canada
| | - Arnaud Droit
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Quebec City, Canada
| | - Claude Robert
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
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Saridakis E. The genetic informational network: how DNA conveys semantic information. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2021; 43:112. [PMID: 34734317 DOI: 10.1007/s40656-021-00470-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
The question of whether "genetic information" is a merely causal factor in development or can be made sense of semantically, in a way analogous to a language or other type of representation, has generated a long debate in the philosophy of biology. It is intimately connected with another intense debate, concerning the limits of genetic determinism. In this paper I argue that widespread attempts to draw analogies between genetic information and information contained in books, blueprints or computer programs, are fundamentally inadequate. In development, gene exons are the central part of an intricate and densely ramified semantic Genetic Informational Network. DNA in the entire genome is in a state of continuous positive and negative feedback with itself and with its 'environment', and is 'read' and acted upon by the cell in various alternative and complementary ways. The linear combinatorial coding relation between codons and amino acids is but one aspect of semantic genetic information, which is, when considered in its entirety, a far wider and richer concept.
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Affiliation(s)
- Emmanuel Saridakis
- Laboratory of Structural and Supramolecular Chemistry, Institute of Nanoscience and Nanotechnology, National Centre for Scientific Research "DEMOKRITOS", 15310, Athens, Greece.
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8
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Quantitative neurogenetics: applications in understanding disease. Biochem Soc Trans 2021; 49:1621-1631. [PMID: 34282824 DOI: 10.1042/bst20200732] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 12/31/2022]
Abstract
Neurodevelopmental and neurodegenerative disorders (NNDs) are a group of conditions with a broad range of core and co-morbidities, associated with dysfunction of the central nervous system. Improvements in high throughput sequencing have led to the detection of putative risk genetic loci for NNDs, however, quantitative neurogenetic approaches need to be further developed in order to establish causality and underlying molecular genetic mechanisms of pathogenesis. Here, we discuss an approach for prioritizing the contribution of genetic risk loci to complex-NND pathogenesis by estimating the possible impacts of these loci on gene regulation. Furthermore, we highlight the use of a tissue-specificity gene expression index and the application of artificial intelligence (AI) to improve the interpretation of the role of genetic risk elements in NND pathogenesis. Given that NND symptoms are associated with brain dysfunction, risk loci with direct, causative actions would comprise genes with essential functions in neural cells that are highly expressed in the brain. Indeed, NND risk genes implicated in brain dysfunction are disproportionately enriched in the brain compared with other tissues, which we refer to as brain-specific expressed genes. In addition, the tissue-specificity gene expression index can be used as a handle to identify non-brain contexts that are involved in NND pathogenesis. Lastly, we discuss how using an AI approach provides the opportunity to integrate the biological impacts of risk loci to identify those putative combinations of causative relationships through which genetic factors contribute to NND pathogenesis.
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Ghazali N, Abd Rahman N, Ahmad A, Sulong S, Kannan TP. Identification of Copy Number Variation Among Nonsyndromic Cleft Lip and or Without Cleft Palate With Hypodontia: A Genome-Wide Association Study. Front Physiol 2021; 12:637306. [PMID: 33732167 PMCID: PMC7959817 DOI: 10.3389/fphys.2021.637306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/18/2021] [Indexed: 12/27/2022] Open
Abstract
Nonsyndromic cleft lip and or without cleft palate (NSCL/P) with the hypodontia is a common developmental abnormality in humans and animals. This study identified the genetic aberration involved in both NSCL/P and hypodontia pathogenesis. A cross-sectional study using genome-wide study copy number variation-targeted CytoScan 750K array carried out on salivary samples from 61 NSCL/P and 20 noncleft with and without hypodontia Malay subjects aged 7-13 years old. Copy number variations (CNVs) of SKI and fragile histidine triad (FHIT) were identified in NSCL/P and noncleft children using quantitative polymerase chain reaction (qPCR) as a validation analysis. Copy number calculated (CNC) for each gene determined with Applied Biosystems CopyCaller Software v2.0. The six significant CNVs included gains (12q14.3, 15q26.3, 1p36.32, and 1p36.33) and losses (3p14.2 and 4q13.2) in NSCL/P with hypodontia patients compared with the NSCL/P only. The genes located in these regions encoded LEMD3, IGF1R, TP73, SKI, FHIT, and UGT2β15. There were a significant gain and loss of both SKI and FHIT copy number in NSCL/P with hypodontia compared with the noncleft group (p < 0.05). The results supported that CNVs significantly furnish to the development of NSCL/P with hypodontia.
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Affiliation(s)
- Norliana Ghazali
- School of Dental Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | | | - Azlina Ahmad
- School of Dental Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
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Hu S, Zhang H, Liu Y, Liu M, Li J, Liao S. Whole-exome sequencing of de novo genetic variants in a Chinese family with a sporadic case of congenital nonsyndromic hearing loss. F1000Res 2021; 10:61. [PMID: 34567527 PMCID: PMC8422347 DOI: 10.12688/f1000research.27739.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/18/2021] [Indexed: 02/05/2023] Open
Abstract
Background: We examined the genetic variants of a Chinese family with a 22-month-old infant with sporadic non-syndromic sensorineural hearing loss (NSHL). Methods: The whole-exome sequence data in the family, especially the de novo variants presented in the patient, were analyzed and the effect of the disease-causing genetic variants on the protein expression level and cellular localization were examined by cell-based functional assay. Results: The infant had no known NSHL-causing variants, except two compound heterozygous variants in connexin26 gene GJB2; one was the c.79G>A, c.341A>G haplotype from the asymptomatic mother who was benign, and the other was a de novo pathogenic c.262G>C (p.A88P). In vitro, GJB2 with c.262G>C was weakly expressed and displayed a punctate distribution in the cytoplasm and cytomembrane, while wild type GJB2 was robustly expressed in the cytomembrane. We deduced that the de novo pathogenic GJB2 c.262G>C exacerbated loss-of-function in the context of leaky variants c.79G>A, c.341A>G in the patient. Interestingly, further analysis of exome sequences revealed that the occurrence of de novo pathogenic variants in the infant was frequent. Among the total~47,000 variants, 143 were de novo in the patient, whereas among all 74 variants predicted to be pathogenic/likely pathogenic, 21 were heterozygous and two were homozygous de novo. The occurrence rate of de novo deleterious variants was much higher (31.1%, 23/74) than that in total (0.34%, 143/47,000). It is notable that most genes with de novo deleterious variants were environment-sensitive, such as GJB2, MNK1, MNK2, MUC4, RAD21 and DNA copy number variations. Conclusions: The full picture of genetic variants in the exome might help us to interpret the NSHL-causing variants. More research is needed into the causes of de novo deleterious variants and gene-environment interactions in congenital NSHL.
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Affiliation(s)
- Sijing Hu
- Diabetes Center & Institute of Organ Transplantation, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China, 610072, China
| | - Hao Zhang
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital,, West China Medical School, Sichuan University,, Chengdu, China, 610041, China
| | - Yunqiang Liu
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital,, West China Medical School, Sichuan University,, Chengdu, China, 610041, China
| | - Mohan Liu
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital,, West China Medical School, Sichuan University,, Chengdu, China, 610041, China
| | - Jingjing Li
- Diabetes Center & Institute of Organ Transplantation, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China, 610072, China
| | - Shunyao Liao
- Diabetes Center & Institute of Organ Transplantation, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China, 610072, China
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11
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Hu S, Zhang H, Liu Y, Liu M, Li J, Liao S. Whole-exome sequencing of de novo genetic variants in a Chinese family with a sporadic case of congenital nonsyndromic hearing loss. F1000Res 2021; 10:61. [PMID: 34567527 PMCID: PMC8422347 DOI: 10.12688/f1000research.27739.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/06/2021] [Indexed: 04/04/2024] Open
Abstract
Background: We examined the genetic variants of a Chinese family with a 22-month-old infant with sporadic non-syndromic sensorineural hearing loss (NSHL). Methods: The whole-exome sequence data in the family, especially the de novo variants presented in the patient, were analyzed and the effect of the disease-causing genetic variants on the protein expression level and cellular localization were examined by cell-based functional assay. Results: The infant had no known NSHL-causing variants, except two compound heterozygous variants in connexin26 gene GJB2; one was the c.79G>A, c.341A>G haplotype from the asymptomatic mother which was benign, and the other was a de novo pathogenic c.262G>C (p.A88P). In vitro, GJB2 with c.262G>C was weakly expressed and displayed a punctate distribution in the cytoplasm and cytomembrane, while wild type GJB2 was robustly expressed in the cytomembrane. We deduced that the de novo pathogenic GJB2 c.262G>C exacerbated loss-of-function in the context of leaky variants c.79G>A, c.341A>G in the patient. Interestingly, further analysis of exome sequences revealed that the occurrence of de novo pathogenic variants in the infant was frequent. Among the total~47,000 variants, 143 were de novo in the patient, whereas among all 74 variants predicted to be pathogenic/likely pathogenic, 21 were heterozygous and two were homozygous de novo. The occurrence rate of de novo deleterious variants was much higher (31.1%, 23/74) than that in total (0.34%, 143/47,000). It is notable that most genes with de novo deleterious variants were environment-sensitive, such as GJB2, MNK1, MNK2, MUC4, RAD21 and DNA copy number variations. Conclusions: The full picture of genetic variants in the exome might help us to interpret the NSHL-causing variants. More research is needed into the causes of de novo deleterious variants and gene-environment interactions in congenital NSHL.
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Affiliation(s)
- Sijing Hu
- Diabetes Center & Institute of Organ Transplantation, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China, 610072, China
| | - Hao Zhang
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital,, West China Medical School, Sichuan University,, Chengdu, China, 610041, China
| | - Yunqiang Liu
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital,, West China Medical School, Sichuan University,, Chengdu, China, 610041, China
| | - Mohan Liu
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital,, West China Medical School, Sichuan University,, Chengdu, China, 610041, China
| | - Jingjing Li
- Diabetes Center & Institute of Organ Transplantation, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China, 610072, China
| | - Shunyao Liao
- Diabetes Center & Institute of Organ Transplantation, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China, 610072, China
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12
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Binversie EE, Baker LA, Engelman CD, Hao Z, Moran JJ, Piazza AM, Sample SJ, Muir P. Analysis of copy number variation in dogs implicates genomic structural variation in the development of anterior cruciate ligament rupture. PLoS One 2020; 15:e0244075. [PMID: 33382735 PMCID: PMC7774950 DOI: 10.1371/journal.pone.0244075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/02/2020] [Indexed: 11/19/2022] Open
Abstract
Anterior cruciate ligament (ACL) rupture is an important condition of the human knee. Second ruptures are common and societal costs are substantial. Canine cranial cruciate ligament (CCL) rupture closely models the human disease. CCL rupture is common in the Labrador Retriever (5.79% prevalence), ~100-fold more prevalent than in humans. Labrador Retriever CCL rupture is a polygenic complex disease, based on genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers. Dissection of genetic variation in complex traits can be enhanced by studying structural variation, including copy number variants (CNVs). Dogs are an ideal model for CNV research because of reduced genetic variability within breeds and extensive phenotypic diversity across breeds. We studied the genetic etiology of CCL rupture by association analysis of CNV regions (CNVRs) using 110 case and 164 control Labrador Retrievers. CNVs were called from SNPs using three different programs (PennCNV, CNVPartition, and QuantiSNP). After quality control, CNV calls were combined to create CNVRs using ParseCNV and an association analysis was performed. We found no strong effect CNVRs but found 46 small effect (max(T) permutation P<0.05) CCL rupture associated CNVRs in 22 autosomes; 25 were deletions and 21 were duplications. Of the 46 CCL rupture associated CNVRs, we identified 39 unique regions. Thirty four were identified by a single calling algorithm, 3 were identified by two calling algorithms, and 2 were identified by all three algorithms. For 42 of the associated CNVRs, frequency in the population was <10% while 4 occurred at a frequency in the population ranging from 10–25%. Average CNVR length was 198,872bp and CNVRs covered 0.11 to 0.15% of the genome. All CNVRs were associated with case status. CNVRs did not overlap previous canine CCL rupture risk loci identified by GWAS. Associated CNVRs contained 152 annotated genes; 12 CNVRs did not have genes mapped to CanFam3.1. Using pathway analysis, a cluster of 19 homeobox domain transcript regulator genes was associated with CCL rupture (P = 6.6E-13). This gene cluster influences cranial-caudal body pattern formation during embryonic limb development. Clustered genes were found in 3 CNVRs on chromosome 14 (HoxA), 28 (NKX6-2), and 36 (HoxD). When analysis was limited to deletion CNVRs, the association was strengthened (P = 8.7E-16). This study suggests a component of the polygenic risk of CCL rupture in Labrador Retrievers is associated with small effect CNVs and may include aspects of stifle morphology regulated by homeobox domain transcript regulator genes.
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Affiliation(s)
- Emily E. Binversie
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lauren A. Baker
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Corinne D. Engelman
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Zhengling Hao
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - John J. Moran
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexander M. Piazza
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Susannah J. Sample
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Peter Muir
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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13
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Tester DJ, Kim CSJ, Hamrick SK, Ye D, O'Hare BJ, Bombei HM, Fitzgerald KK, Haglund-Turnquist CM, Atkins DL, Nunez LAO, Law I, Temple J, Ackerman MJ. Molecular characterization of the calcium release channel deficiency syndrome. JCI Insight 2020; 5:135952. [PMID: 32663189 PMCID: PMC7455073 DOI: 10.1172/jci.insight.135952] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/01/2020] [Indexed: 11/26/2022] Open
Abstract
We identified a potentially novel homozygous duplication involving the promoter region and exons 1–4 of the gene encoding type 2 cardiac ryanodine receptor (RYR2) that is responsible for highly penetrant, exertion-related sudden deaths/cardiac arrests in the Amish community without an overt phenotype to suggest RYR2-mediated catecholaminergic polymorphic ventricular tachycardia (CPVT). Homozygous RYR2 duplication (RYR2-DUP) induced pluripotent stem cell cardiomyocytes (iPSC-CMs) were generated from 2 unrelated patients. There was no difference in baseline Ca2+ handling measurements between WT-iPSC-CM and RYR2-DUP-iPSC-CM lines. However, compared with WT-iPSC-CMs, both patient lines demonstrated a dramatic reduction in caffeine-stimulated and isoproterenol-stimulated (ISO-stimulated) Ca2+ transient amplitude, suggesting RyR2 loss of function. There was a greater than 50% reduction in RYR2 transcript/RyR2 protein expression in both patient iPSC-CMs compared with WT. Delayed afterdepolarization was observed in the RYR2-DUP-iPSC-CMs but not in the WT-iPSC-CMs. Compared with WT-iPSC-CMs, there was significantly elevated arrhythmic activity in the RYR2-DUP-iPSC-CMs in response to ISO. Nadolol, propranolol, and flecainide reduced erratic activity by 8.5-fold, 6.8-fold, and 2.4-fold, respectively, from ISO challenge. Unlike the gain-of-function mechanism observed in RYR2-mediated CPVT, the homozygous multiexon duplication precipitated a dramatic reduction in RYR2 transcription and RyR2 protein translation, a loss of function in calcium handling, and a calcium-induced calcium release apparatus that is insensitive to catecholamines and caffeine. Molecular and functional characterization of the calcium release channel deficiency syndrome in patient-specific induced pluripotent stem cell-cardiomyocytes.
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Affiliation(s)
- David J Tester
- Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics; Division of Heart Rhythm Services, Department of Cardiovascular Medicine; and Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - C S John Kim
- Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics; Division of Heart Rhythm Services, Department of Cardiovascular Medicine; and Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Samantha K Hamrick
- Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics; Division of Heart Rhythm Services, Department of Cardiovascular Medicine; and Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Dan Ye
- Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics; Division of Heart Rhythm Services, Department of Cardiovascular Medicine; and Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Bailey J O'Hare
- Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics; Division of Heart Rhythm Services, Department of Cardiovascular Medicine; and Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Hannah M Bombei
- Division of Cardiology, University of Iowa Stead Family Children's Hospital, Iowa City, Iowa, USA
| | - Kristi K Fitzgerald
- Nemours Cardiac Center, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Carla M Haglund-Turnquist
- Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics; Division of Heart Rhythm Services, Department of Cardiovascular Medicine; and Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Dianne L Atkins
- Division of Cardiology, University of Iowa Stead Family Children's Hospital, Iowa City, Iowa, USA
| | - Luis A Ochoa Nunez
- Division of Cardiology, University of Iowa Stead Family Children's Hospital, Iowa City, Iowa, USA
| | - Ian Law
- Division of Cardiology, University of Iowa Stead Family Children's Hospital, Iowa City, Iowa, USA
| | - Joel Temple
- Nemours Cardiac Center, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Michael J Ackerman
- Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics; Division of Heart Rhythm Services, Department of Cardiovascular Medicine; and Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA
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14
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Wang Z, Guo J, Guo Y, Yang Y, Teng T, Yu Q, Wang T, Zhou M, Zhu Q, Wang W, Zhang Q, Yang H. Genome-Wide Detection of CNVs and Association With Body Weight in Sheep Based on 600K SNP Arrays. Front Genet 2020; 11:558. [PMID: 32582291 PMCID: PMC7297042 DOI: 10.3389/fgene.2020.00558] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/07/2020] [Indexed: 01/30/2023] Open
Abstract
Copy number variations (CNVs) are important genomic structural variations and can give rise to significant phenotypic diversity. Herein, we used high-density 600K SNP arrays to detect CNVs in two synthetic lines of sheep (DS and SHH) and in Hu sheep (a local Chinese breed). A total of 919 CNV regions (CNVRs) were detected with a total length of 48.17 Mb, accounting for 1.96% of the sheep genome. These CNVRs consisted of 730 gains, 102 losses, and 87 complex CNVRs. These CNVRs were significantly enriched in the segmental duplication (SD) region. A CNVR-based cluster analysis of the three breeds revealed that the DS and SHH breeds share a close genetic relationship. Functional analysis revealed that some genes in these CNVRs were also significantly enriched in the olfactory transduction pathway (oas04740), including members of the OR gene family such as OR6C76, OR4Q2, and OR4K14. Using association analyses and previous gene annotations, we determined that a subset of identified genes was likely to be associated with body weight, including FOXF2, MAPK12, MAP3K11, STRBP, and C14orf132. Together, these results offer valuable information that will guide future efforts to explore the genetic basis for body weight in sheep.
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Affiliation(s)
- Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Jing Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Yuanyuan Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Teng Teng
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Tao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Meng Zhou
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Qiusi Zhu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Wenwen Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Qin Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
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15
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Jamaluddin J, Mohd Khair NK, Vinodamaney SD, Othman Z, Abubakar S. Copy number variation of CCL3L1 among three major ethnic groups in Malaysia. BMC Genet 2020; 21:1. [PMID: 31900126 PMCID: PMC6942282 DOI: 10.1186/s12863-019-0803-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 12/17/2019] [Indexed: 11/30/2022] Open
Abstract
Background C-C motif Chemokine Ligand 3 Like 1 (CCL3L1) is a multiallelic copy number variable, which plays a crucial role in immunoregulatory and hosts defense through the production of macrophage inflammatory protein (MIP)-1α. Variable range of the CCL3L1 copies from 0 to 14 copies have been documented in several different populations. However, there is still lack of report on the range of CCL3L1 copy number exclusively among Malaysians who are a multi-ethnic population. Thus, this study aims to extensively examine the distribution of CCL3L1 copy number in the three major populations from Malaysia namely Malay, Chinese and Indian. A diploid copy number of CCL3L1 for 393 Malaysians (Malay = 178, Indian = 90, and Chinese = 125) was quantified using Paralogue Ratio Tests (PRTs) and then validated with microsatellites analysis. Results To our knowledge, this is the first report on the CCL3L1 copy number that has been attempted among Malaysians and the Chinese ethnic group exhibits a diverse pattern of CCL3L1 distribution copy number from the Malay and Indian (p < 0.0001). The CCL3L1 ranged from 0 to 8 copies for both the Malay and Indian ethnic groups while 0 to 10 copies for the Chinese ethnic. Consequently, the CCL3L1 copy number among major ethnic groups in the Malaysian population is found to be significantly varied when compared to the European population (p < 0.0001). The mean/median reported for the Malay, Chinese, Indian, and European are 2.759/2.869, 3.453/3.290, 2.437/1.970 and 2.001/1.940 respectively. Conclusion This study reveals the existence of genetic variation of CCL3L1 in the Malaysian population, and suggests by examining genetic diversity on the ethnicity, and specific geographical region could help in reconstructing human evolutionary history and for the prediction of disease risk related to the CCL3L1 copy number.
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Affiliation(s)
- Jalilah Jamaluddin
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Nur Khairina Mohd Khair
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Shameni Devi Vinodamaney
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Zulkefley Othman
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Suhaili Abubakar
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia.
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16
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Obara Y, Sato H, Nakayama T, Kato T, Ishii K. Midnolin is a confirmed genetic risk factor for Parkinson's disease. Ann Clin Transl Neurol 2019; 6:2205-2211. [PMID: 31588691 PMCID: PMC6856597 DOI: 10.1002/acn3.50914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 09/12/2019] [Indexed: 12/31/2022] Open
Abstract
Objective Genetic analysis of patients with familial Parkinson’s disease (PD) identified many causative genes. However, the majority of PD cases are sporadic, and the mechanisms of onset still remain unclear. Previously, we found that Midnolin (MIDN) is associated with PD in a Yamagata (Japan) cohort study and that MIDN regulates neurite outgrowth and Parkin expression in neuronal cells. In the present study, we aimed to replicate the genetic association between MIDN and PD in a large British population cohort. Methods In this replication study, we analyzed the copy number variations and single‐nucleotide polymorphisms of the MIDN gene in a large British population on a case–control genome‐wide association study dataset including 2,860 controls and 2,168 PD patients. Results There was significant copy number loss in the MIDN gene with an odds ratio of 4.35 (P < 2.2 × 10−16). Furthermore, there were many patients in both the British and Yamagata case groups who have a long spanning deletion. The odds ratio dramatically increased to 22.3 (P = 3.59 × 10−15) when a deletion spanning more than 50,000 bp was defined as the copy number loss. There were no significant differences between the controls and study cases for two relatively frequent single‐nucleotide polymorphisms (rs3746106 and rs3746107). Interpretation We showed the strong genetic association of MIDN with PD development in a British population and in a Japanese population, suggesting MIDN is a confirmed and universal genetic risk factor for PD.
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Affiliation(s)
- Yutaro Obara
- Department of Pharmacology, Yamagata University School of Medicine, Yamagata, Japan
| | - Hidenori Sato
- Genome Informatics Unit, Institution for Promotion of Medical Science Research, Yamagata University School of Medicine, Yamagata, Japan
| | - Takahiro Nakayama
- Research Institute of Bio-system informatics, Tohoku Chemical Co., LTD, Morioka, Japan
| | - Takeo Kato
- Yamagata City Institute of Public Health, Yamagata, Japan
| | - Kuniaki Ishii
- Department of Pharmacology, Yamagata University School of Medicine, Yamagata, Japan
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17
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Abstract
BACKGROUND Biological networks describes the mechanisms which govern cellular functions. Temporal networks show how these networks evolve over time. Studying the temporal progression of network topologies is of utmost importance since it uncovers how a network evolves and how it resists to external stimuli and internal variations. Two temporal networks have co-evolving subnetworks if the evolving topologies of these subnetworks remain similar to each other as the network topology evolves over a period of time. In this paper, we consider the problem of identifying co-evolving subnetworks given a pair of temporal networks, which aim to capture the evolution of molecules and their interactions over time. Although this problem shares some characteristics of the well-known network alignment problems, it differs from existing network alignment formulations as it seeks a mapping of the two network topologies that is invariant to temporal evolution of the given networks. This is a computationally challenging problem as it requires capturing not only similar topologies between two networks but also their similar evolution patterns. RESULTS We present an efficient algorithm, Tempo, for solving identifying co-evolving subnetworks with two given temporal networks. We formally prove the correctness of our method. We experimentally demonstrate that Tempo scales efficiently with the size of network as well as the number of time points, and generates statistically significant alignments-even when evolution rates of given networks are high. Our results on a human aging dataset demonstrate that Tempo identifies novel genes contributing to the progression of Alzheimer's, Huntington's and Type II diabetes, while existing methods fail to do so. CONCLUSIONS Studying temporal networks in general and human aging specifically using Tempo enables us to identify age related genes from non age related genes successfully. More importantly, Tempo takes the network alignment problem one huge step forward by moving beyond the classical static network models.
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Affiliation(s)
- Rasha Elhesha
- University of Florida, CISE Department, Gainesville, Florida, 32611, US
| | - Aisharjya Sarkar
- University of Florida, CISE Department, Gainesville, Florida, 32611, US
| | - Christina Boucher
- University of Florida, CISE Department, Gainesville, Florida, 32611, US
| | - Tamer Kahveci
- University of Florida, CISE Department, Gainesville, Florida, 32611, US.
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18
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Anuar ND, Kurscheid S, Field M, Zhang L, Rebar E, Gregory P, Buchou T, Bowles J, Koopman P, Tremethick DJ, Soboleva TA. Gene editing of the multi-copy H2A.B gene and its importance for fertility. Genome Biol 2019; 20:23. [PMID: 30704500 PMCID: PMC6357441 DOI: 10.1186/s13059-019-1633-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 01/16/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Altering the biochemical makeup of chromatin by the incorporation of histone variants during development represents a key mechanism in regulating gene expression. The histone variant H2A.B, H2A.B.3 in mice, appeared late in evolution and is most highly expressed in the testis. In the mouse, it is encoded by three different genes. H2A.B expression is spatially and temporally regulated during spermatogenesis being most highly expressed in the haploid round spermatid stage. Active genes gain H2A.B where it directly interacts with polymerase II and RNA processing factors within splicing speckles. However, the importance of H2A.B for gene expression and fertility are unknown. RESULTS Here, we report the first mouse knockout of this histone variant and its effects on fertility, nuclear organization, and gene expression. In view of the controversy related to the generation of off-target mutations by gene editing approaches, we test the specificity of TALENs by disrupting the H2A.B multi-copy gene family using only one pair of TALENs. We show that TALENs do display a high level of specificity since no off-target mutations are detected by bioinformatics analyses of exome sequences obtained from three consecutive generations of knockout mice and by Sanger DNA sequencing. Male H2A.B.3 knockout mice are subfertile and display an increase in the proportion of abnormal sperm and clogged seminiferous tubules. Significantly, a loss of proper RNA Pol II targeting to distinct transcription-splicing territories and changes to pre-mRNA splicing are observed. CONCLUSION We have produced the first H2A.B knockout mouse using the TALEN approach.
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Affiliation(s)
- Nur Diana Anuar
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Sebastian Kurscheid
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Matt Field
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.,Present Address: James Cook University, PO Box 6811, Cairns, QLD, 4870, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Lei Zhang
- Sangamo Therapeutics, 501 Canal Blvd, Richmond, CA, 94804, USA
| | - Edward Rebar
- Sangamo Therapeutics, 501 Canal Blvd, Richmond, CA, 94804, USA
| | - Philip Gregory
- Sangamo Therapeutics, 501 Canal Blvd, Richmond, CA, 94804, USA.,Present Address: bluebird bio, 60 Binney St, Cambridge, MA, 02142, USA
| | - Thierry Buchou
- CNRS UMR 5309, Inserm U1209, Universite' Grenoble Alpes, Institute for Advanced Biosciences, 38700, Grenoble, France
| | - Josephine Bowles
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Tremethick
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
| | - Tatiana A Soboleva
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
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19
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De Toni L, Šabovic I, Cosci I, Ghezzi M, Foresta C, Garolla A. Testicular Cancer: Genes, Environment, Hormones. Front Endocrinol (Lausanne) 2019; 10:408. [PMID: 31338064 PMCID: PMC6626920 DOI: 10.3389/fendo.2019.00408] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/07/2019] [Indexed: 12/19/2022] Open
Abstract
Testicular cancer (TC) represents one of the most peculiar clinical challenges at present. In fact, currently treatments are so effective ensuring a 5 years disease-free survival rate in nearly 95% of patients. On the other hand however, TC represents the most frequent newly diagnosed form of cancer in men between the ages of 14 and 44 years, with an incidence ranging from <1 to 9.9 affected individuals per 100,000 males across countries, while the overall incidence is also increasing worldwide. Furthermore, cancer survivors show a 2% risk of developing cancer in the contralateral testis within 15 years of initial diagnosis. This complex and multifaceted scenario requires a great deal of effort to understand the clinical base of available evidence. It is now clear that genetic, environmental and hormonal risk factors concur and mutually influence both the development of the disease and its prognosis, in terms of response to treatment and the risk of recurrence. In this paper, the most recent issues describing the relative contribution of the aforementioned risk factors in TC development are discussed. In addition, particular attention is paid to the exposure to environmental chemical substances and thermal stress, whose role in cancer development and progression has recently been investigated at the molecular level.
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Affiliation(s)
- Luca De Toni
- Unit of Andrology and Reproductive Medicine, Department of Medicine, University of Padova, Padova, Italy
| | - Iva Šabovic
- Unit of Andrology and Reproductive Medicine, Department of Medicine, University of Padova, Padova, Italy
| | - Ilaria Cosci
- Unit of Andrology and Reproductive Medicine, Department of Medicine, University of Padova, Padova, Italy
- Department of Clinical and Experimental Oncology, IOV-IRCCS, Padova, Italy
| | - Marco Ghezzi
- Unit of Andrology and Reproductive Medicine, Department of Medicine, University of Padova, Padova, Italy
| | - Carlo Foresta
- Unit of Andrology and Reproductive Medicine, Department of Medicine, University of Padova, Padova, Italy
- *Correspondence: Carlo Foresta
| | - Andrea Garolla
- Unit of Andrology and Reproductive Medicine, Department of Medicine, University of Padova, Padova, Italy
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20
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Vijay A, Garg I, Ashraf MZ. Perspective: DNA Copy Number Variations in Cardiovascular Diseases. Epigenet Insights 2018; 11:2516865718818839. [PMID: 30560231 PMCID: PMC6291864 DOI: 10.1177/2516865718818839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 12/27/2022] Open
Abstract
Human genome contains many variations, often called mutations, which are difficult to detect and have remained a challenge for years. A substantial part of the genome encompasses repeats and when such repeats are in the coding region they may lead to change in the gene expression profile followed by pathological conditions. Structural variants are alterations which change one or more sequence feature in the chromosome such as change in the copy number, rearrangements, and translocations of a sequence and can be balanced or unbalanced. Copy number variants (CNVs) may increase or decrease the copies of a given region and have a pivotal role in the onset of many diseases including cardiovascular disorders. Cardiovascular disorders have a magnitude of well-established risk factors and etiology, but their correlation with CNVs is still being studied. In this article, we have discussed history of CNVs and a summary on the diseases associated with CNVs. To detect such variations, we shed light on the number of techniques introduced so far and their limitations. The lack of studies on cardiovascular diseases to determine the frequency of such variants needs clinical studies with larger cohorts. This review is a compilation of articles suggesting the importance of CNVs in multitude of cardiovascular anomalies. Finally, future perspectives for better understanding of CNVs and cardiovascular disorders have also been discussed.
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Affiliation(s)
- Aatira Vijay
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Iti Garg
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Mohammad Zahid Ashraf
- Genomics Division, Defence Institute of Physiology and Allied Sciences, DRDO, Delhi, India
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Prunier J, Giguère I, Ryan N, Guy R, Soolanayakanahally R, Isabel N, MacKay J, Porth I. Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations. Mol Ecol 2018; 28:1476-1490. [PMID: 30270494 DOI: 10.1111/mec.14836] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022]
Abstract
Gene copy number variations (CNVs) involved in phenotypic variations have already been shown in plants, but genomewide testing of CNVs for adaptive variation was not doable until recent technological developments. Thus, reports of the genomic architecture of adaptation involving CNVs remain scarce to date. Here, we investigated F1 progenies of an intraprovenance cross (north-north cross, 58th parallel) and an interprovenances cross (north-south cross, 58th/49th parallels) for CNVs using comparative genomic hybridization on arrays of probes targeting gene sequences in balsam poplar (Populus balsamifera L.), a widespread North American forest tree. A total of 1,721 genes were found in varying copy numbers over the set of 19,823 tested genes. These gene CNVs presented an estimated average size of 8.3 kb and were distributed over poplar's 19 chromosomes including 22 hotspot regions. Gene CNVs number was higher for the interprovenance progeny in accordance with an expected higher genetic diversity related to the composite origin of this family. Regression analyses between gene CNVs and seven adaptive trait variations resulted in 23 significant links; among these adaptive gene CNVs, 30% were located in hotspots. One-to-five gene CNVs were found related to each of the measured adaptive traits and annotated for both biotic and abiotic stress responses. These annotations can be related to the occurrence of a higher pathogenic pressure in the southern parts of balsam poplar's distribution, and higher photosynthetic assimilation rates and water-use efficiency at high latitudes. Overall, our findings suggest that gene CNVs typically having higher mutation rates than SNPs may in fact represent efficient adaptive variations against fast-evolving pathogens.
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Affiliation(s)
- Julien Prunier
- Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.,Centre for Forest Research, Université Laval, Québec, Quebec, Canada
| | - Isabelle Giguère
- Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.,Centre for Forest Research, Université Laval, Québec, Quebec, Canada
| | - Natalie Ryan
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert Guy
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Raju Soolanayakanahally
- Indian Head Research Farm, Agriculture and Agri-Food Canada, Indian Head, Saskatchewan, Canada
| | - Nathalie Isabel
- Laurentian Forest Centre, Canadian Forest Service, Natural Resources Canada, Québec, Quebec, Canada
| | - John MacKay
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Ilga Porth
- Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.,Centre for Forest Research, Université Laval, Québec, Quebec, Canada
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De novo vs. inherited copy number variations in multiple sclerosis susceptibility. Cell Mol Immunol 2018; 15:812-814. [PMID: 29429997 DOI: 10.1038/cmi.2017.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/09/2017] [Accepted: 12/09/2017] [Indexed: 11/08/2022] Open
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Fernández R, Guillamón A, Gómez-Gil E, Esteva I, Almaraz MC, Cortés-Cortés J, Lamas B, Lema E, Pásaro E. Analyses of karyotype by G-banding and high-resolution microarrays in a gender dysphoria population. Genes Genomics 2018; 40:465-473. [DOI: 10.1007/s13258-017-0646-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 12/29/2017] [Indexed: 12/31/2022]
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Karimi K, Esmailizadeh A, Wu DD, Gondro C. Mapping of genome-wide copy number variations in the Iranian indigenous cattle using a dense SNP data set. ANIMAL PRODUCTION SCIENCE 2018. [DOI: 10.1071/an16384] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The objective of this study was to present the first map of the copy number variations (CNVs) in Iranian indigenous cattle based on a high-density single nucleotide polymorphism (SNP) dataset. A total of 90 individuals were genotyped using the Illumina BovineHD BeadChip containing 777 962 SNPs. The QuantiSNP algorithm was used to perform a genome-wide CNV detection across autosomal genome. After merging the overlapping CNV, a total of 221 CNV regions were identified encompassing 36.4 Mb or 1.44% of the bovine autosomal genome. The length of the CNV regions ranged from 3.5 to 2252.8 Kb with an average of 163.8 Kb. These regions included 147 loss (66.52%) and 74 gain (33.48%) events containing a total of 637 annotated Ensembl genes. Gene ontology analysis revealed that most of genes in the CNV regions were involved in environmental responses, disease susceptibility and immune system functions. Furthermore, 543 of these genes corresponded to the human orthologous genes, which involved in a wide range of biological functions. Altogether, 73% of the 221 CNV regions overlapped either completely or partially with those previously reported in other cattle studies. Moreover, novel CNV regions involved several quantitative trait loci (QTL)-related to adaptative traits of Iranian indigenous cattle. These results provided a basis to conduct future studies on association between CNV regions and phenotypic variations in the Iranian indigenous cattle.
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Rocca MS, Di Nisio A, Marchiori A, Ghezzi M, Opocher G, Foresta C, Ferlin A. Copy number variations of E2F1: a new genetic risk factor for testicular cancer. Endocr Relat Cancer 2017; 24:119-125. [PMID: 28104681 DOI: 10.1530/erc-16-0514] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 01/18/2017] [Indexed: 01/24/2023]
Abstract
Testicular germ cell tumor (TGCT) is one of the most heritable forms of cancer. In last years, many evidence suggested that constitutional genetic factors, mainly single nucleotide polymorphisms, can increase its risk. However, the possible contribution of copy number variations (CNVs) in TGCT susceptibility has not been substantially addressed. Indeed, an increasing number of studies have focused on the effect of CNVs on gene expression and on the role of these structural genetic variations as risk factors for different forms of cancer. E2F1 is a transcription factor that plays an important role in regulating cell growth, differentiation, apoptosis and response to DNA damage. Therefore, deficiency or overexpression of this protein might significantly influence fundamental biological processes involved in cancer development and progression, including TGCT. We analyzed E2F1 CNVs in 261 cases with TGCT and 165 controls. We found no CNVs in controls, but 17/261 (6.5%) cases showed duplications in E2F1 Blot analysis demonstrated higher E2F1 expression in testicular samples of TGCT cases with three copies of the gene. Furthermore, we observed higher phosphorylation of Akt and mTOR in samples with E2F1 duplication. Interestingly, normal, non-tumoral testicular tissue in patient with E2F1 duplication showed lower expression of E2F1 and lower AKT/mTOR phosphorylation with respect to adjacent tumor tissue. Furthermore, increased expression of E2F1 obtained in vitro in NTERA-2 testicular cell line induced increased AKT/mTOR phosphorylation. This study suggests for the first time an involvement of E2F1 CNVs in TGCT susceptibility and supports previous preliminary data on the importance of AKT/mTOR signaling pathway in this cancer.
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Affiliation(s)
| | - Andrea Di Nisio
- Department of MedicineDIMED University of Padua, Padua, Italy
| | | | - Marco Ghezzi
- Department of MedicineDIMED University of Padua, Padua, Italy
| | - Giuseppe Opocher
- Department of MedicineDIMED University of Padua, Padua, Italy
- Familial Tumor UnitVeneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Carlo Foresta
- Department of MedicineDIMED University of Padua, Padua, Italy
| | - Alberto Ferlin
- Department of MedicineDIMED University of Padua, Padua, Italy
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Cuccaro D, De Marco EV, Cittadella R, Cavallaro S. Copy Number Variants in Alzheimer's Disease. J Alzheimers Dis 2017; 55:37-52. [PMID: 27662298 PMCID: PMC5115612 DOI: 10.3233/jad-160469] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2016] [Indexed: 12/18/2022]
Abstract
Alzheimer's disease (AD) is a devastating disease mainly afflicting elderly people, characterized by decreased cognition, loss of memory, and eventually death. Although risk and deterministic genes are known, major genetics research programs are underway to gain further insights into the inheritance of AD. In the last years, in particular, new developments in genome-wide scanning methodologies have enabled the association of a number of previously uncharacterized copy number variants (CNVs, gain or loss of DNA) in AD. Because of the exceedingly large number of studies performed, it has become difficult for geneticists as well as clinicians to systematically follow, evaluate, and interpret the growing number of (sometime conflicting) CNVs implicated in AD. In this review, after a brief introduction of this type of structural variation, and a description of available databases, computational analyses, and technologies involved, we provide a systematic review of all published data showing statistical and scientific significance of pathogenic CNVs and discuss the role they might play in AD.
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Affiliation(s)
- Denis Cuccaro
- Institute of Neurological Sciences, National Research Council, Section of Catania, Italy
| | | | - Rita Cittadella
- Institute of Neurological Sciences, National Research Council, Section of Mangone, Italy
| | - Sebastiano Cavallaro
- Institute of Neurological Sciences, National Research Council, Section of Catania, Italy
- Institute of Neurological Sciences, National Research Council, Section of Mangone, Italy
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Singh P, Dass JFP. A multifaceted computational report on the variants effect on KIR2DL3 and IFNL3 candidate gene in HCV clearance. Mol Biol Rep 2016; 43:1101-17. [PMID: 27461217 DOI: 10.1007/s11033-016-4044-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 07/14/2016] [Indexed: 12/15/2022]
Abstract
HCV infection causes acute and chronic liver diseases including, cirrhosis and hepatocellular carcinoma. Following HCV infection, spontaneous clearance occurs in approximately 20 % of the population dependant upon HCV genotype. In this study, functional and non-functional variant analysis was executed for the classical and the latest HCV clearance candidate genes namely, KIR2DL3 and IFNL3. Initially, the functional effects of non-synonymous SNPs were assigned on exposing to homology based tools, SIFT, PolyPhen-2 and PROVEAN. Further, UTR and splice sites variants were scanned for the gene expression and regulation changes. Subsequently, the haplotype and CNV were also identified. The mutation H77Y of KIR2DL3 and R157Q, H156Y, S63L, R157W, F179V, H128R, T101M, R180C, and F176I of IFNL3 results in conservation, RMSD, total energy, stability, and secondary structures revealed a negative impact on the structural fitness. UTRscan and the splice site result indicate functional change, which may affect gene regulation and expression. The graphical display of selected population shows alleles like rs270779, rs2296370, rs10423751, rs12982559, rs9797797, and rs35987710 of KIR2DL3 and rs12972991, rs12980275, rs4803217, rs8109886, and rs8099917 of IFNL3 are in high LD with a measure of [Formula: see text] broadcasting its protective effect in HCV clearance. Similarly, CNV report suggests major DNA fragment loss that could have a profound impact on the gene expression affecting the overall phenotype. This roundup report specifies the effect of NK cell receptor, KIR2DL3 and IFNL3 variants that can have a better prospect in GWAS and immunogenetic studies leading to better understanding of HCV clearance and progression.
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Affiliation(s)
- Pratichi Singh
- Bioinformatics Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - J Febin Prabhu Dass
- Bioinformatics Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India.
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A Highly Polymorphic Copy Number Variant in the NSF Gene is Associated with Cocaine Dependence. Sci Rep 2016; 6:31033. [PMID: 27498889 PMCID: PMC4976312 DOI: 10.1038/srep31033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/12/2016] [Indexed: 12/25/2022] Open
Abstract
Cocaine dependence is a complex psychiatric disorder involving both genetic and environmental factors. Several neurotransmitter systems mediate cocaine’s effects, dependence and relapse, being the components of the neurotransmitter release machinery good candidates for the disorder. Previously, we identified a risk haplotype for cocaine dependence in the NSF gene, encoding the protein N-Ethylmaleimide-Sensitive Factor essential for synaptic vesicle turnover. Here we examined the possible contribution to cocaine dependence of a large copy number variant (CNV) that encompasses part of the NSF gene. We performed a case-control association study in a discovery sample (359 cases and 356 controls) and identified an association between cocaine dependence and the CNV (P = 0.013), that was confirmed in the replication sample (508 cases and 569 controls, P = 7.1e-03) and in a pooled analysis (P = 1.8e-04), with an over-representation of low number of copies in cases. Subsequently, we studied the functional impact of the CNV on gene expression and found that the levels of two NSF transcripts were significantly increased in peripheral blood mononuclear cells (PBMC) along with the number of copies of the CNV. These results, together with a previous study from our group, support the role of NSF in the susceptibility to cocaine dependence.
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Zhou LS, Li J, Yang J, Liu CL, Xie XH, He YN, Liu XX, Xin WS, Zhang WC, Ren J, Ma JW, Huang LS. Genome-wide mapping of copy number variations in commercial hybrid pigs using a high-density SNP genotyping array. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795415120145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Saeed S, Bonnefond A, Manzoor J, Shabbir F, Ayesha H, Philippe J, Durand E, Crouch H, Sand O, Ali M, Butt T, Rathore AW, Falchi M, Arslan M, Froguel P. Genetic variants in LEP, LEPR, and MC4R explain 30% of severe obesity in children from a consanguineous population. Obesity (Silver Spring) 2015; 23:1687-95. [PMID: 26179253 DOI: 10.1002/oby.21142] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 03/24/2015] [Accepted: 04/10/2015] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Single gene mutations leading to severe obesity have so far been identified in 3-5% cases in European populations. However, prevalence of these pathogenic mutations has not systematically been examined in specific consanguineous populations. Here we describe the incidence of obesity-associated mutations through a step-wise sequence analysis, in a cohort of 73 Pakistani children with severe obesity from consanguineous families. METHODS Initially, all subjects were screened for mutations in coding regions of leptin (LEP) and melanocortin 4 receptor (MC4R) genes by direct sequencing. Subjects negative for mutation in these genes were screened using microdroplet PCR enrichment and NGS. Genomic structural variation was assessed by genotyping. Serum leptin, insulin, and cortisol were determined by ELISA. RESULTS Among 73 children with severe obesity (BMI SDS > 3.0), we identified 22 probands and 5 relatives, carrying 10 different loss-of-function homozygous mutations in LEP, leptin receptor (LEPR), and MC4R genes, including 4 novel variants. Hypercortisolemia was significantly emphasized in LEP mutation carriers. CONCLUSIONS The prevalence of pathogenic mutations in genes known to directly influence leptin-melanocortin signaling is 30% in our cohort. The results of this study emphasize the desirability of undertaking systematic and in-depth genetic analysis of cases with severe obesity in specific consanguineous populations.
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Affiliation(s)
- Sadia Saeed
- Department of Genomics of Common Disease, Imperial College London, London, UK
| | - Amélie Bonnefond
- European Genomic Institute for Diabetes (EGID), Lille, France
- CNRS-Umr8199, Lille Pasteur Institute, Lille, France
- Lille University, Lille, France
| | - Jaida Manzoor
- Department of Paediatric Endocrinology, Children's Hospital, Lahore, Pakistan
| | - Faiza Shabbir
- Department of Biological Sciences, Forman Christian College, Lahore, Pakistan
| | - Hina Ayesha
- Department of Paediatrics, Punjab Medical College, Faisalabad, Pakistan
| | - Julien Philippe
- European Genomic Institute for Diabetes (EGID), Lille, France
- CNRS-Umr8199, Lille Pasteur Institute, Lille, France
- Lille University, Lille, France
| | - Emmanuelle Durand
- European Genomic Institute for Diabetes (EGID), Lille, France
- CNRS-Umr8199, Lille Pasteur Institute, Lille, France
- Lille University, Lille, France
| | - Hutokshi Crouch
- Department of Genomics of Common Disease, Imperial College London, London, UK
| | - Olivier Sand
- European Genomic Institute for Diabetes (EGID), Lille, France
- CNRS-Umr8199, Lille Pasteur Institute, Lille, France
- Lille University, Lille, France
| | - Muhammad Ali
- Department of Paediatrics, Mayo Hospital, King Edward Medical University, Lahore, Pakistan
| | - Taeed Butt
- Department of Paediatrics, Fatima Memorial Hospital, Lahore, Pakistan
| | - Ahsan W Rathore
- Department of Paediatric Endocrinology, Children's Hospital, Lahore, Pakistan
| | - Mario Falchi
- Department of Genomics of Common Disease, Imperial College London, London, UK
| | - Muhammad Arslan
- Department of Biological Sciences, Forman Christian College, Lahore, Pakistan
- Centre for Research in Molecular Medicine, the University of Lahore, Lahore, Pakistan
| | - Philippe Froguel
- Department of Genomics of Common Disease, Imperial College London, London, UK
- European Genomic Institute for Diabetes (EGID), Lille, France
- CNRS-Umr8199, Lille Pasteur Institute, Lille, France
- Lille University, Lille, France
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Improved Detection and Characterization of Copy Number Variations Among Diverse Pig Breeds by Array CGH. G3-GENES GENOMES GENETICS 2015; 5:1253-61. [PMID: 25908567 PMCID: PMC4478553 DOI: 10.1534/g3.115.018473] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
As a major component of genomic variation, copy number variations (CNVs) are considered as promising markers for some phenotypic and economically important traits in domestic animals. Using a custom-designed 1M array CGH (aCGH), we performed CNV discovery in 12 pig samples from one Asian wild boar population, six Chinese indigenous breeds, and two European commercial breeds. In total, we identified 758 CNV regions (CNVRs), covering 47.43 Mb of the pig genome sequence. Of the total porcine genes, 1295 genes were completely or partially overlapped with the identified CNVRs, which enriched in the terms related to sensory perception of the environment, neurodevelopmental processes, response to external stimuli, and immunity. Further probing the potential functions of these genes, we also found a suite of genes related important traits, which make them a promising resource for exploring the genetic basis of phenotype differences among diverse pig breeds. Compared with previous relevant studies, the current study highlights that different platforms can complement each other, and the combined implementation of different platforms is beneficial to achieve the most comprehensive CNV calls. CNVs detected in diverse populations herein are essentially complementary to the CNV map in the pig genome, which would be helpful for understanding the pig genome variants and investigating the associations between various phenotypes and CNVs.
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Startek M, Szafranski P, Gambin T, Campbell IM, Hixson P, Shaw CA, Stankiewicz P, Gambin A. Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination. Nucleic Acids Res 2015; 43:2188-98. [PMID: 25613453 PMCID: PMC4344489 DOI: 10.1093/nar/gku1394] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Nonallelic homologous recombination (NAHR), occurring between low-copy repeats (LCRs) >10 kb in size and sharing >97% DNA sequence identity, is responsible for the majority of recurrent genomic rearrangements in the human genome. Recent studies have shown that transposable elements (TEs) can also mediate recurrent deletions and translocations, indicating the features of substrates that mediate NAHR may be significantly less stringent than previously believed. Using >4 kb length and >95% sequence identity criteria, we analyzed of the genome-wide distribution of long interspersed element (LINE) retrotransposon and their potential to mediate NAHR. We identified 17 005 directly oriented LINE pairs located <10 Mbp from each other as potential NAHR substrates, placing 82.8% of the human genome at risk of LINE-LINE-mediated instability. Cross-referencing these regions with CNVs in the Baylor College of Medicine clinical chromosomal microarray database of 36 285 patients, we identified 516 CNVs potentially mediated by LINEs. Using long-range PCR of five different genomic regions in a total of 44 patients, we confirmed that the CNV breakpoints in each patient map within the LINE elements. To additionally assess the scale of LINE-LINE/NAHR phenomenon in the human genome, we tested DNA samples from six healthy individuals on a custom aCGH microarray targeting LINE elements predicted to mediate CNVs and identified 25 LINE-LINE rearrangements. Our data indicate that LINE-LINE-mediated NAHR is widespread and under-recognized, and is an important mechanism of structural rearrangement contributing to human genomic variability.
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Affiliation(s)
- Michał Startek
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Patricia Hixson
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Anna Gambin
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawińskiego street, 02-106 Warsaw, Poland
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Analysis of genome-wide copy number variations in Chinese indigenous and western pig breeds by 60 K SNP genotyping arrays. PLoS One 2014; 9:e106780. [PMID: 25198154 PMCID: PMC4157799 DOI: 10.1371/journal.pone.0106780] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 08/07/2014] [Indexed: 12/28/2022] Open
Abstract
Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs.
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Complexity of gene expression evolution after duplication: protein dosage rebalancing. GENETICS RESEARCH INTERNATIONAL 2014; 2014:516508. [PMID: 25197576 PMCID: PMC4150538 DOI: 10.1155/2014/516508] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/03/2014] [Indexed: 11/17/2022]
Abstract
Ongoing debates about functional importance of gene duplications have been recently intensified by a heated discussion of the “ortholog conjecture” (OC). Under the OC, which is central to functional annotation of genomes, orthologous genes are functionally more similar than paralogous genes at the same level of sequence divergence. However, a recent study challenged the OC by reporting a greater functional similarity, in terms of gene ontology (GO) annotations and expression profiles, among within-species paralogs compared to orthologs. These findings were taken to indicate that functional similarity of homologous genes is primarily determined by the cellular context of the genes, rather than evolutionary history. Subsequent studies suggested that the OC appears to be generally valid when applied to mammalian evolution but the complete picture of evolution of gene expression also has to incorporate lineage-specific aspects of paralogy. The observed complexity of gene expression evolution after duplication can be explained through selection for gene dosage effect combined with the duplication-degeneration-complementation model. This paper discusses expression divergence of recent duplications occurring before functional divergence of proteins encoded by duplicate genes.
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Jiang J, Wang J, Wang H, Zhang Y, Kang H, Feng X, Wang J, Yin Z, Bao W, Zhang Q, Liu JF. Global copy number analyses by next generation sequencing provide insight into pig genome variation. BMC Genomics 2014; 15:593. [PMID: 25023178 PMCID: PMC4111851 DOI: 10.1186/1471-2164-15-593] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 07/04/2014] [Indexed: 01/10/2023] Open
Abstract
Background Copy number variations (CNVs) confer significant effects on genetic innovation and phenotypic variation. Previous CNV studies in swine seldom focused on in-depth characterization of global CNVs. Results Using whole-genome assembly comparison (WGAC) and whole-genome shotgun sequence detection (WSSD) approaches by next generation sequencing (NGS), we probed formation signatures of both segmental duplications (SDs) and individualized CNVs in an integrated fashion, building the finest resolution CNV and SD maps of pigs so far. We obtained copy number estimates of all protein-coding genes with copy number variation carried by individuals, and further confirmed two genes with high copy numbers in Meishan pigs through an enlarged population. We determined genome-wide CNV hotspots, which were significantly enriched in SD regions, suggesting evolution of CNV hotspots may be affected by ancestral SDs. Through systematically enrichment analyses based on simulations and bioinformatics analyses, we revealed CNV-related genes undergo a different selective constraint from those CNV-unrelated regions, and CNVs may be associated with or affect pig health and production performance under recent selection. Conclusions Our studies lay out one way for characterization of CNVs in the pig genome, provide insight into the pig genome variation and prompt CNV mechanisms studies when using pigs as biomedical models for human diseases. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-593) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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Longpre KM, Kinstlinger NS, Mead EA, Wang Y, Thekkumthala AP, Carreno KA, Hot A, Keefer JM, Tully L, Katz LS, Pietrzykowski AZ. Seasonal variation of urinary microRNA expression in male goats (Capra hircus) as assessed by next generation sequencing. Gen Comp Endocrinol 2014; 199:1-15. [PMID: 24457251 DOI: 10.1016/j.ygcen.2014.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 12/03/2013] [Accepted: 01/08/2014] [Indexed: 01/09/2023]
Abstract
Testosterone plays a key role in preparation of a male domesticated goat (Capra hircus) to breeding season including changes in the urogenital tract of a male goat (buck). microRNAs are important regulators of cellular metabolism, differentiation and function. They are powerful intermediaries of hormonal activity in the body, including the urogenital tract. We investigated seasonal changes in expression of microRNAs in goat buck urine and their potential consequences using next generation sequencing (microRNA-Seq). We determined the location of each microRNA gene in the goat genome. Testosterone was measured by radioimmunoassay and the androgen receptor binding sites (ARBS) in the promoters of the microRNA genes were determined by MatInspector. The overall impact of regulated microRNAs on cellular physiology was assessed by mirPath. We observed high testosterone levels during the breeding season and changes in the expression of forty microRNAs. Nineteen microRNAs were upregulated, while twenty-one were downregulated. We identified several ARBS in the promoters of regulated microRNAs. Notably, the mostly inhibited microRNA, miR-1246, has a unique set of several gene copy variants associated with a cluster of androgen receptor binding sites. Concomitant changes in regulated microRNA expression could promote transcription, proliferation and differentiation of urogenital tract cells. Together, these findings indicate that in a domesticated goat (Capra hircus), there are specific changes in the microRNA expression profile in buck urine during breeding season, which could be attributable to high testosterone levels during breeding, and could help in preparation of the urogenital tract for high metabolic demands of that season.
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Affiliation(s)
- Kristy M Longpre
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Noah S Kinstlinger
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Edward A Mead
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Yongping Wang
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Austin P Thekkumthala
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Katherine A Carreno
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Azra Hot
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Jennifer M Keefer
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Luke Tully
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Larry S Katz
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Andrzej Z Pietrzykowski
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA.
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Wang J, Jiang J, Wang H, Kang H, Zhang Q, Liu JF. Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds. PLoS One 2014; 9:e87571. [PMID: 24475311 PMCID: PMC3903766 DOI: 10.1371/journal.pone.0087571] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 12/20/2013] [Indexed: 11/18/2022] Open
Abstract
Copy number variations (CNVs) are important forms of genomic variation, and have attracted extensive attentions in humans as well as domestic animals. In the study, using a custom-designed 2.1 M array comparative genomic hybridization (aCGH), genome-wide CNVs were identified among 12 individuals from diverse pig breeds, including one Asian wild population, six Chinese indigenous breeds and two modern commercial breeds (Yorkshire and Landrace), with one individual of the other modern commercial breed, Duroc, as the reference. A total of 1,344 CNV regions (CNVRs) were identified, covering 47.79 Mb (∼1.70%) of the pig genome. The length of these CNVRs ranged from 3.37 Kb to 1,319.0 Kb with a mean of 35.56 Kb and a median of 11.11 Kb. Compared with similar studies reported, most of the CNVRs (74.18%) were firstly identified in present study. In order to confirm these CNVRs, 21 CNVRs were randomly chosen to be validated by quantitative real time PCR (qPCR) and a high rate (85.71%) of confirmation was obtained. Functional annotation of CNVRs suggested that the identified CNVRs have important function, and may play an important role in phenotypic and production traits difference among various breeds. Our results are essential complementary to the CNV map in the pig genome, which will provide abundant genetic markers to investigate association studies between various phenotypes and CNVs in pigs.
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Affiliation(s)
- Jiying Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jicai Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haifei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huimin Kang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Feng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail:
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Wang J, Wang H, Jiang J, Kang H, Feng X, Zhang Q, Liu JF. Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays. PLoS One 2013; 8:e68683. [PMID: 23935880 PMCID: PMC3720780 DOI: 10.1371/journal.pone.0068683] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/03/2013] [Indexed: 11/25/2022] Open
Abstract
Copy number variations (CNVs) are important forms of genetic variation complementary to SNPs, and can be considered as promising markers for some phenotypic and economically important traits or diseases susceptibility in domestic animals. In the present study, we performed a genome-wide CNV identification in 14 individuals selected from diverse populations, including six types of Chinese indigenous breeds, one Asian wild boar population, as well as three modern commercial foreign breeds. We identified 63 CNVRs in total, which covered 9.98 Mb of polymorphic sequence and corresponded to 0.36% of the genome sequence. The length of these CNVRs ranged from 3.20 to 827.21 kb, with an average of 158.37 kb and a median of 97.85 kb. Functional annotation revealed these identified CNVR have important molecular function, and may play an important role in exploring the genetic basis of phenotypic variability and disease susceptibility among pigs. Additionally, to confirm these potential CNVRs, we performed qPCR for 12 randomly selected CNVRs and 8 of them (66.67%) were confirmed successfully. CNVs detected in diverse populations herein are essential complementary to the CNV map in the pig genome, which provide an important resource for studies of genomic variation and the association between various economically important traits and CNVs.
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Affiliation(s)
- Jiying Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Haifei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jicai Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huimin Kang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaotian Feng
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Feng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail:
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Metzger J, Philipp U, Lopes MS, da Camara Machado A, Felicetti M, Silvestrelli M, Distl O. Analysis of copy number variants by three detection algorithms and their association with body size in horses. BMC Genomics 2013; 14:487. [PMID: 23865711 PMCID: PMC3720552 DOI: 10.1186/1471-2164-14-487] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 07/15/2013] [Indexed: 12/14/2022] Open
Abstract
Background Copy number variants (CNVs) have been shown to play an important role in genetic diversity of mammals and in the development of many complex phenotypic traits. The aim of this study was to perform a standard comparative evaluation of CNVs in horses using three different CNV detection programs and to identify genomic regions associated with body size in horses. Results Analysis was performed using the Illumina Equine SNP50 genotyping beadchip for 854 horses. CNVs were detected by three different algorithms, CNVPartition, PennCNV and QuantiSNP. Comparative analysis revealed 50 CNVs that affected 153 different genes mainly involved in sensory perception, signal transduction and cellular components. Genome-wide association analysis for body size showed highly significant deleted regions on ECA1, ECA8 and ECA9. Homologous regions to the detected CNVs on ECA1 and ECA9 have also been shown to be correlated with human height. Conclusions Comparative analysis of CNV detection algorithms was useful to increase the specificity of CNV detection but had certain limitations dependent on the detection tool. GWAS revealed genome-wide associated CNVs for body size in horses.
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Affiliation(s)
- Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany
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Kondrashov FA. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc Biol Sci 2012; 279:5048-57. [PMID: 22977152 PMCID: PMC3497230 DOI: 10.1098/rspb.2012.1108] [Citation(s) in RCA: 391] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 08/21/2012] [Indexed: 01/13/2023] Open
Abstract
A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications.
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Affiliation(s)
- Fyodor A Kondrashov
- Institució Catalana de Recerca i Estudis Avançats, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra, 88 Dr Aiguader, Barcelona 08003, Spain.
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Grace C, Nacheva EP. Significance Analysis of Microarrays (SAM) Offers Clues to Differences Between the Genomes of Adult Philadelphia Positive ALL and the Lymphoid Blast Transformation of CML. Cancer Inform 2012; 11:173-83. [PMID: 23071388 PMCID: PMC3448499 DOI: 10.4137/cin.s9258] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Philadelphia positive malignant disorders are a clinically divergent group of leukemias. These include chronic myeloid leukemia (CML) and de novo acute Philadelphia positive (Ph(+)) leukemia of both myeloid, and lymphoid origin. Recent whole genome screening of Ph(+)ALL in both children and adults identified an almost obligatory cryptic loss of Ikaros, required for the normal B cell maturation. Although similar losses were found in lymphoid blast crisis the genetic background of the transformation in CML is still poorly defined. We used Significance Analysis of Microarrays (SAM) to analyze comparative genomic hybridization (aCGH) data from 30 CML (10 each of chronic phase, myeloid and lymphoid blast stage), 10 Ph(+)ALL adult patients and 10 disease free controls and were able to: (a) discriminate between the genomes of lymphoid and myeloid blast cells and (b) identify differences in the genome profile of de novo Ph(+)ALL and lymphoid blast transformation of CML (BC/L). Furthermore we were able to distinguish a sub group of Ph(+) ALL characterized by gains in chromosome 9 and recurrent losses at several other genome sites offering genetic evidence for the clinical heterogeneity. The significance of these results is that they not only offer clues regarding the pathogenesis of Ph(+) disorders and highlight the potential clinical implications of a set of probes but also demonstrates what SAM can offer for the analysis of genome data.
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Clop A, Vidal O, Amills M. Copy number variation in the genomes of domestic animals. Anim Genet 2012; 43:503-17. [PMID: 22497594 DOI: 10.1111/j.1365-2052.2012.02317.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2011] [Indexed: 12/28/2022]
Abstract
Copy number variation (CNV) might be one of the main contributors to phenotypic diversity and evolutionary adaptation in animals and plants, employing a wide variety of mechanisms, such as gene dosage and transcript structure alterations, to modulate organismal plasticity. In the past 4 years, considerable advances have been made in the characterization of the genomic architecture of CNV in domestic species. First, low-resolution CNV maps were produced for cattle, goat, sheep, pig, dog, chicken, duck and turkey, showing that these structural polymorphisms comprise a significant part of these genomes. Furthermore, CNVs have been associated with several pigmentation (white coat in horse, pig and sheep) and morphological (late feathering and pea comb in chicken) traits, as well as with susceptibility to a wide array of diseases and developmental disorders, for example osteopetrosis, anhidrotic ectodermal dysplasia, copper toxicosis, intersexuality, cone degeneration, periodic fever and dermoid sinus, among others. In the future, development of high-resolution tools for CNV detection and typing combined with the implementation of databases integrating CNV, QTL and gene expression data will be essential to identify and measure the impact of this source of structural variation on the many phenotypes that are relevant to animal breeders and veterinary practitioners.
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Affiliation(s)
- A Clop
- Department of Medical and Molecular Genetics, King's College London, Great Maze Pond, SE1 9RT, London, UK
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Prosdocimi F, Linard B, Pontarotti P, Poch O, Thompson JD. Controversies in modern evolutionary biology: the imperative for error detection and quality control. BMC Genomics 2012; 13:5. [PMID: 22217008 PMCID: PMC3311146 DOI: 10.1186/1471-2164-13-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 01/04/2012] [Indexed: 12/03/2022] Open
Abstract
Background The data from high throughput genomics technologies provide unique opportunities for studies of complex biological systems, but also pose many new challenges. The shift to the genome scale in evolutionary biology, for example, has led to many interesting, but often controversial studies. It has been suggested that part of the conflict may be due to errors in the initial sequences. Most gene sequences are predicted by bioinformatics programs and a number of quality issues have been raised, concerning DNA sequencing errors or badly predicted coding regions, particularly in eukaryotes. Results We investigated the impact of these errors on evolutionary studies and specifically on the identification of important genetic events. We focused on the detection of asymmetric evolution after duplication, which has been the subject of controversy recently. Using the human genome as a reference, we established a reliable set of 688 duplicated genes in 13 complete vertebrate genomes, where significantly different evolutionary rates are observed. We estimated the rates at which protein sequence errors occur and are accumulated in the higher-level analyses. We showed that the majority of the detected events (57%) are in fact artifacts due to the putative erroneous sequences and that these artifacts are sufficient to mask the true functional significance of the events. Conclusions Initial errors are accumulated throughout the evolutionary analysis, generating artificially high rates of event predictions and leading to substantial uncertainty in the conclusions. This study emphasizes the urgent need for error detection and quality control strategies in order to efficiently extract knowledge from the new genome data.
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Affiliation(s)
- Francisco Prosdocimi
- Department of Integrated Structural Biology, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) CNRS/INSERM/Université de Strasbourg, 1 rue Laurent Fries, Illkirch, F-67404, France
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Ceulemans S, van der Ven K, Del-Favero J. Targeted screening and validation of copy number variations. Methods Mol Biol 2012; 838:311-28. [PMID: 22228019 DOI: 10.1007/978-1-61779-507-7_15] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The accessibility of genome-wide screening technologies considerably facilitated the identification and characterization of copy number variations (CNVs). The increasing amount of available data describing these variants, clearly demonstrates their abundance in the human genome. This observation shows that not only SNPs, but also CNVs and other structural variants strongly contribute to genetic variation. Even though not all structural variants have an obvious phenotypic effect, there is evidence that CNVs influence gene dosage and hence can have profound effects on human disease susceptibility, disease manifestation, and disease severity. Therefore, CNV screening and analysis methodologies, specifically focusing on disease-related CNVs are actively progressing. This chapter specifically describes different techniques currently available for the targeted screening and validation of CNVs. We not only provide an overview of all these CNV analysis methods, but also address their strong and weak points. Methods covered include fluorescence in situ hybridization (FISH), quantitative real-time PCR (qPCR), paralogue ratio test (PRT), molecular copy-number counting (MCC), and multiplex PCR-based approaches, such as multiplex amplifiable probe hybridization (MAPH), multiplex ligation-dependent probe amplification (MLPA), multiplex PCR-based real-time invader assay (mPCR-RETINA), quantitative multiplex PCR of short fluorescent fragments (QMPSF), and multiplex amplicon quantification (MAQ). We end with some general remarks and conclusions, furthermore briefly addressing the future perspectives.
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Affiliation(s)
- Shana Ceulemans
- Applied Molecular Genomics Unit, VIB, Department of Molecular Genetics, Flanders, Belgium
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Trewick AL, Moustafa JSES, de Smith AJ, Froguel P, Greve G, Njølstad PR, Coin LJM, Blakemore AIF. Accurate single-nucleotide polymorphism allele assignment in trisomic or duplicated regions by using a single base-extension assay with MALDI-TOF mass spectrometry. Clin Chem 2011; 57:1188-95. [PMID: 21677093 DOI: 10.1373/clinchem.2010.159558] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND The accurate assignment of alleles embedded within trisomic or duplicated regions is an essential prerequisite for assessing the combined effects of single-nucleotide polymorphisms (SNPs) and genomic copy number. Such an integrated analysis is challenging because heterozygotes for such a SNP may be one of 2 genotypes-AAB or ABB. Established methods for SNP genotyping, however, can have difficulty discriminating between the 2 heterozygous trisomic genotypes. We developed a method for assigning heterozygous trisomic genotypes that uses the ratio of the height of the 2 allele peaks obtained by mass spectrometry after a single-base extension assay. METHODS Eighteen COL6A2 (collagen, type VI, alpha 2) SNPs were analyzed in euploid and trisomic individuals by means of a multiplexed single-base extension assay that generated allele-specific oligonucleotides of differing M(r) values for detection by MALDI-TOF mass spectrometry. Reference data (mean and SD) for the allele peak height ratios were determined from heterozygous euploid samples. The heterozygous trisomic genotypes were assigned by calculating the z score for each trisomic allele peak height ratio and by considering the sign (+/-) of the z score. RESULTS Heterozygous trisomic genotypes were assigned in 96.1% (range, 89.9%-100%) of the samples for each SNP analyzed. The genotypes obtained were reproduced in 95 (97.5%) of 97 loci retested in a second assay. Subsequently, the origin of nondisjunction was determined in 108 (82%) of 132 family trios with a Down syndrome child. CONCLUSIONS This approach enabled reliable genotyping of heterozygous trisomic samples and the determination of the origin of nondisjunction in Down syndrome family trios.
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Affiliation(s)
- Anne L Trewick
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, UK
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Sbacchi S, Acquadro F, Calò I, Calì F, Romano V. Functional annotation of genes overlapping copy number variants in autistic patients: focus on axon pathfinding. Curr Genomics 2011; 11:136-45. [PMID: 20885821 PMCID: PMC2874223 DOI: 10.2174/138920210790886880] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 12/12/2009] [Accepted: 12/15/2009] [Indexed: 12/30/2022] Open
Abstract
We have used Gene Ontology (GO) and pathway analyses to uncover the common functions associated to the genes overlapping Copy Number Variants (CNVs) in autistic patients. Our source of data were four published studies [1-4]. We first applied a two-step enrichment strategy for autism-specific genes. We fished out from the four mentioned studies a list of 2928 genes overall overlapping 328 CNVs in patients and we first selected a sub-group of 2044 genes after excluding those ones that are also involved in CNVs reported in the Database of Genomic Variants (enrichment step 1). We then selected from the step 1-enriched list a sub-group of 514 genes each of which was found to be deleted or duplicated in at least two patients (enrichment step 2). The number of statistically significant processes and pathways identified by the Database for Annotation, Visualization and Integrated Discovery and Ingenuity Pathways Analysis softwares with the step 2-enriched list was significantly higher compared to the step 1-enriched list. In addition, statistically significant GO terms, biofunctions and pathways related to nervous system development and function were exclusively identified by the step 2-enriched list of genes. Interestingly, 21 genes were associated to axon growth and pathfinding. The latter genes and other ones associated to nervous system in this study represent a new set of autism candidate genes deserving further investigation. In summary, our results suggest that the autism’s “connectivity genes” in some patients affect very early phases of neurodevelopment, i.e., earlier than synaptogenesis.
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Affiliation(s)
- Silvia Sbacchi
- Dipartimento di Oncologia Sperimentale e Applicazioni Cliniche, Università degli Studi di Palermo, Palermo
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Liu MM, Agrón E, Chew E, Meyerle C, Ferris FL, Chan CC, Tuo J. Copy number variations in candidate genes in neovascular age-related macular degeneration. Invest Ophthalmol Vis Sci 2011; 52:3129-35. [PMID: 21273533 PMCID: PMC3109020 DOI: 10.1167/iovs.10-6735] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Revised: 12/13/2010] [Accepted: 12/19/2010] [Indexed: 01/11/2023] Open
Abstract
PURPOSE The pathogenesis of age-related macular degeneration (AMD) is strongly influenced by genetic factors, and single nucleotide polymorphisms have been consistently linked to AMD. Copy number variation (CNV), or variation in the number of copies of a particular segment of DNA, may also contribute to AMD pathogenesis. This study evaluated CNVs in candidate genes that have been reported to be linked to AMD. METHODS Study participants were 131 patients with neovascular AMD and 103 elderly persons without AMD who were evaluated by retinal specialists at the National Eye Institute. DNA was collected from peripheral whole blood, and duplex RT-PCR based copy number (CN) assays were performed for the genes CCR3, CFH, CX3CR1, ERCC6, HTRA1, and VEGF. Quantitative CNs (CN = 0, 1, 2, or 3+) were determined. RESULTS Novel CNVs were discovered in CCR3, CX3CR1, and ERCC6. The unadjusted data suggested that CN = 3+ for CX3CR1 might be mildly protective against AMD, but this trend did not persist after adjustment for age. AMD patients appeared to have an elevated mean CFH CN relative to controls (2.13 [95% confidence interval (CI), 2.05-2.21] vs. 2.01 [95% CI, 1.92-2.09 copies]; P = 0.05). No significant associations between CNV and AMD were observed for the remaining genes. CONCLUSIONS The methods described are suitable for quantitative characterization of CNV in candidate genes. The authors identified CNVs in AMD-associated genes but did not find strong evidence for a link with neovascular AMD.
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Affiliation(s)
- Melissa M. Liu
- From the Laboratory of Immunology and
- the Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elvira Agrón
- the Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Emily Chew
- the Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Catherine Meyerle
- the Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Frederick L. Ferris
- the Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, Maryland; and
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Fechtel K, Osterbur ML, Kehrer-Sawatzki H, Stenson PD, Cooper DN. Delineating the Hemostaseome as an aid to individualize the analysis of the hereditary basis of thrombotic and bleeding disorders. Hum Genet 2011; 130:149-66. [PMID: 21537949 DOI: 10.1007/s00439-011-0984-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Accepted: 04/05/2011] [Indexed: 01/22/2023]
Abstract
Next-generation sequencing and genome-wide association studies represent powerful tools to identify genetic variants that confer disease risk within populations. On their own, however, they cannot provide insight into how these variants contribute to individual risk for diseases that exhibit complex inheritance, or alternatively confer health in a given individual. Even in the case of well-characterized variants that confer a significant disease risk, more healthy individuals carry the variant, with no apparent ill effect, than those who manifest disease. Access to low-cost genome sequence data promises to provide an unprecedentedly detailed view of the nature of the hereditary component of complex diseases, but requires the large-scale comparison of sequence data from individuals with and without disease to deliver a clinical calibration. The provision of informatics support remains problematic as there are currently no means to interpret the data generated. Here, we initiate this process, a prerequisite for such a study, by narrowing the focus from an entire genome to that of a single biological system. To this end, we examine the 'Hemostaseome,' and more specifically focus on DNA sequence changes pertaining to those human genes known to impact upon hemostasis and thrombosis that can be analyzed coordinately, and on an individual basis, to interrogate how specific combinations of variants act to confer disease predisposition. As a first step, we delineate known members of the Hemostaseome and explore the nature of the genetic variants that may cause disease in individuals whose hemostatic balance has become shifted toward either a prothrombotic or anticoagulant phenotype.
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Affiliation(s)
- Kim Fechtel
- 3rd Millennium Inc., Waltham, MA 02451, USA.
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Cooper DN, Chen JM, Ball EV, Howells K, Mort M, Phillips AD, Chuzhanova N, Krawczak M, Kehrer-Sawatzki H, Stenson PD. Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Hum Mutat 2010; 31:631-55. [PMID: 20506564 DOI: 10.1002/humu.21260] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The number of reported germline mutations in human nuclear genes, either underlying or associated with inherited disease, has now exceeded 100,000 in more than 3,700 different genes. The availability of these data has both revolutionized the study of the morbid anatomy of the human genome and facilitated "personalized genomics." With approximately 300 new "inherited disease genes" (and approximately 10,000 new mutations) being identified annually, it is pertinent to ask how many "inherited disease genes" there are in the human genome, how many mutations reside within them, and where such lesions are likely to be located? To address these questions, it is necessary not only to reconsider how we define human genes but also to explore notions of gene "essentiality" and "dispensability."Answers to these questions are now emerging from recent novel insights into genome structure and function and through complete genome sequence information derived from multiple individual human genomes. However, a change in focus toward screening functional genomic elements as opposed to genes sensu stricto will be required if we are to capitalize fully on recent technical and conceptual advances and identify new types of disease-associated mutation within noncoding regions remote from the genes whose function they disrupt.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom.
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Cooper MT, Conant AW, Kennison JA. Molecular genetic analysis of Chd3 and polytene chromosome region 76B-D in Drosophila melanogaster. Genetics 2010; 185:811-22. [PMID: 20439780 PMCID: PMC2907203 DOI: 10.1534/genetics.110.115121] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 04/20/2010] [Indexed: 01/08/2023] Open
Abstract
The Drosophila melanogaster Chd3 gene encodes a member of the CHD group of SNF2/RAD54 ATPases. CHD proteins are conserved from yeast to man and many are subunits of chromatin-remodeling complexes that facilitate transcription. Drosophila CHD3 proteins are not found in protein complexes, but as monomers that remodel chromatin in vitro. CHD3 colocalize with elongating RNA polymerase II on salivary gland polytene chromosomes. Since the role of Chd3 in development was unknown, we isolated and characterized the essential genes within the 640-kb region of the third chromosome (polytene chromosome region 76B-D) that includes Chd3. We recovered mutations in 24 genes that are essential for zygotic viability. We found that transposon-insertion mutants for 46% of the essential genes are included in the Drosophila Gene Disruption Project collection. None of the essential genes that we identified are in a 200-kb region that includes Chd3. We generated a deletion of Chd3 by targeted gene replacement. This deletion had no effect on either viability or fertility.
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Affiliation(s)
| | | | - James A. Kennison
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland 20892-2785
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