Characterisation and functional predictions of canine long non-coding RNAs

Abstract

Long non-coding RNAs (lncRNAs) are a family of heterogeneous RNAs that play major roles in multiple biological processes. We recently identified an extended repertoire of more than 10,000 lncRNAs of the domestic dog however, predicting their biological functionality remains challenging. In this study, we have characterised the expression profiles of 10,444 canine lncRNAs in 26 distinct tissue types, representing various anatomical systems. We showed that lncRNA expressions are mainly clustered by tissue type and we highlighted that 44% of canine lncRNAs are expressed in a tissue-specific manner. We further demonstrated that tissue-specificity correlates with specific families of canine transposable elements. In addition, we identified more than 900 conserved dog-human lncRNAs for which we show their overall reproducible expression patterns between dog and human through comparative transcriptomics. Finally, co-expression analyses of lncRNA and neighbouring protein-coding genes identified more than 3,400 canine lncRNAs, suggesting that functional roles of these lncRNAs act as regulatory elements. Altogether, this genomic and transcriptomic integrative study of lncRNAs constitutes a major resource to investigate genotype to phenotype relationships and biomedical research in the dog species.

Figure 1

(a) Comparative analysis of log10 transcription (TPM + 1) levels between mRNAs (red) and lncRNAs (blue) genes in 26 canine tissues. (b) Proportions of tissue-specific lncRNAs (blue) and mRNAs (red) amongst expressed genes in each tissue with testis tissue represented in the separated panel (top right). (c) Hierarchical clustering of 26 tissues based on Spearman correlations measured from lncRNA expression data.

Figure 2

(a) Proportion of transposable elements (LINEs, SINEs, LTRs and DNA transposon in green, purple, orange and yellow respectively) with respect to the entire dog genome, lncRNA exons and mRNA exons (from left to right). (b) Canonical correlations between lncRNAs’ expression in the 26 tissues (column) and TE families in exons and promoters (row).

Figure 3

The Circos plot provides the visualisation of dog-human orthologous relationships of lncRNAs and their comparative transcriptomic-based expression patterns. Here, we provide plot for canine chromosome 1 the largest chromosome which allows to summarize the most amount of information. Tracks are described from the outside to the inside. Track1: Labels of canine lncRNAs identified with human orthologues are described at the most outside track of the figure. Track2: Level of expression of canine lncRNAs is shown by the blue histogram. Track3: The tissue in which lncRNA is expressed in dogs. The 11 tissues are adrenal gland, gut-colon, heart, liver, lung, muscle, ovary, pancreas, skin, spleen and testis and are represented with the colour code as shown in the legend. Track4: Expression of the human orthologous lncRNA is represented. 11 lines are reported. When the human orthologue lncRNA is expressed in the same tissue and with the highest of expression, it is represented by a dark red square on the upper line. When an orthologous human lncRNA is expressed in the same tissue, with the second maximum of abundance, it is represented on the second line in lighter red. When an orthologous human lncRNA is not expressed in the same tissue, it is represented by a grey square. Track5: The green layout depicts the canine chromosome, the red layout represents the human chromosomes. Track6: For the innermost part, coloured lines link the dog-human orthologous relationships of lncRNAs. Grey lines represent the orthologous relationships of protein-coding genes.

Figure 4

Bar charts representing the expression of the 3 lncRNAs in 11 matched dog-human tissues. (a) High conservation of expression, (b) intermediate conservation of expression, (c) low conservation of expression.

Figure 5

(a) Correlation plot of the lncRNA:mRNA pair (RLOC_000018074:EGFR) in the 26 tissues. (b) UCSC screenshot representing the genomic localisation of the RLOC_000018074:EGFR pair transcribed in a divergent orientation with the promoter mark (H3K4me3) from published data.