猪全基因组范围ETS基因家族成员的鉴定、进化与表达分析

Genome-wide identification, evolutionary and expression analysis of the ETS transcription factor family in the pig

ETS转录因子家族在动物中广泛存在,参与细胞分化调控、细胞周期控制、细胞凋亡等多个生物学过程。文章采用生物信息学方法系统分析猪ETS家族成员进化关系和调控图谱,结合RNA-Seq数据分析其组织表达规律。研究利用Pfam鉴定ETS保守结构域序列检索猪(Sus scrofa)蛋白序列,最终在猪基因组上鉴定得到23个ETS家族基因。分析ETS家族基因、蛋白一级结构和高级结构及亚细胞定位预测。基于最大似然法,构建ETS家族系统发育树发现,可分为11个子家族,子家族成员保守结构域、基因结构、理化性质相似。通过生信分析构建由ETS家族、靶基因和miRNA构成的基因调控网络,筛选出40个"ETS家族基因-miRNA-靶基因"前馈回路。转录表达谱提示ETS家族基因在成年公猪和母猪28种不同类型组织中均有表达,且ETS1基因在免疫组织(淋巴、脾脏)和外周血单核细胞中高表达,SPIC基因在免疫组织(淋巴、脾脏)高表达。研究结果为揭示ETS家族成员生物学功能奠定基础。

The ETS proteins are a family of transcription factors(TFs) that regulate a variety of biological processes. Genome-wide analyses were carried on to explore the evolutionary and regulatory relationship of the ETS gene family, integrating RNA-seq data. Twenty-three ETS genes in pig genome were identified, the Pfam ETS motif was screened. A phylogenetic tree based on maximum likelihood was constructed using the amino acid sequences of the ETS domain of the ETS proteins, which could be further divided into eleven subgroups. The sequence conserved motifs, the exon-intron structural patterns,and physico-chemical properties of the ETS genes and proteins in pig further supported the phylogenetic classification among these ETS gene family. A gene regulationary network was constructed containing ETS genes, target genes and mi RNA, and 40 "ETS gene-miRNA–target genes" feedforward loops were identified. The expression profiles showed that the ETS family members were ubiquitously expressed in 28 normal adult Duroc pig tissues, and highly expression of ETS1 and SPIC genes were in immune tissues(lymph, spleen). The research offered foundation for biology function of the ETS family.