上颌尖牙阻生患者牙龈组织的转录组特征分析

Transcriptome analysis of the gingival tissue from impacted maxillary permanent canine

目的:采集和分析上颌尖牙阻生患者牙龈组织的转录组信息,为其地域差异和病因基因理论奠定基础。方法:使用Resequencing Illumina Hi Seq 2000测序平台,采集遵义地区5例成人(25~35岁)上颌尖牙阻生患者牙龈组织的转录组信息,并采用FPKM方法计算基因在牙龈组织中的表达量。通过转录组比对,将基因映射至数据库进行功能注释。基于注释信息,挖掘上颌尖牙阻生患者的转录组特征。结果:高通量测序共获得223 530 890个高质量测序数据,FPKM方法鉴定出19 352个基因表达(FPKM>0),其中99.63%的基因FPKM值小于1 000。转录组比对显示每个样本约15 412个基因发生了可变剪切,剪切次数约为16 167次。这些可变剪切类型中外显子选择性跳跃剪切所占比例最低(6.72%),外显子跳跃剪切比例最高(48.82%)。此外,利用这批转录组数据共检测出386 414个单核苷酸多态性位点(SNP),其中转换是最主要的突变类型(76.31%)。基因本体论(GO)注释显示,转录组SNP涉及到广泛的生物功能,且尤其富集于生物学过程和细胞组分。京都基因与基因组百科全书(KEGG)通路分析显示,SNP所在基因除了富集于代谢途径、细胞内吞、细胞凋亡、细胞衰老等相关通路,更多的基因则富集于癌症、信号通路以及免疫系统相关通路。结论:基于阻生尖牙牙龈组织的转录组研究显示牙龈和牙发育密切相关。

Objective: To collect and analyze the whole genome transcription information of gingival tissue of patients with impacted maxillary canine,and lay a foundation for the gene theory of the etiology. Methods: Using resequecing Illumina hiseq 2000 sequencing platform,the transcriptome information of gingival tissue of 5 adult patients(25-35 years old)with impacted maxillary canines in Zunyi area was collected by high-throughput sequencing. The expression level and difference of gene in gingival tissue were analyzed and calculated by FPKM method. Results: 223 530 890 high quality sequencing data were obtained,and 19 352 genes were indentified to be expressed in the gingival tissue,among which 99.63% of genes’ FPKM values were lower than 1 000. 15 412 genes had alternative splicing(AS),and the aplicing times were 16 167. Mutually exclusive exons were found to be the rarest AS type(6.72%). While skipped exons found to be the major type(48.82%). Using these transcriptome data,386 414 SNPs were called,among which transitions were the main type(76.31%). According to GO database,transcriptome SNPs were involved in a wide range of biological functions,and are especially enriched in biological processes and cell components;KEGG pathway analysis shows that the genes of SNPs are enriched in metabolic pathways,endocytosis,apoptosis,cell aging and other related pathways,and more genes are enriched in cancer,signaling pathways and immune system related pathways. Conclusions: Genome transcription information of gingival tissue of patients with impacted maxillary canine showed gingiva were closely related to the development of teeth.