Project description:Somatic cell nuclear transfer has brought considerable chances to breed excellent breeds and protect endanger animals, while also produced numerous fail embryos and abnormal individuals due to inefficient epigenetic modification at the same time. To understand some mechanisms of abnormal piglets with phenotypes such as macroglossia, standing and walking disabilities in our study and find some differences between abnormal piglets and conventionally bred normal piglets, DNA methylation profile and genome-wide gene expression were conducted in two groups, using methylated DNA immunoprecipitation binding highthroughput sequencing (MeDIP-Seq) and RNA sequencing(RNA-Seq). We generated and provided a genome-wide DNA methylation and gene expression profile for abnormal cloned and conventionally bred piglets. We detected a total of 1493 genes differentially expressed in two groups and 382 of these genes also differentially methylated in two groups. Analysis of relationship between DNA methylation and gene expression revealed that DNA methylation levels had significantly negative and monotonic correlation with gene expression levels in particular regions of genes while no obvious monotonic correlation in other regions. Besides, we found some interesting genes and pathways such as MYH7 and mTOR signalling pathway that may played essential role in muscle growth and development. Briefly, these results provide reliable data for future epigenetic studies and may help to uncover the mechanism of failure clones via SCNT. We dissected the leg muscle from the cloned piglets and the conventionally bred piglets, and analyzed the difference of MeDIP-seq and RNA-seq between the two groups. As for data of abnormal cloned piglets, we downloaded it from GEO under Super-Series accession No. GSE51477, including SubSeries accession No.GSE51282 for RNA-seq data (No. GSM1241829 for abnormal cloned group) and SubSeries accession No. GSE51476 for MeDIP-seq data (No. GSM1246252 for abnormal cloned group).

Project description:Backgroud:Epigenetic modifications (especially altered DNA methylation) resulting in altered gene expression may be one reason for development failure or the abnormality of the cloned animals, but the underlying mechanism of the abnormal phenotype in the cloned piglets remains unrevealed. Some cloned piglets in our study showed abnormal phenotypes such as big tongue (longer and thicker), limp, and exomphalos, which is similar to the human BWS syndrome. Here we conducted DNA methylation (DNAm) immunoprecipitation binding high throughput sequencing (MeDIP-seq) and RNA sequencing (RNA-seq) of muscle tissues of cloned piglets to investigate the relationship of abnormal DNAm with gene dysregulation and the unusual phenotypes in cloned piglets. Results:Analysis of the methylomes revealed that abnormal cloned piglets suffered more hypomethylated differentially methylated regions (DMRs) than hypermethylated DMRs compared to the normal cloned piglets. The DNAm level in the CpG Island was higher in the abnormal cloned piglets. Some repetitive elements, such as SINE/tRNA-Glu Satellite/centr also showed significant differences. Besides we detected 1,711 differentially expressed genes (DEGs) between the two groups, of which 243 genes also changed methylation level in the abnormal cloned piglets. The altered DNA methylation mainly affected the low and silent expression genes. We also found some interesting pathways and genes, such as MAPK signalling pathway, hypertrophic cardiomyopathy pathway, TPM3 gene and the imprinted gene PLAGL1, which may played important roles in the abnormal phenotype development. Conclusions;The abnormal cloned piglets showed substantial change both in the DNAm and the gene expression levels. Our data may provide new insights into understanding the molecular mechanisms of the reprogramming of genetic information in cloned animals. We dissected the biceps femoris muscle from the abnormal cloned piglets and the normal cloned piglets, and analyzed the difference of MeDIP-seq and RNA-seq between the two groups.

Project description:Emerging knowledge shows the importance of early life events in programming the intestinal mucosal immune system and development of the intestinal barrier function. These processes depend heavily on close interactions between gut microbiota and host cells in the intestinal mucosa. In turn, development of the intestinal microbiota is largely dependent on available nutrients and substrates required for the specific microbial community structures to expand. It is currently not known what the specificities are of intestinal microbial community structures in relation to the programming of the intestinal mucosal immune system and development of the intestinal barrier function. The objective of the present study was to investigate the effect of a nutritional intervention on intestinal development of suckling piglets by daily oral administration of fructooligosaccharides (FOS) over a period of 12 days. At the microbiota community level a clear “bifidogenic” effect of the FOS administration was observed in colon digesta at day 14. The former, however, did not translate into significant changes of local gene expression in the colonic mucosa. In the jejunum, significant changes were observed for microbiota composition at day 14, and microbiota diversity at day 25. In addition, significant differentially expressed gene sets in mucosal tissues of jejunum were identified at both days 14 and 25 of age. At the age of 14 days, lower activity of cell cycle-related processes and a higher activity of extracellular matrix processes were observed in jejunal scrapings of piglets supplemented with FOS compared to control piglets. At day 25, lower activity of immune-related processes in jejunal tissue were seen in piglets supplemented with FOS. Histological parameters, villi height and crypt depth, were significantly different at day 25 between the experimental and control group, where piglets supplemented with FOS had higher villi and deeper crypts. We conclude that oral FOS administration during the suckling period of piglets has significant bifidogenic effects on the microbiota in the colon and on gene expression in jejunal mucosa scrapings. We hypothesize that FOS supplementation of suckling piglets results in a higher butyrate production in the colon due to the increase in bifidobacteria and lactobacilli in the hindgut. We further speculate that a higher butyrate production in colonic digesta relates to changes in gene expression in the jejunum by thus far unknown mechanisms.

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