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.
Highlights
In the past decade, human whole-genome transcriptional study discovered that approximately two-thirds of genomic DNA is pervasively transcribed (Djebali et al, 2012)
Still less than 2% of the mammalian genome translates into the proteins, indicating that a considerable portion of the mammalian genome is transcribed into non-coding RNAs and do not function in LncRNAs Regulate Lactation of Yak protein-coding (Kopp and Mendell, 2018)
In order to identify novel Long non-coding RNA (lncRNA) in mammary gland of yak, five cDNA libraries were sequenced using Illumina Hiseq 2500 platform, and 503.07 and 299.23 million raw paired-end reads were obtained in lactation and dry stages, respectively
Summary
Human whole-genome transcriptional study discovered that approximately two-thirds of genomic DNA is pervasively transcribed (Djebali et al, 2012). Still less than 2% of the mammalian genome translates into the proteins, indicating that a considerable portion of the mammalian genome is transcribed into non-coding RNAs (ncRNAs) and do not function in LncRNAs Regulate Lactation of Yak protein-coding (Kopp and Mendell, 2018). LncRNAs are a heterogeneous group of non-protein-coding transcripts of greater than 200 nucleotides, which expression levels are usually lower than that of protein-coding genes (Hezroni et al, 2015; Ulitsky, 2016). Based on their position in the genome, lncRNAs can be categorized as long intergenic ncRNA (lincRNAs), enhancer RNAs (eRNAs), intronic lncRNAs, anti-sense lncRNAs and promoter-associated short RNAs (pasRNA) (Weikard et al, 2017). The regulatory roles of lncRNAs are gradually being revealed in a diverse spectrum of biological processes such as genomic imprinting (Sleutels et al, 2002), RNA splicing (Gonzalez et al, 2015), chromosome conformation (Rinn and Chang, 2012), epigenetic regulation (Vizoso and Esteller, 2012), transcriptional control (Salmena et al, 2011), and allosterically regulating enzymatic activity (Quinn and Chang, 2016)
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