Dataset Information

Comparison of gene expression and genome-wide DNA methylation profiling between phenotypically normal cloned pigs and conventionally bred controls.

ABSTRACT: Animal breeding via Somatic Cell Nuclear Transfer (SCNT) has enormous potential in agriculture and biomedicine. However, concerns about whether SCNT animals are as healthy or epigenetically normal as conventionally bred ones are raised as the efficiency of cloning by SCNT is much lower than natural breeding or In-vitro fertilization (IVF). Thus, we have conducted a genome-wide gene expression and DNA methylation profiling between phenotypically normal cloned pigs and control pigs in two tissues (muscle and liver), using Affymetrix Porcine expression array as well as modified methylation-specific digital karyotyping (MMSDK) and Solexa sequencing technology. Typical tissue-specific differences with respect to both gene expression and DNA methylation were observed in muscle and liver from cloned as well as control pigs. Gene expression profiles were highly similar between cloned pigs and controls, though a small set of genes showed altered expression. Cloned pigs presented a more different pattern of DNA methylation in unique sequences in both tissues. Especially a small set of genomic sites had different DNA methylation status with a trend towards slightly increased methylation levels in cloned pigs. Molecular network analysis of the genes that contained such differential methylation loci revealed a significant network related to tissue development. In conclusion, our study showed that phenotypically normal cloned pigs were highly similar with normal breeding pigs in their gene expression, but moderate alteration in DNA methylation aspects still exists, especially in certain unique genomic regions.

SUBMITTER: Gao F

PROVIDER: S-EPMC3191147 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Comparison of gene expression and genome-wide DNA methylation profiling between phenotypically normal cloned pigs and conventionally bred controls.

Gao Fei F Luo Yonglun Y Li Shengting S Li Jian J Lin Lin L Nielsen Anders Lade AL Sørensen Charlotte Brandt CB Vajta Gábor G Wang Jun J Wang Jun J Zhang Xiuqing X Du Yutao Y Yang Huanming H Bolund Lars L

PloS one 20111011 10

Animal breeding via Somatic Cell Nuclear Transfer (SCNT) has enormous potential in agriculture and biomedicine. However, concerns about whether SCNT animals are as healthy or epigenetically normal as conventionally bred ones are raised as the efficiency of cloning by SCNT is much lower than natural breeding or In-vitro fertilization (IVF). Thus, we have conducted a genome-wide gene expression and DNA methylation profiling between phenotypically normal cloned pigs and control pigs in two tissues ...[more]

PMID: 22022462

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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).

Dataset Information

Comparison of gene expression and genome-wide DNA methylation profiling between phenotypically normal cloned pigs and conventionally bred controls.

Publications

Comparison of gene expression and genome-wide DNA methylation profiling between phenotypically normal cloned pigs and conventionally bred controls.

Similar Datasets

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