Abstract
Recently, numerous studies including various tissues have been carried out on long non-coding RNAs (lncRNAs), but still, its variability has not yet been fully understood. In this study, we characterised the inter-individual variability of lncRNAs in pigs, in the context of number, length and expression. Transcriptomes collected from muscle tissue belonging to six Polish Landrace boars (PL1–PL6), including half-brothers (PL1–PL3), were investigated using bioinformatics (lncRNA identification and functional analysis) and statistical (lncRNA variability) methods. The number of lncRNA ranged from 1289 to 3500 per animal, and the total number of common lncRNAs among all boars was 232. The number, length and expression of lncRNAs significantly varied between individuals, and no consistent pattern has been found between pairs of half-brothers. In detail, PL5 exhibits lower expression than the others, while PL4 has significantly higher expression than PL2–PL3 and PL5–PL6. Noteworthy, comparing the inter-individual variability of lncRNA and mRNA expression, they exhibited concordant patterns. The enrichment analysis for common lncRNA target genes determined a variety of biological processes that play fundamental roles in cell biology, and they were mostly related to whole-body homeostasis maintenance, energy and protein synthesis as well as dynamics of multiple nucleoprotein complexes. The high variability of lncRNA landscape in the porcine genome has been revealed in this study. The inter-individual differences have been found in the context of three aspects: the number, length and expression of lncRNAs, which contribute to a better understanding of its complex nature.
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Transcriptomic data were deposited in the NCBI Sequence Read Archive with BioProject Number PRJNA804745.
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Acknowledgements
The computational power was provided by Poznan Supercomputing and Networking Centre. Muscle samples of Polish Landrace boars were kindly provided by slaughterhouse RTA SZWAGRZAK in Zloczew, Poland.
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The work was funded by the Wroclaw University of Environmental and Life Sciences (Poland) as the PhD research program “Innowacyjny Naukowiec, no. N060/0035/20”.
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MM provided the concept and funding for the study. BH and MM implemented the bioinformatic pipeline as well as wrote the draft of the manuscript. JS contributed to the concept of the study and improved the manuscript. The ideas standing behind statistical analyses were provided and performed by MF. All authors read and approved the final manuscript version.
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Supplementary information
Supplementary file 1
The bioinformatic pipeline applied to detect lncRNA in transcriptomic data. (PDF 111 kb)
Supplementary file 2
The statistical analysis description of the inter-individual variability in the context of the number, length, and expression level of lnc- and mRNAs. (PDF 156 kb)
Supplementary file 3
The IDs of lncRNAs from the RNA Central database overlapping with lncRNA with logFC≥2 identified in this study. (XLSX 11 kb)
Supplementary file 4
(a) The total number of mRNA per boar (PL1-PL6). The highest number of mRNA was determined for the PL4 individual (7,679), while the lowest for PL1 (10,053). (b) Boxplots represent the mRNA length (bp) per individual (PL1-PL6). The average lncRNA length is marked with a cross. (PDF 209 kb)
Supplementary file 5
The results of the pairwise comparison of mRNA expression using Wilcoxon test with Bonferroni correction. P-values < 0.05 are marked in grey. (DOCX 25 kb)
Supplementary file 6
The list of over-/under-represented Gene Ontology processes for lncRNA target genes based on (a) co-expression and (b) co-localisation. (XLSX 13 kb)
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Hofman, B., Szyda, J., Frąszczak, M. et al. Long non-coding RNA variability in porcine skeletal muscle. J Appl Genetics (2024). https://doi.org/10.1007/s13353-024-00860-5
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DOI: https://doi.org/10.1007/s13353-024-00860-5