Tol2转座子介导斑马鱼rps26基因附近增强子捕获及注解分析

Enhancer trapping nearby rps26 gene in zebrafish mediated by the Tol2 transposon and it’s annotation

摘要:

随着人类等生物大规模基因组测序工作的完成，认识和理解基因组上表达调控元件成为后基因组时代的重要研究任务，增强子捕获技术是一种鉴定基因组上增强子元件及其对基因表达调控机制的有效方法。本研究选择Tol2转座子系统介导制备的稳定增强子捕获品系TK4系 (头部和躯干特异性GFP表达)，利用Splinkerette PCR (sp-PCR)、原位杂交和比较基因组学等技术手段进行所捕获增强子的解析研究。将TK4系的F1代与野生型斑马鱼杂交，收集受精卵，于6 hpf (Hour post fertilization)、24 hpf、48 hpf、3 dpf (Day post fertilization)、4 dpf、5 dpf六个发育阶段通过荧光显微镜检测绿色荧光蛋白报告基因的表达模式；然后通过sp-PCR方法克隆到Tol2转座子插入位点斑马鱼基因组侧翼序列，经比对分析表明插入位点位于基因组23号染色体27749253位置，在rps26基因的intron1中，且报告基因插入方向与基因方向相反。在插入位点100 kb的基因组范围内有7个基因，分别为arf3a、wnt10b、wnt1、rps26、IKZF4、dnajc22和lmbr1l。通过VISTA程序对不同脊椎动物基因组同源序列比对结果显示，在rps26基因下游有2个潜在保守的非编码序列区CNS1 (Conserved non-coding sequence)和CNS2，为可能的增强子元件。胚胎原位杂交表明：rps26基因的两个转录本有母源性表达，rps26-201在合子中的表达早于rps26-001，而TK4系斑马鱼的GFP在早期 (6 hpf) 不表达，后期rps26与GFP的表达模式既存在相似性，也存在差异性，提示两者可能既接受共同的增强子调控，但也存在不同增强子调控，所获得的2个潜在的增强子 (CNS1和CNS2) 可能对附近的基因 (包括rps26) 发挥差异的时空表达调控作用。本研究首次成功获得rps26基因附近2个潜在增强子，为深入研究这两个增强子对基因组附近基因的表达调控机制奠定基础，本研究所采用的结合技术手段也为增强子解析提供参考。

Abstract:

With the completion of large-scale genome sequencing of human beings and other organisms, understanding the expression of control elements on the genome has become an important research task in the post-genome era. The enhancer trapping technology is an effective method for identifying enhancer elements in the genome and understanding its mechanism for gene expression regulation. In this study, we selected the stable enhancer trapping line TK4 (head and trunk specific GFP expression), which is generated with the mediation of Tol2 transposon system, and analyzed the trapped enhancers with the techniques of Splinkerette PCR (sp-PCR), in situ hybridization and comparative genomics. We crossed F1 individuals of TK4 line with wild-type zebrafish, collected fertilized eggs, and then detected the expression pattern of green fluorescent protein reporter gene by fluorescence microscopy at six different developmental stages, 6 hpf (hour post fertilization), 24 hpf, 48 hpf, 3 dpf (day post fertilization), 4 dpf and 5 dpf . The zebrafish genome flank sequence near the insertion site of Tol2 transposon was cloned by sp-PCR, and the results revealed that the insertion located at the position 27749253 of chromosome 23, and the transgene inserted reversely inside the intron 1 of rps26 gene. Within the 100 kb region of the insertion site, totally, seven genes including arf3a, wnt10b, wnt1, rps26, IKZF4, dnajc22 and lmbr1l were identified. Comparative genomic analysis by VISTA program revealed that there were two potential enhancer elements in the downstream of rps26 gene, which were conserved non-coding sequence (CNS) 1 and CNS2. The results of in situ hybridization showed that two transcripts of rps26 gene were maternal expression, the expression of rps26-201 in zygote was earlier than that of rps26-001, and the GFP signal of TK4 line zebrafish was not detectable before 6hpf, the expression patterns of rps26 and GFP at the late stages display similarity, and also represent differences, which suggested that the expression of rps26 and GFP may be controlled by the same enhancer, and also by the different enhancer, and two potential enhancers (CNS1 and CNS2) may play a differential regulation roles on the spatial and temporal expression of nearby genes (including rps26). In this study, we successfully obtained two potential enhancers near rps26 gene for the first time, which laid a foundation for further study of the regulation mechanism between these two enhancers and nearby genes in the genome, and the combination technique used in this study also provides a reference for enhancer analysis.