Dysregulation of genome-wide gene expression and DNA methylation in abnormal cloned piglets

Abstract

BackgroundEpigenetic modifications (especially altered DNA methylation) resulting in altered gene expression may be one reason for development failure or abnormalities in cloned animals, but the underlying mechanism of the abnormal phenotype in cloned piglets remains unknown. Some cloned piglets in our study showed abnormal phenotypes such as large tongue (longer and thicker), weak muscles, and exomphalos. Here we conducted DNA methylation (DNAm) immunoprecipitation and 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.ResultsAnalysis of the methylomes revealed that abnormal cloned piglets suffered more hypomethylation than hypermethylation compared to the normal cloned piglets, although 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 differences. 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 silently expressed genes. There were differences in both pathways and genes, such as the MAPK signalling pathway, the hypertrophic cardiomyopathy pathway, and the imprinted gene PLAGL1; all of which may play important roles in development of the abnormal phenotype.ConclusionsThe abnormal cloned piglets showed substantial changes both in the DNAm and the gene expression. Our data may provide new insights into understanding the molecular mechanisms of the reprogramming of genetic information in cloned animals.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-811) contains supplementary material, which is available to authorized users.

Artificial cloning of domestic animals

“…As remarked by other authors, nature allows a certain amount of flexibility in the epigenome and gene expression during growth and development (28). As might be anticipated, clones that fail during gestation and/or have physiological abnormalities have been found to have abnormal epigenetic patterns whereas those that thrive have a comparatively normal pattern (28,36). It is also interesting to note that the gestational losses and abnormalities observed in SCNT were also noted during the development of in vitro embryo production and culture techniques in domestic species in the 1990s.…”

“…Due to the cost and extended generation times for domestic species, most of these studies, so far, have focused on early embryonic and fetal development. As with epigenetic patterns described above, many of these studies report either the normal expression of key genes after a reconstructed embryo passes a developmental checkpoint (e.g., blastocyst formation) or abnormal gene expression after failure to pass such checkpoints (28,36). These experiments focused mainly on how SCNT worked or did not work, and few use SCNT to explore questions regarding developmental regulation of genes.…”

Comparison of skeletal muscle miRNA and mRNA profiles among three pig breeds

“…The raw sequence data were assessed and tags that contained adaptors, were of low quality, or showed more than 10 % unidentified nucleotides, were removed. Only clean reads were used for subsequent analysis, and the unique reads were used for identifying differentially expressed genes with log 2 ratio ≥1 and false discovery rate (FDR) ≤0.001 Li et al 2014). …”

Genome-wide gene expression and DNA methylation differences in abnormally cloned and normally natural mating piglets

“…; Li et al . ). Some studies also identified and functionally/biologically characterised differentially methylated genes (DMGs) or differentially expressed genes (DEGs) that may participate in muscle development of pigs and cattle (Huang et al .…”