Genome-wide identification of tissuespecific long non-coding RNA in three farm animal species

- The goal of the FAANG Consortium (Functional Annotation of Animal Genomes) is to functionally annotate animal genomes, including the annotation of lncRNAs.
- As one of the FAANG pilot projects, lncRNAs were identified across eight tissues in two adult male biological replicates from chickens, cattle, and pigs..
- About half of the identified lncRNAs were not previously reported in the NCBI annotations for these species.
- RNA-seq data has revealed that while less than 5% of the human genome consists of protein coding sequences, most of the genome is tran- scribed [1–3].
- A recent review of lncRNA in livestock species pro- vides a comprehensive overview of the current progress in the field [58].
- Many of the lncRNA studies in livestock were performed using samples from varied developmental.
- however, a larger per- centage of the lncRNAs from pig were previously anno- tated.
- least 50% of the predicted lncRNA.
- Figure 1d shows the distri- bution of the lengths of lncRNAs and mRNAs, which were similar within each species.
- The exonic and in- tronic lncRNAs were then categorized based on whether they were on the same strand (sense) or opposite strand (antisense) of the protein-coding gene (Fig.
- In all three species, about 25% of the lncRNAs that were included in this analysis overlap the genic region, with the other 75% divided evenly between upstream or downstream location relative to the protein-coding gene..
- The Spearman correlation of the expression of the lncRNAs with their nearest genes was used to provide evidence for potential cis- regulatory function.
- LncRNAs expressed from novel loci were in regions of the genome that no annotated transcript originated.
- e Distribution of the number of exons of both lncRNAs and protein-coding genes.
- f Distribution of the number of isoforms of both lncRNAs and protein-coding genes.
- c Percentage of intergenic lncRNAs that are upstream or downstream and on the same strand or opposite strand of the nearest gene.
- A GO term analysis of the genes associated with conserved lncRNAs showed that they have functions fundamental to cell biology (Fig.
- Multiple sequence align- ments performed on each of the groups of lncRNAs (Additional file 21) showed some regions of conserva- tion between the species, although not at the magnitude of what would be expected of orthologous protein-coding genes..
- The quality of the reference genomes and.
- function of these lncRNAs was predicted by examining GO term enrichment of the nearest protein-coding genes..
- One of the main goals of this study was to identify the conservation of lncRNAs across three evolutionarily.
- a Phylogenetic tree of the five animal species used for conservation analysis.
- This will further our understanding of the epigenetic regulation of protein-coding genes by lncRNAs..
- Note that the coding potential scores were not used in the prediction of the lncRNA, but were calculated and provided as a confidence metric.
- where N is the number of tissues and x i is the expression of the lncRNA x in tissue i normalized by the maximum expression value.
- To generate multiple sequence alignments of the lncRNAs in the conserved groups, ClustalW (2.1) was used with default parameters [79]..
- The genomic locations of the exons of all chicken lncRNAs.
- The genomic locations of the exons of all cattle lncRNAs.
- The genomic locations of the exons of all pig lncRNAs.
- The “ TSI Both ” column is the F1 score of the TSI from both replicates.
- This file contains tables from the DAVID analysis tool for each of the eight tissues, showing GO terms enriched by genes associated with tissue-specific lncRNAs in cattle.
- This file contains tables from the DAVID analysis tool for each of the eight tissues, showing GO terms enriched by genes associated with tissue-specific lncRNAs in pigs.
- A multiple sequence alignment file generated by ClustalW is included for each of the 39 groups of lncRNAs associated with orthologous genes across all five species.
- Gel images from a few RT-PCRs to verify a few of the predicted lncRNAs.
- Author Hans Cheng is a member of the editorial board (Associate Editor) of this journal..
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