Dysregulation of Genome-Wide DNA Methylation and Gene Expression in Abnormally Cloned Piglets

INTRODUCTION

Somatic cell nuclear transfer (SCNT) has considerable applications in agriculture and regenerative medicine. Until recently, the low efficiency of this technology has limited its further application. Studies have demonstrated that abnormal phenotypes in cloned animals are caused mainly by epigenetic modifications especially the DNA methylation.

MATERIALS AND METHODS

The biceps femoris muscle from three normal cloned piglets and three abnormal cloned piglets and three conventionally bred piglets were collected methylation sequencing and gene profiling sequencing using MeDIP-seq and RNA-seq. All piglets were newborn and slaughtered, and the three abnormal cloned piglets have some abnormal phenotype symptoms such as macroglossia, can’t stand walk and light weight, which is similar to that of the BWS patients.

RESULTS

The abnormally cloned piglets (ACPS) suffered demethylation in the entire genome. The number of differentially methylated regions (DMRs) between normal cloned piglets (NCPS) and conventionally bred piglets (CBPS) was higher than that from the comparison of ACPS and NCPS. RNA-seq data revealed that ACPS had 1,711 differentially expressed genes (DEGs) compared with normal cloned piglets. A total of 244 genes showed altered expression between NCPS and CBPS. Combined analyses of differentially methylated genes (DMGs) and DEGs revealed that only 243 genes showed changes in methylation and gene expression. Among these genes, gene expression as well as the DNA methylation of the imprinted gene PLAGL1 was altered. Pathway analysis revealed the MAPK signaling pathway was the most prominent altered pathway.

DISCUSSION AND CONCLUSION

1.The abnormally cloned piglets (ACPS) suffered demethylation in the entire genome. 2.DNA methylation was altered enormously between normal cloned piglets and conventionally bred piglets, but their gene expression level was similar. 3. Cloned abnormal large-tongue piglets revealed altered expression of several genes, and these DEGs were not only regulated by modification of DNA methylation, but also by other factors involved in this process.

KEY WORDS：SCNT; piglets; DNA methylation; gene expression, whole genome profiling

ACKNOWLEDGMENT

The work was supported by the National Natural Science Foundation of China (31072010), the National Basic Research Program of China (973 Program, 2013CB835205)。

Changchun Li: Corresponding author, email: lichangchun@mail.hzau.edu.cn