Transcriptome Analysis Reveals the Potential Role of Long Non-coding RNAs in Mammary Gland of Yak During Lactation and Dry Period

Abstract

The mammary gland is a remarkably dynamic organ of milk synthesis and secretion, and it experiences drastic structural and metabolic changes during the transition from dry periods to lactation, which involves the expression and regulation of numerous genes and regulatory factors. Long non-coding RNA (lncRNA) has considered as a novel type of regulatory factors involved in a variety of biological processes. However, their role in the lactation cycle of yak is still poorly understood. To reveal the involved mechanism, Ribo-zero RNA sequencing was employed to profile the lncRNA transcriptome in mammary tissue samples from yak at two physiological stages, namely lactation (LP) and dry period (DP). Notably, 1,599 lncRNA transcripts were identified through four rigorous steps and filtered through protein-coding ability. A total of 59 lncRNAs showed significantly different expression between two stages. Accordingly, the results of qRT-PCR were consistent with that of the transcriptome data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that target genes of differentially expressed lncRNAs (DELs) were involved in pathways related to lactation, such as ECM-receptor interaction, PI3K-Akt signaling pathway, biosynthesis of amino acids and focal adhesion etc. Finally, we constructed a lncRNA-gene regulatory network containing some well known candidate genes for milk yield and quality traits. This is the first study to demonstrate a global profile of lncRNA expression in the mammary gland of yak. These results contribute to a valuable resource for future genetic and molecular studies on improving milk yield and quality, and help us to gain a better understanding of the molecular mechanisms underlying lactogenesis and mammary gland development of yak.

Characterization of RNA Editome in the Mammary Gland of Yaks during the Lactation and Dry Periods

“…For identifying RNA editing profiles in the yak mammary gland at the LP and DP, we retrieved five paired-end RNA-seq datasets from our prior work [ 21 ]. Total RNA was extracted using TRIzol reagent (Invitrogen, Waltham, MA, USA) according to the manufacturer’s protocol.…”

“…The mammary gland is an endocrine organ related to milk production and delivery, and its function and physiology are substantially altered in pregnancy [ 18 ]. Next-generation sequencing (NGS) technique has enabled the identification of genes and noncoding RNAs related to lactogenesis, which provides new opportunities to discover the hidden mechanisms of milk synthesis and mammary gland development in yaks [ 19 , 20 , 21 ]. There is, however, no available information on how RNA editing sites affect the lactation regulation and mammary gland development of yaks.…”

Transcriptome and proteome analysis of pregnancy and postpartum anoestrus ovaries in yak

“…The gene expression levels were calculated using the fragments per kilobase of exon per million fragments mapped (FPKM) method with Cufflinks software [ 18 ]. Differentially expressed genes (DEGs) between postpartum anestrus and pregnancy ovaries were identified using DESeq [ 18 ]. The differences in gene abundance between samples were calculated based on the ratio of FPKM values.…”

Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

“…RNA-seq was carried out following standard Illumina protocols as previous reported [ 60 ]. A total of 3 µg RNA per sample was used as input material for RNA sample preparation.…”

“…Data analysis was conducted by the Novogene Gene Regulation Department (Beijing, China) as previous reported [ 60 ]. Raw read data in FASTQ format were processed using custom Perl scripts.…”