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Yuan B, Qi Y, Zhang X, Hu J, Fan Y, Ji X. The relationship of MITF gene expression and promoter methylation with plumage colour in quail. Br Poult Sci 2024; 65:259-264. [PMID: 38578288 DOI: 10.1080/00071668.2024.2326962] [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: 10/11/2023] [Accepted: 01/16/2024] [Indexed: 04/06/2024]
Abstract
1. This study focused on the relationship between MITF mRNA expression and plumage colour in quail and the effect of promoter methylation on the expression of MITF mRNA.2. The CDS region of MITF mRNA was cloned by RT-PCR, followed by DNA sequencing. The RT-qPCR method was used to analyse the expression levels of MITF mRNA in dorsal skin tissue in Korean quail and Beijing white quail. The promoter region of the MITF gene was cloned, and the CpG island was predicted by the CpGplot program. The methylation levels of the CpG island were analysed using BS-PCR technology.3. Quail MITF mRNA contains a 1,476 bp complete ORF, which encodes a 492 amino acid residue protein. The MITF protein has no signal peptide or transmembrane region. The expression of MITF mRNA in dorsal tissue of Korean quail was significantly higher than that in Beijing white quail (p < 0.01). Abundant cis-elements and a 346 bp CpG island were found in the promoter region of the MITF gene. The average methylation level of the CpG island was 22 (22%) in Korean quail, and 46 (30%) in Beijing white quail (p < 0.05).4. The hypermethylation of the MITF gene promoter region in Beijing white quail resulted in a decrease in expression level, which was related to white feather colour.
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Affiliation(s)
- B Yuan
- College of Animal Science, Henan University of Science and Technology, Luoyang, P.R.China
| | - Y Qi
- College of Animal Science, Henan University of Science and Technology, Luoyang, P.R.China
| | - X Zhang
- College of Animal Science, Henan University of Science and Technology, Luoyang, P.R.China
| | - J Hu
- College of Animal Science, Henan University of Science and Technology, Luoyang, P.R.China
| | - Y Fan
- College of Animal Science, Henan University of Science and Technology, Luoyang, P.R.China
| | - Xingyu Ji
- College of Animal Science, Henan University of Science and Technology, Luoyang, P.R.China
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Cossette ML, Stewart DT, Haghani A, Zoller JA, Shafer ABA, Horvath S. Epigenetics and island-mainland divergence in an insectivorous small mammal. Mol Ecol 2023; 32:152-166. [PMID: 36226847 DOI: 10.1111/mec.16735] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 12/29/2022]
Abstract
Geographically isolated populations, specifically island-mainland counterparts, tend to exhibit phenotypic variation in many species. The so-called island syndrome occurs when different environmental pressures lead to insular divergence from mainland populations. This phenomenon can be seen in an island population of Nova Scotia masked shrews (Sorex cinereus), which have developed a specialized feeding habit and digestive enzyme compared to their mainland counterparts. Epigenetic modifications, such as DNA methylation (DNAm), can impact phenotypes by altering gene expression without changing the DNA sequence. Here, we used a de novo masked shrew genome assembly and a mammalian methylation array profiling 37 thousand conserved CpGs to investigate morphological and DNA methylation patterns between island and mainland populations. Island shrews were morphologically and epigenetically different than their mainland counterparts, exhibiting a smaller body size. A gene ontology enrichment analyses of differentially methylated CpGs implicated developmental and digestive system related pathways. Based on our shrew epigenetic clock, island shrews might also be aging faster than their mainland counterparts. This study provides novel insight on phenotypic and epigenetic divergence in island-mainland mammal populations and suggests an underlying role of methylation in island-mainland divergence.
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Affiliation(s)
- Marie-Laurence Cossette
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Donald T Stewart
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, California, USA
| | - Aaron B A Shafer
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, California, USA
- Altos Labs, San Diego, California, USA
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Ma J, Zhang L, Huang Y, Shen F, Wu H, Yang Z, Hou R, Song Z, Yue B, Zhang X. Epigenomic profiling indicates a role for DNA methylation in the postnatal liver and pancreas development of giant pandas. Genomics 2022; 114:110342. [PMID: 35306168 DOI: 10.1016/j.ygeno.2022.110342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 02/14/2022] [Accepted: 03/13/2022] [Indexed: 01/14/2023]
Abstract
Giant pandas are unique within Carnivora with a strict bamboo diet. Here, the epigenomic profiles of giant panda liver and pancreas tissues collected from three important feeding stages were investigated using BS-seq. Few differences in DNA methylation profiles were exhibited between no feeding and suckling groups in both tissues. However, we observed a tendency toward a global loss of DNA methylation in the gene-body and promoter region of metabolism-related genes from newborn to adult. Correlation analysis revealed a significant negative correlation between the changes in methylation levels within gene promoters and gene expression. The majority of genes related to nutrition metabolism had lost DNA methylation with increased mRNA expression in adult giant pandas. The few galactose metabolism and unsaturated fatty acid metabolism related genes that were hypomethylated and highly-expressed at early stages of giant panda development may meet the nutritional requirement of this species' highly altricial neonates.
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Affiliation(s)
- Jinnan Ma
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Liang Zhang
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Yan Huang
- China Conservation and Research Center for the Giant Panda, 98 Tongjiang Road, Dujiangyan, Chengdu, Sichuan 611800, China
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Honglin Wu
- China Conservation and Research Center for the Giant Panda, 98 Tongjiang Road, Dujiangyan, Chengdu, Sichuan 611800, China
| | - Zhisong Yang
- Sichuan Academy of Giant Panda, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Zhaobin Song
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China.
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Hernaiz A, Sanz A, Sentre S, Ranera B, Lopez-Pérez O, Zaragoza P, Badiola JJ, Filali H, Bolea R, Toivonen JM, Martín-Burriel I. Genome-Wide Methylation Profiling in the Thalamus of Scrapie Sheep. Front Vet Sci 2022; 9:824677. [PMID: 35252421 PMCID: PMC8888973 DOI: 10.3389/fvets.2022.824677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
Scrapie is a neurodegenerative disorder belonging to the group of transmissible spongiform encephalopathy (TSE). Scrapie occurs in sheep and goats, which are considered good natural animal models of these TSE. Changes in DNA methylation occur in the central nervous system (CNS) of patients suffering from prion-like neurodegenerative diseases, such as Alzheimer's disease. Nevertheless, potential DNA methylation alterations have not yet been investigated in the CNS of any prion disease model or naturally infected cases, neither in humans nor in animals. Genome-wide DNA methylation patterns were studied in the thalamus obtained from sheep naturally infected with scrapie at a clinical stage (n = 4) and from controls (n = 4) by performing a whole-genome bisulfite sequencing (WGBS) analysis. Ewes carried the scrapie-susceptible ARQ/ARQ PRNP genotype and were sacrificed at a similar age (4–6 years). Although the average genomic methylation levels were similar between the control and the scrapie animals, we identified 8,907 significant differentially methylated regions (DMRs) and 39 promoters (DMPs). Gene Ontology analysis revealed that hypomethylated DMRs were enriched in genes involved in transmembrane transport and cell adhesion, whereas hypermethylated DMRs were related to intracellular signal transduction genes. Moreover, genes highly expressed in specific types of CNS cells and those previously described to be differentially expressed in scrapie brains contained DMRs. Finally, a quantitative PCR (qPCR) validation indicated differences in the expression of five genes (PCDH19, SNCG, WDR45B, PEX1, and CABIN1) that matched the methylation changes observed in the genomic study. Altogether, these results suggest a potential regulatory role of DNA methylation in prion neuropathology.
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Affiliation(s)
- Adelaida Hernaiz
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza-IA2, IIS, Zaragoza, Spain
| | - Arianne Sanz
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza-IA2, IIS, Zaragoza, Spain
| | - Sara Sentre
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza-IA2, IIS, Zaragoza, Spain
| | - Beatriz Ranera
- Facultad de Ciencias de la Salud, Universidad San Jorge, Zaragoza, Spain
| | - Oscar Lopez-Pérez
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza-IA2, IIS, Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Facultad de Veterinaria, Universidad de Zaragoza-IA2, IIS, Zaragoza, Spain
| | - Pilar Zaragoza
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza-IA2, IIS, Zaragoza, Spain
| | - Juan J. Badiola
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Facultad de Veterinaria, Universidad de Zaragoza-IA2, IIS, Zaragoza, Spain
| | - Hicham Filali
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Facultad de Veterinaria, Universidad de Zaragoza-IA2, IIS, Zaragoza, Spain
| | - Rosa Bolea
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Facultad de Veterinaria, Universidad de Zaragoza-IA2, IIS, Zaragoza, Spain
| | - Janne M. Toivonen
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza-IA2, IIS, Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Inmaculada Martín-Burriel
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza-IA2, IIS, Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Facultad de Veterinaria, Universidad de Zaragoza-IA2, IIS, Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Inmaculada Martín-Burriel
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Cao Q, Feng Y, Dai X, Huang L, Li J, Tao P, Crabbe MJC, Zhang T, Qiao Q. Dynamic Changes of DNA Methylation During Wild Strawberry ( Fragaria nilgerrensis) Tissue Culture. FRONTIERS IN PLANT SCIENCE 2021; 12:765383. [PMID: 34917103 PMCID: PMC8669611 DOI: 10.3389/fpls.2021.765383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Tissue culture is an important tool for asexual propagation and genetic transformation of strawberry plants. In plant tissue culture, variation of DNA methylation is a potential source of phenotypic variation in regenerated plants. However, the genome wide dynamic methylation patterns of strawberry tissue culture remain unclear. In this study, we used whole-genome bisulfite sequencing (WGBS) to study genomic DNA methylation changes of a wild strawberry Fragaria nilgerrensis at six stages: from explants of shoot tips to outplanting and acclimation. Global methylation levels showed that CG sites exhibited the highest methylation level in all stages with an average of 49.5%, followed by CHG (33.2%) and CHH (12.4%). Although CHH accounted for the lowest proportion of total cytosine methylation, it showed the most obvious methylation change and the most of these changes occurred in the transposable element regions. The overall methylation levels alternately decreased and increased during the entire tissue culture process and the distribution of DNA methylation was non-uniform among different genetic regions. Furthermore, much more differentially methylated regions (DMRs) were detected in dedifferentiation and redifferentiation stages and most of them were transposable elements, suggesting these processes involved activating or silencing of amounts of transposons. The functional enrichment of the DMR-related genes indicated that genes involved in hormone metabolic processes, plant development and the stress response changed methylation throughout the tissue culture process. Finally, the quantitative real-time PCR (qRT-PCR) was conducted to examine the association of methylation and gene expression of a set of different methylated genes. Our findings give deeper insight into the epigenetic regulation of gene expression during the plant tissue cultures process, which will be useful in the efficient control of somaclonal variations and in crop improvement.
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Affiliation(s)
- Qiang Cao
- School of Agriculture, Yunnan University, Kunming, China
| | - Yuxi Feng
- School of Agriculture, Yunnan University, Kunming, China
| | - Xiongwei Dai
- School of Agriculture, Yunnan University, Kunming, China
| | - Lin Huang
- School of Agriculture, Yunnan University, Kunming, China
| | - Jiamin Li
- School of Agriculture, Yunnan University, Kunming, China
| | - Pang Tao
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - M. James C. Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom
- Institute of Biomedical and Environmental Science and Technology, School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Qin Qiao
- School of Agriculture, Yunnan University, Kunming, China
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