A catalogue of novel bovine long noncoding RNA across 18 tissues

Abstract

Long non-coding RNA (lncRNA) have been implicated in diverse biological roles including gene regulation and genomic imprinting. Identifying lncRNA in bovine across many differing tissue would contribute to the current repertoire of bovine lncRNA, and help further improve our understanding of the evolutionary importance and constraints of these transcripts. Additionally, it could aid in identifying sites in the genome outside of protein coding genes where mutations could contribute to variation in complex traits. This is particularly important in bovine as genomic predictions are increasingly used in genetic improvement for milk and meat production. Our aim was to identify and annotate novel long non coding RNA transcripts in the bovine genome captured from RNA Sequencing (RNA-Seq) data across 18 tissues, sampled in triplicate from a single cow. To address the main challenge in identifying lncRNA, namely distinguishing lncRNA transcripts from unannotated genes and protein coding genes, a lncRNA identification pipeline with a number of filtering steps was developed. A total of 9,778 transcripts passed the filtering pipeline. The bovine lncRNA catalogue includes MALAT1 and HOTAIR, both of which have been well described in human and mouse genomes. We attempted to validate the lncRNA in libraries from three additional cows. 726 (87.47%) liver and 1,668 (55.27%) blood class 3 lncRNA were validated with stranded liver and blood libraries respectively. Additionally, this study identified a large number of novel unknown transcripts in the bovine genome with high protein coding potential, illustrating a clear need for better annotations of protein coding genes.

Long noncoding RNA repertoire in chicken liver and adipose tissue

“…For example, Wang et al [33] reported 2805 lncRNA transcripts in the pig endometrium (using 12 porcine samples and 85–105 million reads per sample), and Billerey et al [34] reported approximately 1300 lncRNA transcripts in bovine muscle (using nine samples with 15 million to 45 million reads per sample). In contrast, multi-tissue studies reported a larger number of lncRNA transcripts, generally above 10,000, with a wide variation depending on the sequenced tissues and the tools used for the lncRNA detection (9778 lncRNA transcripts reported by Koufariotis et al [16] in 18 bovine tissues (using 1.87 million 120-bp stranded paired-end reads and CPC/CNCI tools for lncRNA prediction [24, 35]), and 20,163 lncRNA transcripts reported by Li et al [36] in 13 maize tissues (using 1.17 million 35- to 110-bp unstranded paired- and single-end reads and the CPC tool for lncRNA prediction [24]).…”

“…Given that approximately 80% of the variants associated with human complex traits map outside of protein-coding exons of which 40% are in intergenic regions [12, 13], identifying the lncRNA repertoire is crucial to better understand the “genotype to phenotype” relationships in livestock [14, 15]. To date, few lncRNA studies have been reported for livestock species, apart from lncRNA studies in bovine [16] and trout [17], and the construction of multi-species databases such as NONCODE [18, 19] and the domestic-animal lncRNA database (ALDB) [20, 21]. Research programs are in progress on several farm species, e.g., in projects conducted within the framework of the Functional Annotation of Animal Genomes initiative [14, 15].…”

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

“…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. Koufariotis et al [133] [136] identified 1336 specific lncRNAs in fetal skin of Youzhou dark goat (dark skin) and Yudong white goat (white skin). Similarly, Chao et al [137] in a study with aim to identify and classify new transcripts in Dorper and small-tail Han sheep muscle transcriptomes predicted with high confidence 1520 transcripts to be lncRNAs.…”

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

“…Particular considerations for lncRNA transcript construction include sample pooling according to species and tissue type. LncRNA expression is known to demonstrate tissue speciicity [66][67][68].…”