DNA methylation signatures of long intergenic noncoding RNAs in porcine adipose and muscle tissues.
Long intergenic noncoding RNAs (lincRNAs) are one of the major unexplored components of genomes. Here we re-analyzed a published methylated DNA immunoprecipitation sequencing (MeDIP-seq) dataset to characterize the DNA methylation pattern of pig lincRNA genes in adipose and muscle tissues. Our study showed that the methylation level of lincRNA genes was higher than that of mRNA genes, with similar trends observed in comparisons of the promoter, exon or intron regions. Different methylation pattern were observed across the transcription start sites (TSS) of lincRNA and protein-coding genes. Furthermore, an overlap was observed between many lincRNA genes and differentially methylated regions (DMRs) identified among different breeds of pigs, which show different fat contents, sexes and anatomic locations of tissues. We identify a lincRNA gene, linc-sscg3623, that displayed differential methylation levels in backfat between Min and Large White pigs at 60 and 120 days of age. We found that a demethylation process occurred between days 150 and 180 in the Min and Large White pigs, which was followed by remethylation between days 180 and 210. These results contribute to our understanding of the domestication of domestic animals and identify lincRNA genes involved in adipogenesis and muscle development.
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.|Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China.
Zhong-Yin
ZY
Zhou
School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.
Aimin
A
Li
Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
Li-Gang
LG
Wang
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.|Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.|Banting and Best Diabetes Centre, University of Toronto, Toronto, Canada.
David M
DM
Irwin
Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China.
Yan-Hu
YH
Liu
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.|Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
Dan
D
Xu
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Xu-Man
XM
Han
Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China.
Lu
L
Wang
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Shi-Fang
SF
Wu
Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
Li-Xian
LX
Wang
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Hai-Bing
HB
Xie
State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.|Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China.|Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China.
Ya-Ping
YP
Zhang
D000273:Adipose Tissue / Q000378:metabolism*; D000818:Animals; D019175:DNA Methylation; D009132:Muscles / Q000378:metabolism*; D062085:RNA, Long Noncoding / Q000235:genetics*; D013552:Swine
D062085:RNA, Long Noncoding