Genome-wide association studies in livestock based on high-resolution genotyping and sequencing have revealed that the majority of signals associated with complex phenotypic traits are located outside of annotated protein-coding regions in the genome. The approaches of next-generation sequencing applied to whole transcriptome and chromatin profiles have provided information about existing genome-wide transcriptional activity and have revealed that the genomes are templates for thousands of long noncoding transcripts (lncRNAs). Despite their lack of coding capacity, many lncRNAs have been found to play functional roles in a variety of biological processes, which is adding a novel regulatory network to the complex structural organization and function of the genome. Here, the authors summarize main features of lncRNAs, provide an overview about computational tools and pipelines used for identification of lncRNAs from whole transcriptome datasets and review the current state of knowledge about lncRNAs in livestock species. Although lncRNAs are increasingly emerging as an integral component of the regulatory information encoded in the genome, the complexity of the transcriptomes in domesticated animals is inadequately characterized in comparison to human and mouse. Progress in elucidating whole transcriptomes of livestock species, including identification, functional annotation and characterization of lncRNAs, will be essential for a better understanding of basic biological processes associated with developmental, metabolic and immunological regulation and adaptation and phenotypic variation of complex traits in domesticated animals.
Computational steps and methods for the identification, functional
characterization and annotation of lncRNAs
GWAS, genome-wide association study; RNA-seq, RNA sequencing; ChIPseq, chromatin immunoprecipitation sequencing; ATACseq, assay for transposase-accessible chromatin sequencing; DNAseseq, DNase hypersensitive sites sequencing; MeDIPseq, methylated DNA immunoprecipitation sequencing; RRBSseq, reduced representation bisulfite sequencing; WGBSseq, whole-genome bisulfite sequencing; CLIPseq, cross-linking immunoprecipitation sequencing; RIPseq, RNA immunoprecipitation sequencing; ChIRPseq, chromatin isolation by RNA purification sequencing.