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

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journal contribution
posted on 06.12.2017, 00:00 by F Gao, Y Luo, Y Du, H Yang, L Bolund, S Li, J Li, L Lin, A Nielsen, C Sorensen, Gabor Vajta
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.

Funding

Other

History

Volume

6

Issue

10

Start Page

1

End Page

13

Number of Pages

13

eISSN

1932-6203

Location

USA

Publisher

Public Library of Science

Language

en-aus

Peer Reviewed

Yes

Open Access

Yes

External Author Affiliations

Aarhus universitet; BGI-Shenzhen; Københavns universitet; Not affiliated to a Research Institute;

Era Eligible

Yes

Journal

PLoS ONE.