Genome-Wide Epigenetic Landscape of Pig lincRNAs and their Evolution During Porcine Domestication

Abstract

Aim: We aimed to identify previously unreported long intergenic noncoding RNAs (lincRNAs) in the porcine liver, an important metabolic tissue, and further illustrate the epigenomic landscapes and the evolution of lincRNAs. Materials & methods: We used porcine omics data and comprehensively analyzed and identified lincRNAs and their methylation, expression and evolutionary patterns during pig domestication. Results: LincRNAs exhibit highly methylated promoter and downstream regions, as well as lower expression levels and higher tissue specificity than protein-coding genes. We identified a batch of lincRNAs with selection signals that are associated with pig domestication, which are more highly expressed in the liver than in other tissues (19:10/8/6/3/2/1/1). Interestingly, the lincRNA linc-sscg1779 and its target gene C6, which is crucial in liver metabolism, are differentially expressed during pig domestication. Conclusion: Although they may originate from noisy transcripts, lincRNAs may be subjected to artificial selection. This phenomenon implies the functional importance of lincRNAs in pig domestication.

Keywords::

• coding gene
• domestication
• evolution
• expression
• lincRNAs
• liver
• methylation
• pig
• selection signal
• wild

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2217/epi-2017-0117

Author contributions

C Li and H Xiang conceived and designed the experiments, explained the data and revised the manuscript. J Li provided assistant in resequencing data download. W Wang, C Zou, Y Cui, Y Fu, C Fang and Y Li provided in writing paper. C Zou provided assistant in lincRNAs identification. C Li analyzed main content of the data and wrote the paper. H Xiang and C Li revised the manuscript.

Acknowledgements

Authors specially thank all of the contributors of the BS-seq data, resequencing data and RNA-seq data.

Financial & competing interests disclosure

The work was supported by a 973 program (2013CB835205), the Research Project of Chinese Ministry of Education (113048A), National Natural Science Foundation of China (NSFC, 31472076) and the Science Fund for Distinguished Young Scholars of Hubei Province of China (2014CFA024). The authors have no other relevant affiliations or financialinvolvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Additional information

Funding

The work was supported by a 973 program (2013CB835205), the Research Project of Chinese Ministry of Education (113048A), National Natural Science Foundation of China (NSFC, 31472076) and the Science Fund for Distinguished Young Scholars of Hubei Province of China (2014CFA024). The authors have no other relevant affiliations or financialinvolvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.