Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Abstract

Background: The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental periods, the biological processes governing mammary gland physiology and internal environmental homeostasis depend on a complex network of genes and regulatory factors. Emerging evidence indicates that lncRNAs have arbitrarily critical functions in regulating gene expression in many organisms; however, the systematic characteristics, expression, and regulatory roles of lncRNAs in the mammary gland tissues of dairy goats have not been determined. Result: In the present study, we profiled long noncoding RNA (lncRNA) expression in the mammary gland tissues of Laoshan dairy goats (Capra hircus) from different lactation periods at the whole-genome level, to identify, characterize and explore the regulatory functions of lncRNAs. A total of 37,249 transcripts were obtained, of which 2381 lncRNAs and 37,249 mRNAs were identified, 22,488 transcripts, including 800 noncoding transcripts and 21,688 coding transcripts, differed significantly (p ≤ 0.01) among the different lactation stages. The results of lncRNA-RNA interaction analysis showed that six known lncRNAs belonging to four families were identified as the precursors of 67 known microRNAs; 1478 and 573 mRNAs were predicted as hypothetical cis-regulation elements and antisense mRNAs, respectively. GO annotation and KEGG analysis indicated that the coexpressed mRNAs were largely enriched in biological processes related to such activities as metabolism, immune activation, and stress,., and most genes were involved in pathways related to such phenomena as inflammation, cancer, signal transduction, and metabolism. Conclusions: Our results clearly indicated that lncRNAs involved in responses to stimuli, multiorganism processes, development, reproductive processes and growth, are closely related to mammary gland development and lactation.

RNA-Seq Reveals the Expression Profiles of Long Non-Coding RNAs in Lactating Mammary Gland from Two Sheep Breeds with Divergent Milk Phenotype

“…These were less than those reported in mammary gland tissue of dairy goats, with an average of 2381 predicted lncRNAs [18]. This likely reflects species-specific expression patterns, and the species-specific expression has been observed in the mammary gland of dairy cows and dairy goats [16,18]. Most lncRNAs identified in the study were expressed at low levels in the ovine mammary gland.…”

“…In the study, a total of 1770 and 1742 lncRNAs were found in mammary gland of lactating GAM and STH ewes, respectively. These were less than those reported in mammary gland tissue of dairy goats, with an average of 2381 predicted lncRNAs [18]. This likely reflects species-specific expression patterns, and the species-specific expression has been observed in the mammary gland of dairy cows and dairy goats [16,18].…”

“…It has been confirmed that lncRNAs play key roles in the development of mammary gland and lactation in mice [12], dairy cows [13][14][15][16][17], dairy goats [6,18], and sows [19]. For example, lncRNA Neat1 is a basal component of paraspeckle nuclear bodies; its genetic ablation led to abnormal morphogenesis of mammary gland and defects in lactation owing to a decreased ability of sustaining high proliferation rates of duct during lobular-alveolar development in mice [12].…”

“…The functions of these differentially expressed lncRNAs can be achieved by targeting mRNAs. For example, 800 differentially expressed lncRNAs were found in the mammary gland of dairy goats between different lactation stages, and the target genes of these differentially expressed lncRNAs were enriched in multi-organism processes, reproductive processes and growth, and responses to stimuli and development that are closely correlated to the lactation and development of the mammary gland [18]. Yang et al [16] found that target genes of differentially expressed lncRNAs in mammary gland tissues between the lactating and non-lactating Holstein cows, were significantly enriched in cell cycle, Janus kinase/signal transducer and activator of transcription (JAK-STAT), cell adhesion, and phosphatidylinositide 3-kinases protein kinase B (PI3K-Akt), and these signaling pathways were related to lactation.…”

Transcriptional Profiles of Long Non-coding RNA and mRNA in Sheep Mammary Gland During Lactation Period

“…For example, Ma et al (2018) profiled mRNA and lncRNA expression in sheep that differed in the deposition of fat in their tails and identified several DE mRNAs and lncRNAs, suggesting that they may play crucial roles in the deposition of tail fat. Ji et al (2020) characterized the mRNA and lncRNA expression profiles in dairy goats from different lactation periods and found that the expression of lncRNAs was tied to mammary gland development and lactation. However, little comparative research of the lncRNAs and mRNAs in sheep lactation has been conducted.…”