基于表达谱芯片筛选鸡不同部位皮肤组织差异表达基因

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

旨在筛选鸡不同部位(背部和腿部)皮肤组织中的差异表达基因,探讨二者皮肤毛囊出现表型差异的分子机制。以处于上市日龄的(63日龄)商品代肉鸡为素材,利用Agilent鸡全基因组表达谱芯片对皮肤厚度、毛囊密度和直径出现显著差异的背部和腿部皮肤组织mRNA表达水平进行检测,对与皮肤毛囊发生发育相关的候选基因及信号通路进行系统筛查,并运用实时荧光定量PCR技术对部分差异表达基因进行验证。结果显示,芯片分析共筛选到差异表达基因676个(|FC|≥2,P<0.05),以腿部皮肤为参照,背部皮肤组织中上调基因223个,下调基因453个。荧光定量PCR验证部分差异表达基因的表达趋势与芯片结果基本一致。GO分析表明,差异表达基因参与细胞增殖和凋亡调控、Wnt信号通路、神经元分化、细胞间黏附调节、细胞命运的确定等生物学过程。KEGG信号通路分析发现,除了部分已知的与皮肤毛囊生长发育相关的信号通路(Wnt和Hedgehog信号通路),ECM受体相互作用、黏着、细胞黏附分子、黏合连接等信号通路也被富集。蛋白互作网络分析表明,这些差异表达基因相互作用形成一个调控网络,可能通过影响皮肤毛囊的生长发育和周期变化来影响皮肤毛囊的性状,推测ECM受体相互作用、黏着、运输等调控通路及DKK1、WNT3A、SHH、FGF1、IGF1等基因可能是参与鸡不同部位皮肤毛囊性状出现差异的重要调控通路和候选基因。

The aims of this study were to screen differentially expressed genes of skin tissue at dif- ferent positions（dorsal and leg）of chicken, and investigate the molecular mechanism of pheno- typic 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.