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Current IssueEditorial BoardOnline First ArticlesArchive

Short Communication

volume 52 issue 6 (june 2018) : 816-819,   Doi: 10.18805/ijar.B-834

Identification and characterization of microRNAs in white and black coated yak

W
Wang-Dui Basang
T
Tian-Wu An
X
Xiao-Lin Luo
Y
Yan-Bin Zhu
L
Luo-Bu Danjiu
S
Shi-Cheng He
G
Guang-Xin E
1Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husandry Science, Lasa, 850009, China.
Cite article:- Basang Wang-Dui, An Tian-Wu, Luo Xiao-Lin, Zhu Yan-Bin, Danjiu Luo-Bu, He Shi-Cheng, E Guang-Xin (2018). Identification and characterization of microRNAs in white and blackcoated yak. Indian Journal of Animal Research. 52(6): 816-819. doi: 10.18805/ijar.B-834.

ABSTRACT

In this study, we used high-throughput technology to provide the first transcriptome dataset for differentially expressed miRNA in mixed pools of dermis tissue from black- and white-coated yak to research the possible molecular mechanisms of yak coat pigmentation. In this study, 92,636,002 and 95,917,842 clear reads were generated through Illumina paired-end sequencing. A total of 78 differentially expressed miRNAs (DEMs) were identified, including 59 upregulated and 19 downregulated miRNAs in the mixed pools of white-coated yak compared with the mixed pools of black-coated yak. In addition, 3634 genes were predicted as putative targets of DEMs. These DEGs related to 59 GO categories and were enriched in 216 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including melanogenesis and the Wnt signaling pathway. The results of the current study indicated that the coat color of the yak involved the transcriptional regulation process of miRNAs. These results provide helpful data to understand the molecular mechanisms of yak coat pigmentation.

REFERENCES

  1. Cao, T.T., Xiang, D., Liu, B.L., Huang, T.X., Tan, B.B., Zeng, C.M., Wang, Z.Y., Ming, X.Y., Zhang, L.Y., Jin, G., Li, F., Wu, J.L., Guan, X.Y., Lu, D., Fu, L. (2017). FZD7 is a novel prognostic marker and promotes tumor metastasis via WNT and EMT signaling pathways in esophageal squamous cell carcinoma. Oncotarget 8(39):65957-65968. 
  2. Corda, G., Sala, G., Lattanzio, R., Iezzi, M., Sallese, M., Fragassi, G., Lamolinara, A., Mirza, H., Barcaroli, D., Ermler, S., Silva, E., Yasaei, H., Newbold, R.F., Vagnarelli, P., Mottolese, M., Natali, P.G., Perracchio, L., Quist, J., Grigoriadis, A., Marra, P., Tutt, A.N., Piantelli, M., Iacobelli, S., De Laurenzi, V., Sala, A. 2017. Functional and prognostic significance of the genomic amplification of frizzled 6 (FZD6) in breast cancer. J Pathol 241(3):350-361. doi: 10.1002/path.4841.
  3. Dong. C., H. Wang., L. Xue., Y. Dong., L. Yang., R. Fan., X. Yu., X. Tian., S. Ma., G.W. Smith. (2012). Coat color determination by miR-137 mediated down-regulation of microphthalmia-associated transcription factor in a mouse model. RNA 18:1679-86.
  4. Huang, T., Alvarez, A.A., Pangeni, R.P., Horbinski, C.M., Lu, S., Kim, S.H., James, C.D., J Raizer, J., A Kessler, J., Brenann, C.W., Sulman, E.P., Finocchiaro, G., Tan, M., Nishikawa, R., Lu, X., Nakano, I., Hu, B., Cheng, S.Y. (2016). A regulatory circuit of miR-125b/miR-20b and Wnt signalling controls glioblastoma phenotypes through FZD6-modulated pathways. Nat Commun 7:12885. doi: 10.1038/ncomms12885.
  5. Irizarry, K.J., Bryden, R.L. (2016). In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites. Adv Bioinformatics, DOI: 10.1155/2016/1286510
  6. Irwandi, R.A., A. Vacharaksa. (2016). The role of microRNA in periodontal tissue: A review of the literature. Arch Oral Biol 72: 66-74. 
  7. Jo, H., Choi, M., Sim, J., Viji, M., Li, S., Lee, Y.H., Kim, Y., Seo, S.Y., Zhou, Y., Lee, K., Kim, W.J., Hong, J.T., Lee, H., Jung, J.K. (2017). Synthesis and biological evaluation of caffeic acid derivatives as potent inhibitors of á-MSH-stimulated melanogenesis. Bioorg Med Chem Lett 27(15):3374-3377. doi: 10.1016/j.bmcl.2017.06.011.
  8. Liu, X., Yan, Y., Ma, W., Wu, S. (2017). Knockdown of frizzled-7 inhibits cell growth and metastasis and promotes chemosensitivity of esophageal squamous cell carcinoma cells by inhibiting Wnt signaling. Biochem Biophys Res Commun 490(3):1112-1118. 
  9. San-Jose, L.M., Ducret, V., Ducrest, A.L., Simon, C., Roulin, A. (2017). Beyond mean allelic effects: A locus at the major color gene MC1R associates also with differing levels of phenotypic and genetic (co)variance for coloration in barn owls. Evolution 71(10):2469-2483. 
  10. Tiwary, S., Xu, L. 2016. FRIZZLED7 Is Required for Tumor Initiation and Metastatic Growth of Melanoma Cells. PLoS One 11(1):e0147638. doi: 10.1371/journal.pone.0147638
  11. Wang, G., Liao, J., Tang, M., Yu, S. (2017). Genetic variation in the MITF promoter affects skin colour and transcriptional activity in black-boned chickens. Br Poult Sci 17:1-7. doi: 10.1080/00071668.2017.1379053.
  12. Wu, Z., Y. Fu., J. Cao., M. Yu., X. Tang., S. Zhao. (2014). Identification of differentially expressed miRNAs between white and black hair follicles by RNA-sequencing in the goat (Capra hircus). Int J Mol Sci 15:9531-45.
  13. Xia, M., Chen, K., Yao, X., Xu Y, Yao J, Yan J, Shao Z, Wang G.Mediator MED23 Links Pigmentation and DNA Repair through the Transcription Factor MITF. Cell Rep. (2017) Aug 22;20(8):1794-1804. doi: 10.1016/j.celrep.2017.07.056.
  14. Yang, L., Wu, X., Wang, Y., Zhang, K., Wu, J., Yuan, Y.C., Deng, X., Chen, L., Kim, C.C., Lau, S., Somlo, G., Yen, Y. (2011). FZD7 has a critical role in cell proliferation in triple negative breast cancer. Oncogene 30(43):4437-46. doi: 10.1038/onc.2011.145.
  15. Yang, S., R. Fan., Z. Shi., K. Ji., J. Zhang., H. Wang., M. Herrid., Q. Zhang., J. Yao., G.W. Smith., C. Dong. (2015). Identification of a novel microRNA important for melanogenesis in alpaca (Vicugna pacos). J Anim Sci 93:1622-31. 
  16. Zhang, M.Q., X. Xu., and S.J. Luo. (2014). The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens). Animal Genetics 45: 652–659
  17. Zhou, Y., Mowlazadeh, H.S., Zoi, I., Sawyer, J.R., Hruby, V.J., Cai, M. (2017). Design of MC1R Selective ã-MSH Analogues with Canonical Amino Acids Leads to Potency and Pigmentation. J Med Chem 60(22):9320-9329. 
  18. Zhou, Y., Mowlazadeh, H.S., Zoi, I., Sawyer, J.R., Hruby, V.J., Cai, M. (2017). Design of MC1R Selective ã-MSH Analogues with Canonical Amino Acids Leads to Potency and Pigmentation.J Med Chem 60(22):9320-9329. doi: 10.1021/acs.jmedchem    .7b01295. 
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Indian Journal of Animal Research
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    Short Communication

    volume 52 issue 6 (june 2018) : 816-819,   Doi: 10.18805/ijar.B-834

    Identification and characterization of microRNAs in white and black coated yak

    W
    Wang-Dui Basang
    T
    Tian-Wu An
    X
    Xiao-Lin Luo
    Y
    Yan-Bin Zhu
    L
    Luo-Bu Danjiu
    S
    Shi-Cheng He
    G
    Guang-Xin E
    1Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husandry Science, Lasa, 850009, China.
    Cite article:- Basang Wang-Dui, An Tian-Wu, Luo Xiao-Lin, Zhu Yan-Bin, Danjiu Luo-Bu, He Shi-Cheng, E Guang-Xin (2018). Identification and characterization of microRNAs in white and blackcoated yak. Indian Journal of Animal Research. 52(6): 816-819. doi: 10.18805/ijar.B-834.

    ABSTRACT

    In this study, we used high-throughput technology to provide the first transcriptome dataset for differentially expressed miRNA in mixed pools of dermis tissue from black- and white-coated yak to research the possible molecular mechanisms of yak coat pigmentation. In this study, 92,636,002 and 95,917,842 clear reads were generated through Illumina paired-end sequencing. A total of 78 differentially expressed miRNAs (DEMs) were identified, including 59 upregulated and 19 downregulated miRNAs in the mixed pools of white-coated yak compared with the mixed pools of black-coated yak. In addition, 3634 genes were predicted as putative targets of DEMs. These DEGs related to 59 GO categories and were enriched in 216 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including melanogenesis and the Wnt signaling pathway. The results of the current study indicated that the coat color of the yak involved the transcriptional regulation process of miRNAs. These results provide helpful data to understand the molecular mechanisms of yak coat pigmentation.

    REFERENCES

    1. Cao, T.T., Xiang, D., Liu, B.L., Huang, T.X., Tan, B.B., Zeng, C.M., Wang, Z.Y., Ming, X.Y., Zhang, L.Y., Jin, G., Li, F., Wu, J.L., Guan, X.Y., Lu, D., Fu, L. (2017). FZD7 is a novel prognostic marker and promotes tumor metastasis via WNT and EMT signaling pathways in esophageal squamous cell carcinoma. Oncotarget 8(39):65957-65968. 
    2. Corda, G., Sala, G., Lattanzio, R., Iezzi, M., Sallese, M., Fragassi, G., Lamolinara, A., Mirza, H., Barcaroli, D., Ermler, S., Silva, E., Yasaei, H., Newbold, R.F., Vagnarelli, P., Mottolese, M., Natali, P.G., Perracchio, L., Quist, J., Grigoriadis, A., Marra, P., Tutt, A.N., Piantelli, M., Iacobelli, S., De Laurenzi, V., Sala, A. 2017. Functional and prognostic significance of the genomic amplification of frizzled 6 (FZD6) in breast cancer. J Pathol 241(3):350-361. doi: 10.1002/path.4841.
    3. Dong. C., H. Wang., L. Xue., Y. Dong., L. Yang., R. Fan., X. Yu., X. Tian., S. Ma., G.W. Smith. (2012). Coat color determination by miR-137 mediated down-regulation of microphthalmia-associated transcription factor in a mouse model. RNA 18:1679-86.
    4. Huang, T., Alvarez, A.A., Pangeni, R.P., Horbinski, C.M., Lu, S., Kim, S.H., James, C.D., J Raizer, J., A Kessler, J., Brenann, C.W., Sulman, E.P., Finocchiaro, G., Tan, M., Nishikawa, R., Lu, X., Nakano, I., Hu, B., Cheng, S.Y. (2016). A regulatory circuit of miR-125b/miR-20b and Wnt signalling controls glioblastoma phenotypes through FZD6-modulated pathways. Nat Commun 7:12885. doi: 10.1038/ncomms12885.
    5. Irizarry, K.J., Bryden, R.L. (2016). In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites. Adv Bioinformatics, DOI: 10.1155/2016/1286510
    6. Irwandi, R.A., A. Vacharaksa. (2016). The role of microRNA in periodontal tissue: A review of the literature. Arch Oral Biol 72: 66-74. 
    7. Jo, H., Choi, M., Sim, J., Viji, M., Li, S., Lee, Y.H., Kim, Y., Seo, S.Y., Zhou, Y., Lee, K., Kim, W.J., Hong, J.T., Lee, H., Jung, J.K. (2017). Synthesis and biological evaluation of caffeic acid derivatives as potent inhibitors of á-MSH-stimulated melanogenesis. Bioorg Med Chem Lett 27(15):3374-3377. doi: 10.1016/j.bmcl.2017.06.011.
    8. Liu, X., Yan, Y., Ma, W., Wu, S. (2017). Knockdown of frizzled-7 inhibits cell growth and metastasis and promotes chemosensitivity of esophageal squamous cell carcinoma cells by inhibiting Wnt signaling. Biochem Biophys Res Commun 490(3):1112-1118. 
    9. San-Jose, L.M., Ducret, V., Ducrest, A.L., Simon, C., Roulin, A. (2017). Beyond mean allelic effects: A locus at the major color gene MC1R associates also with differing levels of phenotypic and genetic (co)variance for coloration in barn owls. Evolution 71(10):2469-2483. 
    10. Tiwary, S., Xu, L. 2016. FRIZZLED7 Is Required for Tumor Initiation and Metastatic Growth of Melanoma Cells. PLoS One 11(1):e0147638. doi: 10.1371/journal.pone.0147638
    11. Wang, G., Liao, J., Tang, M., Yu, S. (2017). Genetic variation in the MITF promoter affects skin colour and transcriptional activity in black-boned chickens. Br Poult Sci 17:1-7. doi: 10.1080/00071668.2017.1379053.
    12. Wu, Z., Y. Fu., J. Cao., M. Yu., X. Tang., S. Zhao. (2014). Identification of differentially expressed miRNAs between white and black hair follicles by RNA-sequencing in the goat (Capra hircus). Int J Mol Sci 15:9531-45.
    13. Xia, M., Chen, K., Yao, X., Xu Y, Yao J, Yan J, Shao Z, Wang G.Mediator MED23 Links Pigmentation and DNA Repair through the Transcription Factor MITF. Cell Rep. (2017) Aug 22;20(8):1794-1804. doi: 10.1016/j.celrep.2017.07.056.
    14. Yang, L., Wu, X., Wang, Y., Zhang, K., Wu, J., Yuan, Y.C., Deng, X., Chen, L., Kim, C.C., Lau, S., Somlo, G., Yen, Y. (2011). FZD7 has a critical role in cell proliferation in triple negative breast cancer. Oncogene 30(43):4437-46. doi: 10.1038/onc.2011.145.
    15. Yang, S., R. Fan., Z. Shi., K. Ji., J. Zhang., H. Wang., M. Herrid., Q. Zhang., J. Yao., G.W. Smith., C. Dong. (2015). Identification of a novel microRNA important for melanogenesis in alpaca (Vicugna pacos). J Anim Sci 93:1622-31. 
    16. Zhang, M.Q., X. Xu., and S.J. Luo. (2014). The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens). Animal Genetics 45: 652–659
    17. Zhou, Y., Mowlazadeh, H.S., Zoi, I., Sawyer, J.R., Hruby, V.J., Cai, M. (2017). Design of MC1R Selective ã-MSH Analogues with Canonical Amino Acids Leads to Potency and Pigmentation. J Med Chem 60(22):9320-9329. 
    18. Zhou, Y., Mowlazadeh, H.S., Zoi, I., Sawyer, J.R., Hruby, V.J., Cai, M. (2017). Design of MC1R Selective ã-MSH Analogues with Canonical Amino Acids Leads to Potency and Pigmentation.J Med Chem 60(22):9320-9329. doi: 10.1021/acs.jmedchem    .7b01295. 
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