Rxivist logo

Assembly and validation of conserved long non-coding RNAs in the ruminant transcriptome

By SJ Bush, Charity Muriuki, Mary E. B. McCulloch, Iseabail L. Farquhar, Emily L. Clark, DA Hume

Posted 25 Jan 2018
bioRxiv DOI: 10.1101/253997 (published DOI: 10.1186/s12711-018-0391-0)

mRNA-like long non-coding RNAs (lncRNA) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. In many cases, therefore, lncRNA detection by RNA-sequencing (RNA-seq) is compromised by stochastic sampling. To account for this and create a catalogue of ruminant lncRNA, we compared de novo assembled lncRNA derived from large RNA-seq datasets in transcriptional atlas projects for sheep and goats with previous lncRNA assembled in cattle and human. Few lncRNA could be reproducibly assembled from a single dataset, even with deep sequencing of the same tissues from multiple animals. Furthermore, there was little sequence overlap between lncRNA assembled from pooled RNA-seq data. We combined positional conservation (synteny) with cross-species mapping of candidate lncRNA to identify a consensus set of ruminant lncRNA and then used the RNA-seq data to demonstrate detectable and reproducible expression in each species. The majority of lncRNA were encoded by single exons, and expressed at < 1 TPM. In sheep, 20-30% of lncRNA had expression profiles significantly correlated with neighbouring protein-coding genes, suggesting association with enhancers. Alongside substantially expanding the ruminant lncRNA repertoire, the outcomes of our analysis demonstrate that stochastic sampling can be partly overcome by combining RNA-seq datasets from related species. This has practical implications for the future discovery of lncRNA in other species.

Download data

  • Downloaded 570 times
  • Download rankings, all-time:
    • Site-wide: 27,500 out of 92,091
    • In genomics: 2,894 out of 5,810
  • Year to date:
    • Site-wide: 70,059 out of 92,091
  • Since beginning of last month:
    • Site-wide: 67,415 out of 92,091

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News