Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing

Abstract

BackgroundDeep RNA sequencing (RNAseq) has opened a new horizon for understanding global gene expression. The functional annotation of non-model mammalian genomes including bovines is still poor compared to that of human and mouse. This particularly applies to tissues without direct significance for milk and meat production, like skin, in spite of its multifunctional relevance for the individual. Thus, applying an RNAseq approach, we performed a whole transcriptome analysis of pigmented and nonpigmented bovine skin to describe the comprehensive transcript catalogue of this tissue.ResultsA total of 39,577 unique primary skin transcripts were mapped to the bovine reference genome assembly. The majority of the transcripts were mapped to known transcriptional units (65%). In addition to the reannotation of known genes, a substantial number (10,884) of unknown transcripts (UTs) were discovered, which had not previously been annotated. The classification of UTs was based on the prediction of their coding potential and comparative sequence analysis, subsequently followed by meticulous manual curation. The classification analysis and experimental validation of selected UTs confirmed that RNAseq data can be used to amend the annotation of known genes by providing evidence for additional exons, untranslated regions or splice variants, by approving genes predicted in silico and by identifying novel bovine loci. A large group of UTs (4,848) was predicted to potentially represent long noncoding RNA (lncRNA). Predominantly, potential lncRNAs mapped in intergenic chromosome regions (4,365) and therefore, were classified as potential intergenic lncRNA. Our analysis revealed that only about 6% of all UTs displayed interspecies conservation and discovered a variety of unknown transcripts without interspecies homology but specific expression in bovine skin.ConclusionsThe results of our study demonstrate a complex transcript pattern for bovine skin and suggest a possible functional relevance of novel transcripts, including lncRNA, in the modulation of pigmentation processes. The results also indicate that the comprehensive identification and annotation of unknown transcripts from whole transcriptome analysis using RNAseq data remains a tremendous future challenge.

Long Noncoding RNA Lnc-SEMT Modulates IGF2 Expression by Sponging miR-125b to Promote Sheep Muscle Development and Growth

“…The central role of miRNAs in skeletal muscle development has been demonstrated by the detrimental consequences of Dicer deletion in embryonic skeletal muscle [42][43][44]. RNA-Seq technology has allowed the discovery and analysis of noncoding RNAs, and differential methods have been developed to identify novel lncRNAs in RNA-Seq data [45,46]. Although many studies have highlighted the important roles of lncRNAs indifferent tissues [47,48], little is known about the biological function and significance of lncRNAsduring skeletal muscle development in sheep.…”

Non-Coding RNA Roles in Ruminant Mammary Gland Development and Lactation

“…A limited number of studies have examined the occurrence and potential functions of lncRNAs in ruminant livestock species [130][131][132]. A pioneer study screened reconstructed transcript assemblies of bovine-specific expressed sequence tags and identified 449 putative lncRNAs located in 405 intergenic regions [130].…”

“…A pioneer study screened reconstructed transcript assemblies of bovine-specific expressed sequence tags and identified 449 putative lncRNAs located in 405 intergenic regions [130]. Following this initial study, Weikard et al [131] used RNA sequencing technique and identified 4848 potential lncRNAs, which were predominantly intergenic (4365) in bovine skin. In another study, Billerey et al [132] characterized 584 lncRNAs in bovine muscle in addition to significant correlated expression between 2083 pairs of lncRNA/protein encoding genes.…”

Long non-coding RNAs and hepatocellular carcinoma

“…There are currently five broad categories of lncRNAs, namely ⅰ) sense or ⅱ) antisense, when overlapping one or more exons of another transcript on the same or opposite Long non-coding RNAs and hepatocellular carcinoma (Review) FU-JUN YU 1 , JIAN-JIAN ZHENG 2 , PEI-HONG DONG 3 and XIAO-MING FAN strand, respectively; ⅲ) bidirectional, when the expression of lncRNA and a neighboring coding transcript on the opposite strand is initiated in close genomic proximity; ⅳ) intronic, when the lncRNA is derived from an intron of a splicing transcript; and ⅴ) intergenic, when it lies in the genomic interval between two genes (21,22). To facilitate the search for lncRNAs, the currently available online databases including ncRNAs are listed in Table I.…”