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Hosseini S, Schmitt AO, Tetens J, Brenig B, Simianer H, Sharifi AR, Gültas M. In Silico Prediction of Transcription Factor Collaborations Underlying Phenotypic Sexual Dimorphism in Zebrafish ( Danio rerio). Genes (Basel) 2021; 12:873. [PMID: 34200177 PMCID: PMC8227731 DOI: 10.3390/genes12060873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 11/17/2022] Open
Abstract
The transcriptional regulation of gene expression in higher organisms is essential for different cellular and biological processes. These processes are controlled by transcription factors and their combinatorial interplay, which are crucial for complex genetic programs and transcriptional machinery. The regulation of sex-biased gene expression plays a major role in phenotypic sexual dimorphism in many species, causing dimorphic gene expression patterns between two different sexes. The role of transcription factor (TF) in gene regulatory mechanisms so far has not been studied for sex determination and sex-associated colour patterning in zebrafish with respect to phenotypic sexual dimorphism. To address this open biological issue, we applied bioinformatics approaches for identifying the predicted TF pairs based on their binding sites for sex and colour genes in zebrafish. In this study, we identified 25 (e.g., STAT6-GATA4; JUN-GATA4; SOX9-JUN) and 14 (e.g., IRF-STAT6; SOX9-JUN; STAT6-GATA4) potentially cooperating TFs based on their binding patterns in promoter regions for sex determination and colour pattern genes in zebrafish, respectively. The comparison between identified TFs for sex and colour genes revealed several predicted TF pairs (e.g., STAT6-GATA4; JUN-SOX9) are common for both phenotypes, which may play a pivotal role in phenotypic sexual dimorphism in zebrafish.
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Affiliation(s)
- Shahrbanou Hosseini
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Göttingen, 37077 Göttingen, Germany;
- Functional Breeding Group, Department of Animal Sciences, University of Göttingen, 37077 Göttingen, Germany;
- Institute of Veterinary Medicine, University of Göttingen, 37077 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
| | - Armin Otto Schmitt
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany
| | - Jens Tetens
- Functional Breeding Group, Department of Animal Sciences, University of Göttingen, 37077 Göttingen, Germany;
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
| | - Bertram Brenig
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Göttingen, 37077 Göttingen, Germany;
- Institute of Veterinary Medicine, University of Göttingen, 37077 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
| | - Henner Simianer
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany
| | - Ahmad Reza Sharifi
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany
- Faculty of Agriculture, South Westphalia University of Applied Sciences, 59494 Soest, Germany
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Liu X, Zhang P, Ji K, Zhang J, Yang S, Du B, Hu S, Fan R. Cyclin-dependent kinase 5 regulates MAPK/ERK signaling in the skin of mice. Acta Histochem 2018; 120:15-21. [PMID: 29132690 DOI: 10.1016/j.acthis.2017.10.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 12/11/2022]
Abstract
Cyclin-dependent kinase 5 (CDK5) is a proline-directed serine/threonine kinase that has been shown to play important roles in many tissues except the nervous system. We previously reported that CDK5 showed differential expression in the transcriptome profiles of the skin of alpacas with different hair colors. To understand the functional role of CDK5 in hair color determination, we constructed CDK5-knockdown mice and identified the effect on the mitogen-activated protein kinase (MAPK) pathway in the mouse skin. Quantitative real-time polymerase chain reaction, co-immunoprecipitation, and western blotting were performed to analyze the effects of CDK5-knockdown on the MAPK pathway in mice. The results showed that MAP3K6 was inhibited by phosphorylated CDK5 through its activator CDK7. The decrease in MAP3K6 levels caused down-regulation of MEK1 and ERK expression, leading to the up-regulation of miR-143-3p, which targets MAP3K6 via Dicer. Taken together, our findings indicate that CDK5 functions in regulating the MAPK pathway. Given that MAP3K6 was inhibited in two directions, this mechanism can provide insight into the contributions of the MAPK/ERK pathway to the inhibition of melanin production.
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Affiliation(s)
- Xuexian Liu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China
| | - Pengqian Zhang
- Department of Ecology Research, Beijing Milu Ecological Research Center, Nanhaizi, Daxing District, Beijing 102600, China
| | - Kaiyuan Ji
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China
| | - Junzhen Zhang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China
| | - Shanshan Yang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China
| | - Bin Du
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China
| | - Shuaipeng Hu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China
| | - Ruiwen Fan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China.
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Du Z, Huang K, Zhao J, Song X, Xing X, Wu Q, Zhang L, Xu C. Comparative Transcriptome Analysis of Raccoon Dog Skin to Determine Melanin Content in Hair and Melanin Distribution in Skin. Sci Rep 2017; 7:40903. [PMID: 28098220 PMCID: PMC5241637 DOI: 10.1038/srep40903] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/13/2016] [Indexed: 02/03/2023] Open
Abstract
The raccoon dog (Nyctereutes procyonoides) is an important canid fur-bearing animal species worldwide. Chinese raccoon dogs that present a white mutation, especially those with a white coat. Exploring melanin biosynthesis in the hair and skin of raccoon dogs is important for understanding the survival and evolutionary mechanisms of them. In this study, we measured the content of melanin in the hair of two types of raccoon dog and generated stained slices of skin tissue. The results indicated that melanin biosynthesis occurs in the wild-type (W) and white-type (B) raccoon dog skin, although less melanin is produced in B skin. We then sequenced the skin transcriptomes of W and B, compared the similarities and differences in expressed genes. A comparison of the gene expression showed 60 up-regulated genes and 127 down-regulated genes in B skin. We analyzed the unigenes and pathways related to the melanogenesis pathway and found that TYR, TYRP1, MC1R, SLC24a5, SLC45a2 and OCA2 were significantly down-regulated in B skin and these results were verified via qRT-PCR. We surmised that the phenotypic characteristics of the white mutation might be caused by the reduced expression of these genes and this finding provides new insights for future experiments in raccoon dogs.
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Affiliation(s)
- Zhanyu Du
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory of Special Economic Animal Molecular Biology, Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Juye Street NO. 4899 130112, Changchun, China
- College of Life Science, Jilin Agricultural University, Xincheng Street NO. 2888 130118, Changchun, China
| | - Kai Huang
- Beijing Gene-Health Huachuang Biotech Co., Ltd, Xueqing Rode NO. 9 100089, Beijing, China
| | - Jiaping Zhao
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory of Special Economic Animal Molecular Biology, Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Juye Street NO. 4899 130112, Changchun, China
| | - Xingchao Song
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory of Special Economic Animal Molecular Biology, Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Juye Street NO. 4899 130112, Changchun, China
| | - Xiumei Xing
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory of Special Economic Animal Molecular Biology, Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Juye Street NO. 4899 130112, Changchun, China
| | - Qiong Wu
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory of Special Economic Animal Molecular Biology, Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Juye Street NO. 4899 130112, Changchun, China
| | - Linbo Zhang
- College of Life Science, Jilin Agricultural University, Xincheng Street NO. 2888 130118, Changchun, China
| | - Chao Xu
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory of Special Economic Animal Molecular Biology, Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Juye Street NO. 4899 130112, Changchun, China
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation, Ministry of Agriculture (nzdsys2016-3), Yuangmingyuan West-Rode NO. 2 100193, Beijing, China
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Cecchi T, Valbonesi A, Passamonti P, Gonzales M, Antonini M, Renieri C. Quantitative variation of melanins in alpaca (Lama pacosL.). ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2011.e30] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Fan R, Xie J, Bai J, Wang H, Tian X, Bai R, Jia X, Yang L, Song Y, Herrid M, Gao W, He X, Yao J, Smith GW, Dong C. Skin transcriptome profiles associated with coat color in sheep. BMC Genomics 2013; 14:389. [PMID: 23758853 PMCID: PMC3689618 DOI: 10.1186/1471-2164-14-389] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/04/2013] [Indexed: 01/06/2023] Open
Abstract
Background Previous molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins. To identify additional genes that may play important roles in coat color regulation, Illumina sequencing technology was used to catalog global gene expression profiles in skin of sheep with white versus black coat color. Results There were 90,006 and 74,533 unigenes assembled from the reads obtained from white and black sheep skin, respectively. Genes encoding for the ribosomal proteins and keratin associated proteins were most highly expressed. A total of 2,235 known genes were differentially expressed in black versus white sheep skin, with 479 genes up-regulated and 1,756 genes down-regulated. A total of 845 novel genes were differentially expressed in black versus white sheep skin, consisting of 107 genes which were up-regulated (including 2 highly expressed genes exclusively expressed in black sheep skin) and 738 genes that were down-regulated. There was also a total of 49 known coat color genes expressed in sheep skin, from which 13 genes showed higher expression in black sheep skin. Many of these up-regulated genes, such as DCT, MATP, TYR and TYRP1, are members of the components of melanosomes and their precursor ontology category. Conclusion The white and black sheep skin transcriptome profiles obtained provide a valuable resource for future research to understand the network of gene expression controlling skin physiology and melanogenesis in sheep.
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Affiliation(s)
- Ruiwen Fan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
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Minvielle F, Cecchi T, Passamonti P, Gourichon D, Renieri C. Plumage colour mutations and melanins in the feathers of the Japanese quail: a first comparison. Anim Genet 2009; 40:971-4. [PMID: 19496774 DOI: 10.1111/j.1365-2052.2009.01929.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The absorbance of melanin content from dorsal feathers was compared between wild-type Japanese quail and nine other quail plumage colours determined by single mutations in one of seven genes: extended brown (MC1R), yellow (ASIP), silver (MITF), lavender (MLPH), roux (TYRP1), imperfect albinism (SLC45A2) and rusty. As compared with wild-type quail, all mutations but extended brown decreased total melanins. The largest decrease was observed in quail with one of the dilution mutations at TYRP1, MLPH or SLCA45A2. No difference in eumelanins was found between the 10 plumage colours. Despite visible colour differences, homozygous and heterozygous mutants at MITF, or the two imperfect albino (white) and cinnamon (pale yellow) alleles at SLC45A2, could not be differentiated on the basis of melanins. In contrast, the two white phenotypes caused by mutations at MITF and SLC45A2, or the two reddish plumage colours caused by the roux and rusty non-allelic mutations had different total melanin contents. The results showed that rusty was not likely to be a dilution mutation.
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Affiliation(s)
- F Minvielle
- INRA/AgroParisTech, UMR 1313 Génétique animale et biologie intégrative, 78352 Jouy-en-Josas, France.
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Feeley NL, Munyard KA. Characterisation of the melanocortin-1 receptor gene in alpaca and identification of possible markers associated with phenotypic variations in colour. ANIMAL PRODUCTION SCIENCE 2009. [DOI: 10.1071/an09005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The aim of this study was to determine if any correlation exists between melanocortin-1 receptor (MC1R) polymorphisms and skin and fibre colour in alpacas. Primers capable of amplifying the entire alpaca MC1R gene were designed from a comparative alignment of Bos taurus and Mus musculus MC1R gene sequences. The complete MC1R gene of 41 alpacas exhibiting a range of fibre colours, and which were sourced from farms across Australia, was sequenced from PCR products. Twenty-one single nucleotide polymorphisms were identified within MC1R. Two of these polymorphisms (A82G and C901T) have the potential to reduce eumelanin production by disrupting the activity of MC1R. No agreement was observed between fibre colour alone and MC1R genotype in the 41 animals in this study. However, when the animals were assigned to groups based on the presence or absence of eumelanin in their fibre and skin, only animals that had at least one allele with the A82/C901 combination expressed eumelanin. We propose that A82/C901 is the wild-type dominant ‘E’ MC1R allele, while alpacas with either G82/T901 or G82/Y901 are homozygous for the recessive ‘e’ MC1R allele and are therefore unable to produce eumelanin.
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Characterization of the effect of Melanocortin 1 Receptor, a member of the hair color genetic locus, in alpaca (Lama pacos) fleece color differentiation. Small Rumin Res 2008. [DOI: 10.1016/j.smallrumres.2008.07.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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