Investigation of lncRNA in Bos taurus mammary tissue during dry and lactation periods

Authors: MARCEAU, ALEXIS - University Of Maryland; WANG, JUNJIAN - North Carolina State University; IQBAL, VICTORIA - University Of Maryland; JIANG, JICAI - North Carolina State University; Liu, Ge - George; MA, LI - University Of Maryland

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/8/2023
Publication Date: 9/12/2023
Citation: Marceau, A., Wang, J., Iqbal, V., Jiang, J., Liu, G., Ma, L. 2023. Investigation of lncRNA in Bos taurus mammary tissue during dry and lactation periods. Genes. 14(9):1789. https://doi.org/10.3390/genes14091789.
DOI: https://doi.org/10.3390/genes14091789

Interpretive Summary: Long non-coding RNAs (lncRNAs) play important roles in controlling gene expression. We identified and compared mammary lncRNAs in dry and lactating cows, revealing their functional roles in mammary tissue development and transition of lactation. These results fill our knowledge gaps and provide the foundation for incorporating new knowledge into the future animal breeding program. Farmers, scientists, and policy planners who need to improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: This study aims to collect publicly available RNA-Seq data from Bos taurus samples representing dry and lactating mammary tissue, identify a list of candidate lncRNA transcripts, and to analyze the lncRNA transcripts regarding their genome features, functional annotation, and enrichment with GWAS signals. Specifically, our analysis consists of expression level data, conservation scores, sequence similarity functional analysis, co-expression gene clustering, and multi-trait GWAS enrichment analysis. Overall, connections between lncRNA and their potential functional roles in the lactation process can be revealed, allowing improvement of cattle genetic information. RNA-Seq data from 103 samples of Bos taurus mammary tissue were gathered from publicly available databases, with 60 samples representing dry mammary tissue and 43 samples representing lactating mammary tissue. The samples were progressively filtered to reveal 214 dry mammary lncRNA candidate transcripts and 517 lactating mammary lncRNA candidate transcripts, of which 53 were determined to be common to both dry and lactating samples. In addition to the uniquely expressed lncRNA between dry and lactating samples, 44 of the 53 common transcripts were differentially expressed. The mammary lncRNA met common lncRNA characteristics such as being shorter, having fewer exons, showing lower expression levels, and exhibiting less sequence conservation across species when compared to gene transcripts identified. lncRNA that demonstrated higher levels of conservation were found to overlap with many gene features of interest, including several transcriptional regulators. Most interestingly, several lncRNA showed sequence similarity to genes associated with strong hair keratin intermediate filaments. In human breast cancer research, strong hair keratin filaments were associated with mammary tissue cellular resilience. Using expression correlation and gene ontology clustering, lncRNA were associated with many traits, notably including several genes/proteins that can be linked to pregnancy. Using large-scale GWAS data to investigate trait enrichment, SNPs overlapping discovered lncRNA showed significant enrichment in milk production and daughter pregnancy rate in both dry and lactating lncRNA. lncRNA are found in Bos taurus mammary tissue in both variable lncRNA profiles and at different expression levels. Many of the transcripts common to both conditions were significantly differentially expressed, indicating lncRNA play a role in the changes in mammary structure and function. Analysis aiming to assign roles to the identified transcripts revealed relationships between lncRNA and transcriptional regulators, expression modifiers, tissue resilience markers, pregnancy symptoms, and much more. These findings indicate there are crucial relationships between the lncRNA found in mammary tissue and the development of the tissue to meet both the animal’s needs and our own production needs; these relationships should be further investigated to ensure we continue to breed the most resilient, efficient dairy cattle.