基于表达谱芯片筛选鸡不同部位皮肤组织差异表达基因

doi:10.11843/j.issn.0366-6964.2018.01.005

Abstract

Abstract:

The aims of this study were to screen differentially expressed genes of skin tissue at different positions(dorsal and leg) of chicken, and investigate the molecular mechanism of phenotypic differences. Commercial broiler chickens (63 days old) were selected as materials, Agilent cDNA microarray analyses were conducted to determine gene expression profiles of dorsal and leg skin tissues with significant differences in skin thickness, hair follicle density and diameter. A systematic identification of candidate genes and signaling pathways associated with skin follicle initiation and development were conducted, and qRT-PCR assays were used to validate the microarray hybridization results. A total of 676 genes were screened (|FC| ≥ 2,P<0.05), compared with the leg skin, among them, 223 were up-regulated expression genes and 453 were down-regulated expression genes in dorsal skin. Real-time PCR results were consistent with microarray results in the expression trend of partial differentially expressed genes (DEGs). GO analysis showed that the DEGs were involved in the regulation of cell proliferation and apoptosis, Wnt signaling pathway, neuronal differentiation, regulation of cell-cell adhesion, cell fate commitment and other biological processes. KEGG pathway analysis revealed that, in addition to partly known signaling pathways associated with skin follicle development(Wnt and Hedgehog signaling pathways), ECM-receptor interaction, Focal adhesion, Cell adhesion molecules (CAMs), Adherens junction signaling pathways were also enriched. Protein interaction network analysis showed that the DEGs genes interacted with each other to form a regulatory network that may affect the skin follicle traits by affecting the growth and development of the skin follicle and the periodic variation. ECM-receptor interaction, Focal adhesion, transporter pathways and DKK1, WNT3A, SHH, FGF1 and IGF1 genes may be important regulatory pathways and candidate genes involved in the differences of skin follicle traits in different positions of the chicken skin.

CLC Number:

S831.2

JI Gai-ge, SHU Jing-ting, SHAN Yan-ju, ZHANG Ming, TU Yun-jie, LIU Yi-fan, JU Xiao-jun, ZOU Jian-min. Identification of Differentially Expressed Genes between Different Positions of Chicken Skin Based on Gene Expression Microarray[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2018, 49(1): 36-45.

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References

[1] RENDL M, POLAK L, FUCHS E. BMP signaling in dermal papilla cells is required for their hair follicle-inductive properties[J]. Genes Dev, 2008, 22(4):543-557.
[2] 狄江, 拉扎提·艾尼瓦尔, 徐新明, 等. 不同羊毛纤维直径细毛羊皮肤组织差异表达基因研究[J]. 畜牧兽医学报, 2013, 44(5):681-689.
DI J, AINIWAER L Z T, XU X M, et al. Genome array on differentially expressed genes of skin tissue in fine wool sheep with different fiber diameter[J]. Acta Veterinaria et Zootechnica Sinica, 2013, 44(5):681-689. (in Chinese)
[3] NORRIS B J, BOWER N I, SMITH W J M, et al. Gene expression profiling of ovine skin and wool follicle development using a combined ovine-bovine skin cDNA microarray[J]. Aust J Exp Agric, 2005, 45(8):867-877.
[4] 陈兴勇, 谢珊珊, 周丽, 等. 皖西白鹅换羽前后基因表达谱差异分析[J]. 畜牧兽医学报, 2013, 44(7):1030-1036.
CHEN X Y, XIE S S, ZHOU L, et al. Identification of differentially expressed genes in skin of Wanxi-white goose during regeneration of downy feather[J]. Acta Veterinaria et Zootechnica Sinica, 2013, 44(7):1030-1036. (in Chinese)
[5] ZHANG J Q, LIU F Z, CAO J T, et al. Skin transcriptome profiles associated with skin color in chickens[J]. PLoS One, 2015, 10(6):e0127301.
[6] 高广琦. 基于红腹锦鸡基因组、转录组测序的羽毛色素调控机制研究[D]. 呼和浩特:内蒙古大学, 2016.
GAO G Q. researches of plumage pigmentation based on golden pheasant genome and transcriptome sequencing[D]. Hohhot:Inner Mongolia University, 2016. (in Chinese)
[7] ZHANG L, NIE Q H, SU Y, et al. MicroRNA profile analysis on duck feather follicle and skin with high-throughput sequencing technology[J]. Gene, 2013, 519(1):77-81.
[8] 乌仁套迪, 巴拉, 宝迪. 河南斗鸡与艾维茵肉鸡皮肤厚度及羽密度的比较[J]. 中国家禽, 2013, 35(14):50-51.
WURENTAODI, BALA, BAODI. Comparison of skin thickness and feather density between Henan Game Fowl and Avian broiler[J]. China Poultry, 2013, 35(14):50-51. (in Chinese)
[9] CHEN X Y, JIANG R S, GENG Z Y. Differential effects of two indigenous broilers exposed to cold stress and characters of follicle density and diameter[J]. Ital J Anim Sci, 2011, 10(1):e8.
[10] PENG H, PARK J K, KATSNELSON J, et al. microRNA-103/107 family regulates multiple epithelial stem cell characteristics[J]. Stem Cells, 2015, 33(5):1642-1656.
[11] SIBILIA M, KROISMAYR R, LICHTENBERGER B M, et al. The epidermal growth factor receptor:from development to tumorigenesis[J]. Differentiation, 2007, 75(9):770-787.
[12] KIZAWA K, ITO M. Characterization of epithelial cells in the hair follicle with S100 proteins[M]//TURKSEN K. Epidermal Cells. New York:Humana Press, 2005:209-222.
[13] WEGER N, SCHLAKE T. IGF-I signalling controls the hair growth cycle and the differentiation of hair shafts[J]. J Invest Dermatol, 2005, 125(5):873-882.
[14] OLSSON J E, KAMACHI Y, PENNING S, et al. Sox18 expression in blood vessels and feather buds during chicken embryogenesis[J]. Gene, 2001, 271(2):151-158.
[15] NAKAYAMA F, HAGIWARA A, KIMURA M, et al. Evaluation of radiation-induced hair follicle apoptosis in mice and the preventive effects of fibroblast growth factor-1[J]. Exp Dermatol, 2009, 18(10):889-892.
[16] HWANG J, MEHRANI T, MILLAR S E, et al. Dlx3 is a crucial regulator of hair follicle differentiation and cycling[J]. Development, 2008, 135(18):3149-3159.
[17] JIANG T X, CHUONG C M. Mechanism of skin morphogenesis. I. Analyses with antibodies to adhesion molecules tenascin, N-CAM, and integrin[J]. Dev Biol, 1992, 150(1):82-98.
[18] TSAI S Y, SENNETT R, REZZA A, et al. Wnt/β-catenin signaling in dermal condensates is required for hair follicle formation[J]. Dev Biol, 2014, 385(2):179-188.
[19] MICHNO K, BORAS-GRANIC K, MILL P, et al. Shh expression is required for embryonic hair follicle but not mammary gland development[J]. Dev Biol, 2003, 264(1):153-165.
[20] BILLONI N, BUAN B, GAUTIER B, et al. Expression of peroxisome proliferator activated receptors (PPARs) in human hair follicles and PPARα involvement in hair growth[J]. Acta Derm Venereol, 2000, 80(5):329-334.
[21] GUO H Y, YANG K, DENG F, et al. Wnt3a promotes melanin synthesis of mouse hair follicle melanocytes[J]. Biochem Biophys Res Commun, 2012, 420(4):799-804.
[22] JIA L W, ZHOU J X, PENG S, et al. Effects of Wnt3a on proliferation and differentiation of human epidermal stem cells[J]. Biochem Biophys Res Commun, 2008, 368(3):483-488.
[23] CHANG C H, TSAI R K, TSAI M H, et al. The roles of Frizzled-3 and Wnt3a on melanocyte development:in vitro studies on neural crest cells and melanocyte precursor cell lines[J]. J Dermatol Sci, 2014, 75(2):100-108.
[24] SHIN H, KWACK M H, SHIN S H, et al. Identification of transcriptional targets of Wnt/β-catenin signaling in dermal papilla cells of human scalp hair follicles:EP2 is a novel transcriptional target of Wnt3a[J]. J Dermatol Sci, 2010, 58(2):91-96.
[25] MI H K, KIM M K, KIM J C, et al. Dickkopf 1 promotes regression of hair follicles[J]. J Invest Dermatol, 2012, 132(6):1554-1560.
[26] SICK S, REINKER S, TIMMER J, et al. WNT and DKK determine hair follicle spacing through a reaction-diffusion mechanism[J]. Science, 2006, 314(5804):1447-1450.
[27] LEI M X, GUO H Y, QIU W M, et al. Modulating hair follicle size with Wnt10b/DKK1 during hair rege-neration[J]. Exp Dermatol, 2014, 23(6):407-413.
[28] GALLEGO M I, BEACHY P A, HENNIGHAUSEN L, et al. Differential requirements for Shh in mammary tissue and hair follicle morphogenesis[J]. Dev Biol, 2002, 249(1):131-139.
[29] TING-BERRETH S A, CHUONG C M. Sonic hedgehog in feather morphogenesis:induction of mesenchymal condensation and association with cell death[J]. Dev Dyn, 1996, 207(2):157-170.
[30] REDDY S, ANDL T, BAGASRA A, et al. Characterization of Wnt gene expression in developing and postnatal hair follicles and identification of Wnt5a as a target of Sonic hedgehog in hair follicle morphogenesis[J]. Mech Dev, 2001, 107(1-2):69-82.
[31] HU B, LEFORT K, QIU W Y, et al. Control of hair follicle cell fate by underlying mesenchyme through a CSL-Wnt5a-FoxN1 regulatory axis[J]. Genes Dev, 2010, 24(14):1519-1532.
[32] UMEDA-IKAWA A, SHIMOKAWA I, DOI K. Time-course expression profiles of hair cycle-associated genes in male mini rats after depilation of telogen-phase hairs[J]. Int J Mol Sci, 2009, 10(5):1967-1977.
[33] STACHELSCHEID H, IBRAHIM H, KOCH L, et al. Epidermal insulin/IGF-1 signaling control interfollicular morphogenesis and proliferative potential through Rac activation[J]. EMBO J, 2008, 27(15):2091-2101.
[34] BOL D K, KIGUCHI K, GIMENEZ-CONTI I, et al. Overexpression of insulin-like growth factor-1 induces hyperplasia, dermal abnormalities, and spontaneous tumor formation in transgenic mice[J]. Oncogene, 1997, 14(14):1725-1734.
[35] HE L, VASILIOU K, NEBERT D W. Analysis and update of the human solute carrier (SLC) gene superfamily[J]. Hum Genomics, 2009, 3(2):195-206.

Identification of Differentially Expressed Genes between Different Positions of Chicken Skin Based on Gene Expression Microarray

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