title: Dysregulation of genome-wide gene expression and DNA methylation in abnormal cloned piglets.
abstract: BACKGROUND
  Epigenetic 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.
  
  
  RESULTS
  Analysis 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.
  
  
  CONCLUSIONS
  The 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.
authors.forename: Guanglei
authors.initials: G
authors.lastname: Li
authors.forename: Qitao
authors.initials: Q
authors.lastname: Jia
authors.forename: Jianguo
authors.initials: J
authors.lastname: Zhao
authors.forename: Xinyun
authors.initials: X
authors.lastname: Li
authors.forename: Mei
authors.initials: M
authors.lastname: Yu
authors.forename: Melissa S
authors.initials: MS
authors.lastname: Samuel
authors.forename: Shuhong
authors.initials: S
authors.lastname: Zhao
authors.forename: Randall S
authors.initials: RS
authors.lastname: Prather
authors.affiliation: Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China. lichangchun@mail.hzau.edu.cn.
authors.forename: Changchun
authors.initials: C
authors.lastname: Li
mesh_terms: D000818:Animals; D019976:Cloning, Organism; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D063990:Gene Ontology; D023281:Genomics; D010641:Phenotype; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D013552:Swine / Q000033:anatomy & histology / Q000235:genetics*; D059467:Transcriptome