藏绵羊不同毛色皮肤组织miRNA表达谱及靶基因分析

doi:10.3864/j.issn.0578-1752.2018.02.014

Abstract

Abstract: 【Objective】 Tibetan sheep is one of three coarse wool sheep breeds in China, distributing mainly in Tibet and its adjacent alpine pastoral areas, such as Qinghai, Gansu, Sichuan, Yunnan. The wool of Tibetan sheep, felt smooth and warm duo to the long and thick fibers, is good raw material for manufacture of Tibetan carpet. Coat color is an important economic traits. However, at present, the mechanism of molecular regulation of sheep coat color is not clear. In this study, the transcriptome of skin tissues of different color (black and white) was sequenced with a aim to explore the role of miRNAs at post-transcriptional levels in different coat color skin tissues and possible regulatory pathways. 【Method】Healthy sheep with black and white coat color was sacrificed to provide skin tissues for RNA extraction and miRNA analysis. Through miRNA sequencing and bioinformatics analysis, miRNA expression profiles of skin tissues of black and white wool color were obtained. Then the differentially expressed miRNAs were screened and the related target genes were predicted. Through the target gene analysis, the signal pathway which is related to Tibetan coat color skin traits were proposed. 【Result】 A total of 85.76 million original reads and 85.08 million clean reads were obtained from the analyzed tissues. Among the clean reads were 334 known miRNAs and 59 newly identified miRNAs and 23 of them were differentially expressed between white and black color tissues. In the 23 differentially expressed miRNAs, 14 and 9 were up-regulated and down-regulated in white skin tissues respectively. miR-2284b and miR-744 were the type that is expressed only in white Tibetan sheep skin, and miR-23b, miR-411a-5p, miR-30c, miR-423-3p, miR-324-5p were the miRNAs that expressed only in black skin. Among them, miR-10a can participate in the regulation of a variety of signaling pathways, involving proliferation, differentiation, apoptosis, cell adhesion. MiR-23b is associated with Wnt, Notch and other signal pathways, which may related to melanin production. MiR-411a-5p, miR103 and miR-200b may also closely relate to regulation of hair color. A total of 981 target genes were predicted to be involved in coat color control, most of which were related to WNT signaling pathway, MAPK pathway, EDNRB signaling pathway and Melanogenesis pathway. The melanogenesis pathway was found to be associated with the WNT signal pathway, the KIT signal pathway, and the EDNRB signal pathway. The synthesis of melanin may be regulated by downstream TYR gene (tyrosinase gene) through MITF gene. Quantitative analysis showed that five miRNAs were up-regulated in black skin tissue, and two miRNAs were up-regulated in white tissues. The quantitative results were consistent with the sequencing results. 【Conclusion】 The miRNA expression profile of the skin of Tibetan sheep were obtained and the miRNAs and signal pathways which may be related to control of coat color were obtained by bioinformatics analysis. These results indicated that the color traits could be regulated by many miRNAs and involved many signal pathways. This may help understand the level of post-transcriptional regulation of the process, and lay the foundation for further functional verification.

Key words: Tibetan sheep, skin tissue, high throughput sequencing, miRNA

WU ZhenYang, TANG XiaoHui, FU YuHua, WANG Sheng, ZHANG Cheng, LI JingJin, YU Mei, DU XiaoYong. Profiles of miRNAs and Target Gene Analysis with White and Black Skin Tissues of the Tibetan Sheep[J].Scientia Agricultura Sinica, 2018, 51(2): 351-362.

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References

[1] BLLANPAIN C, SOTIROPOULOU P A. A dominant role of the hair follicle stem cell niche in regulating melanocyte stemness. Cell Stem Cell, 2010, 6(2):95-96.

[2] LANG D, MASCARENHAS J B, SHEA C R. Melanocytes, melanocyte stem cells, and melanoma stem cells. Clinics in Dermatology, 2013, 31(2):166-178.

[3] LI A. The biology of melanocyte and melanocyte stem cell. Acta Biochimica et Biophysica Sinica, 2014, 46(4):255-260.

[4] GUO H, LEI M, LI Y, LIU Y, TANG Y, XING Y, DENG F, YANG K. Paracrine secreted frizzled-related protein 4 inhibits melanocytes differentiation in hair follicle. Stem Cells International, 2017 , 2017: 1-12.

[5] GUO H, XING Y, LIU Y, LUO Y, DENG F, YANG T, YANG K, LI Y. Wnt/beta-catenin signaling pathway activates melanocyte stem cells in vitro and in vivo. Journal of Dermatological Science, 2016, 83(1): 45-51.

[6] 姜俊兵，于秀菊，田雪，贺俊平，董常生. 干细胞因子及其受体c-KIT 对羊驼毛囊黑色素细胞增殖与分化的影响及其机制. 解剖学报，2011, 42(1):99-103.

JIANG J B, YU X J, TIAN X, HE J P, DONG C S. SCF/c-KIT signal regulates the proliferation and division of alpaca (Lama pacos) hair follicle melanocytes and its mechanism. Acta Anatomica Sinica, 2011, 42(1):99-103.(in Chinese)

[7] GUENTHER C A, TASIC B, LUO L, BEDELL M A, KINGSLEY D M. A molecular basis for classic blond hair color in Europeans. Nature Genetics, 2014, 46(7):748-752.

[8] AUBIN-HOUZELSTEIN G. Notch signaling and the developing hair follicle. Advances in Experimental Medicine and Biology, 2012, 727: 142-160.

[9] WATANABE N, MOTOHASHI T, NISHIOKA M, KAWAMURA N, HIROBE T, KUNISADA T. Multipotency of melanoblasts isolated from murine skin depends on the notch signal. Developmental Dynamics : an Official Publication of the American Association of Anatomists, 2016, 245(4):460-471.

[10] ZHAO Y, WANG P, MENG J, JI Y, XU D, CHEN T, FAN R, YU X,YAO J, DONG C. Microrna-27a-3p inhibits melanogenesis in mouse skin melanocytes by targeting wnt3a. International Journal of Molecular Sciences, 2015, 16(5):10921-10933.

[11] WANG P, ZHAO Y, FAN R, CHEN T, DONG C. Microrna-21a-5p functions on the regulation of melanogenesis by targeting sox5 in mouse skin melanocytes. International Journal of Molecular Sciences, 2016, 17(7):959.

[12] DAI X, RAO C, LI H, CHEN Y, FAN L, GENG H, LI S, QU J, HOU L. Regulation of pigmentation by micrornas: Mitf-dependent microrna-211 targets tgf-beta receptor 2. Pigment Cell & Melanoma Research, 2015, 28(2):217-222.

[13] ZHANG J, LIU Y, ZHU Z, YANG S, JI K, HU S, LIU X, YAO J, FAN R, DONG C. Role of microrna508-3p in melanogenesis by targeting microphthalmia transcription factor in melanocytes of alpaca. Animal, 2017, 11(2):236-243.

[14] DONG C, WANG H, XUE L, DONG Y, YANG L, FAN R, YU X, TIAN X, MA S, SMIH G W. Coat color determination by mir-137 mediated down-regulation of microphthalmia-associated transcription factor in a mouse model. Rna, 2012,18(9):1679-1686.

[15] 马淑慧，薛霖莉，徐刚，侯亚琴，耿建军，曹靖，赫晓燕，王海东，董常生. 黑色素细胞中过量表达miR-137 对TYRP-1 和TYRP-2 的影响. 中国农业科学，2013，46(16)：3452-3459.

MA S H, XUE L L, XU G, HOU Y Q, GEN J J, CAO J, HAO X Y, WANG H D, DONG C S. The influences of over-expressing miR-137 on TYRP-1 and TYRP-2 in melanocytes, Scientia Agricultura Sinica, 2013, 46 (16) :3452-3459.(in Chinese)

[16] JIANG S, YU X, DONG C. Mir-137 affects melanin synthesis in mouse melanocyte by repressing the expression of c-kit and tyrp2 in scf/c-kit signaling pathway. Bioscience, Biotechnology, and Biochemistry, 2016:1-7.

[17] YUAN C, WANG X, GENG R, HE X, QU L, CHEN Y. Discovery of cashmere goat (Capra hircus) micrornas in skin and hair follicles by solexa sequencing. BMC Genomics, 2013,14:511.

[18] LI Z, LAN X, GUO W, SUN J, HUANG Y, WANG J, HUANG T, LEI C, FANG X, CHEN H. Comparative transcriptome profiling of dairy goat micrornas from dry period and peak lactation mammary gland tissues. PloS One, 2012,7(12):e52388.

[19] TIAN X, JIANG J, FAN R, WANG H, MENG X, HE X, HE J, LI H, GENG J, YU X, SONG Y, SONG Y, ZHANG D, YAO J, SMITH G W, DONG C. Identification and characterization of micrornas in white and brown alpaca skin. BMC Genomics, 2012,13(1):555.

[20] WU Z, FU Y, CAO J, YU M, TANG X, ZHAO S H. Identification of Differentially Expressed miRNA between White and Black Hair Follicles by RNA-Sequencing in the Goat. International Journal of Molecular Sciences, 2014, 15 (6) :9531-9545.

[21] ANDER S, HUBER W. Differential expression analysis for sequence count data. Genome Biology, 2010, 11(10): R106.

[22] Friedländer M R, Mackowiak S D, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Research, 2012, 40: 37-52.

[23] ZENG H C, BAE Y, DAWSON B C, CHEN Y, BERTIN T, MUNIVEZ E, CAMPEAU P M, TAO J, CHEN R, LEE B H. Microrna mir-23a cluster promotes osteocyte differentiation by regulating tgf-beta signalling in osteoblasts. Nature Communications, 2017, 8:15000.

[24] GUO X, WANG X. Signaling cross-talk between TGF-β/BMP and other pathways. Cell Research , 2009 , 19 (1) :71-88.

[25] ZHENG J, JIANG H Y, LI J, TANG H C, ZHANG X M, WANG X R, DU J T, LI H B, XU G. Microrna-23b promotes tolerogenic properties of dendritic cells in vitro through inhibiting notch1/nf-kappab signalling pathways. Allergy, 2012,67(3):362-370.

[26] SUN M, HUANG F, YU D, ZHANG Y, XU H, ZHANG L, LI L, DONG L, GUO L, WANG S. Autoregulatory loop between TGF-β1/ miR-411-5p/SPRY4 and MAPK pathway in rhabdomyosarcoma modulates proliferation and differentiation. Cell Death and Disease, 2015, 6: e1859.

[27] FUJIMURA N, TAKETO M M, MORI M, KORINEK V, KOZMIK Z. Spatial and temporal regulation of Wnt/beta-catenin signaling is essential for development of the retinal pigment epithelium. Developmental Biology, 2009, 334: 31-45.

[28] SQUARZONI P, PARVEEN F, ZANETTI L, RISTORATORE F, SPAGNUOLO A. Fgf/mapk/ets signaling renders pigment cell precursors competent to respond to wnt signal by directly controlling ci-tcf transcription. Development, 2011,138(7):1421-1432.

[29] KIM S H, HWANG S Y, YOON J T. Microarray-based analysis of the differential expression of melanin synthesis genes in dark and light-muzzle Korean cattle. PloS One, 2014, 9(5):e96453.

[30] YE J, YANG T, GUO H, TANG Y, DENG F, LI Y, XING Y, YANG L, YANG K. Wnt10b promotes differentiation of mouse hair follicle melanocytes. International Journal of Medical Sciences, 2013, 10(6): 691-698.

[31] PARK T J, KIM M, KIM H, PARK S Y, PARK K C, ORTONNE J P, KANG H Y. Wnt inhibitory factor (wif)-1 promotes melanogenesis in normal human melanocytes. Pigment Cell & Melanoma Research, 2014, 27(1):72-81.

[32] YAMDA T, AKAMATSU H, HASEGAWA S, INOUE Y, DATE Y, MIZUTANI H, YAMAMOTO N, MATSUNAGA K, NAKATA S. Melanocyte stem cells express receptors for canonical wnt-signaling pathway on their surface. Biochemical and Biophysical Research Communications, 2010, 396(4):837-842.

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Profiles of miRNAs and Target Gene Analysis with White and Black Skin Tissues of the Tibetan Sheep

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