Retrotransposon insertion polymorphism of the porcine esr gene and its association with production performances of Large White pigs / 生物工程学报

Estrogen receptor (esr) mediates the effects of estrogen on the expression of related genes, thereby regulating the growth and reproduction of mammals. To investigate the effect of retrotransposon insertion polymorphism (RIP) of the porcine esr gene on porcine growth performance, retrotransposon insertion polymorphism of the esr gene were predicted by comparative genomics and bioinformatics, and PCR was used to verify the insertion polymorphisms in different porcine breeds. Finally, the correlation analysis between the genotypes and performance of Large White pigs was conducted. The results showed that four retrotransposon polymorphic sites were identified in the esr1 and esr2 genes, which are esr1-SINE- RIP1 located in intron 2 of the esr1 gene, esr1-LINE-RIP2 and RIP3-esr1- SINE located in intron 5 of the gene, and esr2-LINE-RIP located in intron 1 of the esr2 gene, respectively. Among them, insertion of a 287 bp of SINE into intron 2 of the esr1 gene significantly affected (P<0.05) the live back fat thickness and 100 kg body weight back fat thickness of Large White pigs. Moreover, the live back fat thickness and back fat thickness at 100 kg body weight of homozygous with insertion (SINE+/+) was significantly greater than that of heterozygous with insertion (SINE+/-) and homozygous without insertion (SINE-/-). Therefore, esr1-SINE-RIP1 could be used as a molecular marker to assist the selection of deposition traits in Large White pigs.

Enhancer trapping nearby rps26 gene in zebrafish mediated by the Tol2 transposon and it's annotation / 生物工程学报

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.

Annotation of the mobilomes of nine teleost species / 生物工程学报

In this study, the mobilomes of nine teleost species were annotated by bioinformatics methods. Both of the mobilome size and constitute displayed a significant difference in 9 species of teleost fishes. The species of mobilome content ranking from high to low were zebrafish, medaka, tilapia, coelacanth, platyfish, cod, stickleback, tetradon and fugu. Mobilome content and genome size were positively correlated. The DNA transposons displayed higher diversity and larger variation in teleost (0.50% to 38.37%), was a major determinant of differences in teleost mobilomes, and hAT and Tc/Mariner superfamily were the major DNA transposons in teleost. RNA transposons also exhibited high diversity in teleost, LINE transposons accounted for 0.53% to 5.75% teleost genomic sequences, and 14 superfamilies were detected. L1, L2, RTE and Rex retrotransposons obtained significant amplification. While LTR displayed low amplification in most teleost with less than 2% of genome coverages, except in zebrafish and stickleback, where LTR reachs 5.58% and 2.51% of genome coverages respectively. And 6 LTR superfamilies (Copia, DIRS, ERV, Gypsy, Ngaro and Pao) were detected in the teleost, and Gypsy exhibits obvious amplication among them. While the SINE represents the weakest ampification types in teleost, only within zebrafish and coelacanth, it represents 3.28% and 5.64% of genome coverages, in the other 7 teleost, it occupies less than 1% of genomes, and tRNA, 5S and MIR families of SINE have a certain degree of amplification in some teleosts. This study shows that the teleost display high diversity and large variation of mobilome, there is a strong correlation with the size variations of genomes and mobilome contents in teleost, mobilome is an important factor in determining the teleost genome size.