基于基因及调控区进化保守性评估细胞和组织发育潜能的定量分析

Quantitative analysis of the developmental potential of cells and tissues based on evolutionary conservation of genes and regulatory regions

目的在DNA序列的保守度层面探讨物种进化与发育之间的关系及其内在规律。方法分析编码基因的氨基酸序列在100个物种中的保守程度,并建立保守率(conservation rate,CR)这一量化基因进化保守程度的指标,进一步使用胚胎干细胞通路特征基因验证保守率与发育潜能的关系。分析早期三胚层(内胚层、中胚层、外胚层)及其对应的成熟器官(肝脏、心脏和大脑等)的转录组测序(RNA sequencing,RNA-seq)数据,寻找差异表达基因,研究其保守性特点。收集人类早期胚层和成熟器官H3组蛋白第27位赖氨酸乙酰化(histone H3 acetylated at lysine 27,H3K27ac)这一增强子表观遗传标志物的染色质免疫共沉淀测序(chromatin immunoprecipitation sequencing,ChIP-seq)数据,寻找增强子位点,使用ROSE程序鉴定各种细胞和组织中的超级增强子(super enhancer,SE)。使用基因通路富集分析研究超级增强子调控的基因与对应的细胞特征的身份相关性,以明确所鉴定的超级增强子是否符合已有研究报道的特点。使用PhastCons程序计算非编码调控区的DNA保守性评分(conservation score,CS),研究其与发育潜能的关系。结果在基因编码区,成功建立保守率这一对基因保守程度进行量化的指标。早期三胚层和成熟器官的基因表达数据分析显示:保守率越高的基因与干性和早期发育过程相关性越大,基因保守率指标能区分出发育前后的组织差异。在基因非编码区,发现调控区的保守性也与发育具有相关性:发育早期三胚层的超级增强子序列的保守性评分显著高于对应的成熟器官的超级增强子序列;但细胞特异的普通增强子(typical enhancer,TE)没有呈现出这样的趋势。结论随着发育进行,在基因编码区特异表达的基因在进化中的保守率下降,非编码调控区的超级增强子DNA保守性评分下降。

Objective To study the relationship between evolution and the developmental process from the perspective of DNA sequence conservation,and explore their inherent principles.Methods First,conservation rate(CR)was established by analyzing the conservation of amino acid sequences of coding genes in 100 species to quantify the evolutionary conservation of genes.The relationship between CR and developmental potential was verified by using the feature genes involved in embryonic stem cells pathways.Secondly,cell type-specific genes and their characteristics in conservation were studied by analyzing the RNA sequencing(RNA-seq)data of the three early germ layers(ectoderm,mesoderm and endoderm)and their corresponding mature organs(brain,heart,liver,etc).Then,chromatin immunoprecipitation sequencing(ChIP-seq)data of enhancer histone H3 acetylated at lysine 27(H3K27ac)from early germ layers and mature organs were collected to search for enhancer sites and identify super enhancers in various cells and tissues by using the ROSE procedure.Functional enrichment and signaling pathway analysis of genes was used to examine the identity correlation between SEs-regulated genes and the corresponding cell characteristics,to clarify whether the SEs identified in this study were consistent with the characteristics reported in previous studies.Finally,PhastCons program was used to calculate the DNA conservation score(CS)of non-coding regulatory regions to study their relationship with developmental potential.Results In the coding region of DNA,CR was successfully established to quantify the conservation of genes.The gene expression data of early germ layers and mature organs showed that the genes with higher conservation rate were more relevant to the stemness and early developmental process,and the differences between the tissues from early and late development could be distinguished by using CR.In the non-coding regions of DNA,it was found that the conservation of regulatory regions was also correlated with development.The CS of the SE sequences in the early developmental germ layers was significantly higher than that of the SE sequences in the corresponding mature organs.However,cell-specific typical enhancers(TEs)did not show such a trend.Conclusion During the developmental process,CR of genes expressed in the coding region decreases,and CS of super-enhancer DNA in the non-coding region decreases.