Non-coding transcriptomic profiles in the sheep mammary gland during different lactation periods

Abstract

Sheep milk production is a dynamic and multifactorial trait regulated by diverse biological mechanisms. To improve the quality and production of sheep milk, it is necessary to understand the underlying non-coding transcriptomic mechanisms. In this study, ribonucleic acid-sequencing (RNA-seq) was used to profile the expression of microRNAs (miRNAs) and circular RNAs (circRNAs) in the sheep mammary gland at three key lactation time points (perinatal period, PP; early lactation, EL; and peak lactation, PL). A total of 2,369 novel circRNAs and 272 miRNAs were profiled, of which 348, 373, and 36 differentially expressed (DE) circRNAs and 30, 34, and 7 DE miRNAs were detected in the comparison of EL vs. PP, PL vs. PP, and PL vs. EL, respectively. A series of bioinformatics analyses including functional enrichment, machine learning prediction, and competing endogenous RNA (ceRNA) network analyses were conducted to identify subsets of the potential candidate miRNAs (e.g., oar_miR_148a, oar_miR_362, and oar_miR_432) and circRNAs (e.g., novel_circ_0011066, novel_circ_0010460, and novel_circ_0006589) involved in sheep mammary gland development. Taken together, this study offers a window into the dynamics of non-coding transcriptomes that occur during sheep lactation and may provide further insights into miRNA and circRNA that influence sheep mammary gland development.

Identification and Characterization of circRNAs in Non-Lactating Dairy Goat Mammary Glands Reveal Their Regulatory Role in Mammary Cell Involution and Remodeling

“…The expression of circRNAs has time-and tissue-specific characteristics. For example, circRNAs are differentially expressed in mammary gland tissues at different developmental stages, which has been confirmed in mammalian mammary gland tissues, such as that from goats [18], sheep [19,20], cattle [21,22], and mice [23], by transcriptome sequencing. In addition, the number of circRNAs in human glandular tissues (adrenal, mammary gland, pancreas, and thyroid), especially in the mammary gland (9665 candidate circRNAs), was higher than that in other adult tissues (colon, heart, kidney, liver, lung, and stomach) [24].…”

Transcriptomic Changes and Regulatory Networks Associated with Resistance to Mastitis in Xinjiang Brown Cattle

“…Liang et al [48] identified 216 ceRNAs, including 26 lncRNAs, 27 miRNAs, and 64 mRNAs, in human mesenchymal stem cell (MSC) adipose differentiation at 0, 3, and 6 d. The mRNAs in the ceRNA network were found to be mainly associated with glucose homeostasis and the response to insulin stimulation, as well as many lipid metabolism-related pathways, such as Ras, hypoxia-inducible factor-1 (HIF-1), PI3K-Akt, and insulin signaling. Chen et al constructed a ceRNA network using RNA-seq data and annotated potential candidate miRNAs and circRNAs involved in udder development in sheep, providing further insights into the influence of miRNAs and circRNAs on udder development in this species [49]. These studies not only identified many key molecular markers but also further demonstrated the integration of data from multiple sources for the construction of a global gene expression network, which could help us to understand the mechanisms underlying the formation of important traits [50].…”

Understanding Circular RNAs in Health, Welfare, and Productive Traits of Cattle, Goats, and Sheep

“…Similarly, Chen et al (2022) [ 61 ] investigated ncRNA profiles in Hu ewes’ mammary glands during different lactation periods (perinatal, 6 days postpartum, and 25 days postpartum) to understand their roles in mammary gland development and lactation. They identified several DE circRNAs: 348 in early lactation vs. perinatal, 373 in peak lactation vs. perinatal, and 36 in peak lactation vs. early lactation.…”