Profiling Long Noncoding RNA of Multi-Tissue TranscriPtome Enhances Porcine Noncoding Genome Annotation

Abstract

Aim: To construct a comprehensive pig noncoding transcriptome and further enhance porcine noncoding genome annotation. Materials & methods: We performed a tissue-based long noncoding RNA (lncRNA) profiling via exploiting 32,212 nonredundant lncRNA isoforms corresponding to 18,676 lncRNA loci across 34 normal pig tissues using high-throughput sequencing. Furthermore, the potential relationship between our identified lncRNAs and known protein-coding genes were globally assessed via a comprehensive computation-based strategy, developing a genome-wide lncRNA-targeted genome draft for further functional studies on noncoding genes. Results & conclusion: Among these lncRNAs, ubiquitously expressed lncRNA appeared at a higher level compared with tissue-specific one. Findings herein provide insight into comprehensive knowledge of porcine noncoding RNAs and further enhance pig noncoding annotation. For ease of accessing the information of the identified lncRNAs, we deposited those with high confidence in the publicly available NONCODE database, providing a valuable resource for facilitating pig noncoding genomic studies.

Graphical abstract

Keywords: :

• lncRNA
• lncRNA function
• NONCODE
• pig

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: https://www.tandfonline.com/doi/suppl/10.2217/epi-2017-0149

Availability of data & materials

The sequenced RNA-seq raw data for 34 pig tissues are available from NCBI Sequence Read Archive with the BioProject number: PRJNA392949.

Author contributions

JF Liu conceived and designed the experiments. P Zhao performed lncRNAs detection and transcriptome analyses. Y Zhao provided NONCODE platform for depositing pig lncRNAs database. W Feng and X Zheng assisted the lncRNA experimental validations. P Zhao, X Zheng, H Wang, H Kang, C Ning and H Du collected samples and prepared for sequencing. JF Liu, P Zhao, X Zheng, W Feng, Y Yu and B Li wrote and revised the paper. All authors declare that they have read and approved the final manuscript.

Acknowledgements

We thank Z Fan, Y Dong and K Yang for sample collection.

Financial & competing interests disclosure

This work was supported by the National High Technology Research and Development Program of China (863 Program, 2013AA102503), the National Natural Science Foundations of China (31661143013) and the Program for Changjiang Scholar and Innovation Research Team in University (IRT1191). The authors have no other relevant affiliations or financial involvement 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.

Ethics approval and consent to participate

The whole sample collection and treatment were conducted in strict accordance with the protocol approved by the Institutional Animal Care and Use Committee (IACUC) of China Agricultural University (permit number: DK1023).

Additional information

Funding

This work was supported by the National High Technology Research and Development Program of China (863 Program, 2013AA102503), the National Natural Science Foundations of China (31661143013) and the Program for Changjiang Scholar and Innovation Research Team in University (IRT1191). The authors have no other relevant affiliations or financial involvement 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.