LncRNAs in domesticated animals: from dog to livestock species

Abstract

Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.

RNA sequencing reveals the emerging role of bronchoalveolar lavage fluid exosome lncRNAs in acute lung injury

“…Also, miRNAs and lncRNAs in BALF exosomes possess different properties according to different underlying diseases ( Lin & Yang, 2018 ; Zhao et al, 2019 ). Long noncoding RNAs in different organisms and tissues are different ( Lagarrigue et al, 2021 ). Human and animal lncRNA annotations are also different.…”

Epigenetics at the interface between environment and DNA: what importance for breeding practices and selection methods?

“…Ces ARN de diverses natures sont des transcrits de l'ADN qui ne sont pas traduits en protéines. Ils sont de tailles variées, allant de quelques dizaines de nucléotides (appelés alors "petits ARN") jusqu'à plusieurs centaines à milliers de bases (appelés alors "ARN longs non codant"), ces derniers étant codés par des gènes aussi nombreux que les gènes codant des protéines (Lagarrigue et al, 2021). Leurs fonctions sont diverses au sein du noyau, telles que la régulation de la conformation de l'ADN, la dégradation de transcrits ou l'interférence avec la machinerie permettant l'expression des gènes.…”

Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep

“…The lncRNA catalogues of livestock species remain under-annotated compared to the mouse or human annotations ( Kosinska-Selbi et al, 2020 ; Lagarrigue et al, 2021 ). Publicly available gene annotations contain more than ten thousand mouse and human lncRNA genes, while the sheep annotation contains 2,229 lncRNA genes in Ensembl v.105 and 4,442 lncRNA genes in NCBI Release 104.…”

“…Publicly available gene annotations contain more than ten thousand mouse and human lncRNA genes, while the sheep annotation contains 2,229 lncRNA genes in Ensembl v.105 and 4,442 lncRNA genes in NCBI Release 104. There is limited genomic overlap between both sources, most likely reflecting the highly specific expression of lncRNAs and the incompleteness of the current annotations ( Lagarrigue et al, 2021 ). The annotation and functional characterisation of livestock lncRNAs is essential, since most trait-associated variants in livestock lie within non-coding genome regions ( Weikard et al, 2017 ).…”

“…The exponential increase in RNA sequencing datasets in the last years offers a valuable opportunity for posing novel scientific questions or improving the statistical significance of the analyses in a cost-efficient manner ( Sielemann et al, 2020 ). This is specially suitable for the profiling of lncRNAs, due to their highly specific expression ( Lagarrigue et al, 2021 ) and for the profiling of the gene expression signatures of immune responses ( Sparks et al, 2016 ). There is a great interest in gene expression meta-analysis methods ( Sweeney et al, 2017 ; Toro-Domínguez et al, 2021 ), which have been successfully applied to profile the transcriptional signatures across respiratory viruses ( Andres-Terre et al, 2015 ) or vaccines ( Li et al, 2014 ) in human blood samples.…”