Review: Long non-coding RNA in livestock

Abstract

Less than 2% of mammalian genomes code for proteins, but ‘the majority of its bases can be found in primary transcripts’ – a phenomenon termed the pervasive transcription, which was first reported in 2007. Even though most of the transcripts do not code for proteins, they play a variety of biological functions, with regulation of gene expression appearing as the most common one. Those transcripts are divided into two groups based on their length: small non-coding RNAs, which are maximally 200 bp long, and long non-coding RNAs (lncRNAs), which are longer than 200 nucleotides. The advances in next-generation sequencing methods provided a new possibility of investigating the full set of RNA molecules in the cell. In this review, we summarized the current state of knowledge on lncRNAs in three major livestock species – Sus scrofa, Bos taurus and Gallus gallus, based on the literature and the content of biological databases. In the NONCODE database, the largest number of identified lncRNA transcripts is available for pigs, but cattle have the largest number of lncRNA genes. Poultry is represented by less than a half of records. Genomic annotation of lncRNAs showed that the majority of them are assigned to introns (pig, poultry) or intergenic (cattle). The comparison with well-annotated human and mouse genomes indicates that such annotation is a result of lack of proper lncRNA annotation data. Since lncRNAs play an important role in genomic studies, their characterization in farm animals’ genomes is critical in bridging the gap between genotype and phenotype.

Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle

“…The growing number of next-generation sequencing data and the development of computational biology have brought the regulatory role of lncRNA in biological processes to light, which may offer a deeper understanding of the phenotypic variation of complex traits in farm animals [2,52]. In this study, we used transcriptomic data from 18 Nellore bulls, to identify lncRNA expressed in five tissues (hypothalamus, pituitary gland, adrenal gland, muscle and liver) of indicine cattle.…”

Transcriptome Analysis Reveals the Profile of Long Non-coding RNAs During Chicken Muscle Development

“…lncRNA is an important member of the group of ncRNAs and plays a critical role in muscle development through the regulation of transcriptional and post-transcriptional gene expression. Previous studies have identified numerous lncRNAs in livestock (such as pig, cattle, and chicken) and have demonstrated that they play key roles in specific developmental stages for different tissues (such as liver, muscle, and adipose tissue) ( Muret et al, 2017 ; Kern et al, 2018 ; Kosinska-Selbi et al, 2020 ). In recent years, several studies have been performed on lncRNA identification and pathway regulation in chicken skeletal muscle development ( Li et al, 2012 , 2017 ; Ren et al, 2018 ).…”

Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle

“…The growing number of next-generation sequencing data and the development of computational biology have brought the regulatory role of lncRNA in biological processes to light, which may offer a deeper understanding of the phenotypic variation of complex traits in farm animals [2,52]. In this study, we used transcriptomic data from 18 Nellore bulls, to identify lncRNA expressed in five tissues (hypothalamus, pituitary, adrenal gland, muscle and liver) of indicine cattle.…”