Abstract
BackgroundLong non-coding RNAs (lncRNAs) are important component of mammalian genomes, where their numbers are even larger than that of protein-coding genes. For example, human (Homo sapiens) (96,308 vs. 20,376) and mouse (Mus musculus) (87,774 vs. 22,630) have more lncRNA genes than protein-coding genes in the NONCODEv5 database. Recently, mammalian lncRNAs were reported to play critical roles in immune response to influenza A virus infections. Such observation inspired us to identify lncRNAs related to immune response to influenza A virus in duck, which is the most important natural host of influenza A viruses.ResultsWe explored features of 62,447 lncRNAs from human, mouse, chicken, zebrafish and elegans, and developed a pipeline to identify lncRNAs using the identified features with transcriptomic data. We then collected 151,970 assembled transcripts from RNA-Seq data of 21 individuals from three tissues and annotated 4094 duck lncRNAs. Comparing to duck protein-coding transcripts, we found that 4094 lncRNAs had smaller number of exons (2.4 vs. 10.2) and longer length of transcripts (1903.0 bp vs. 1686.9 bp) on average. Among them, 3586 (87.6%) lncRNAs located in intergenic regions and 619 lncRNAs showed differential expression in ducks infected by H5N1 virus when compared to control individuals. 58 lncRNAs were involved into two co-expressional modules related to anti-influenza A virus immune response. Moreover, we confirmed that eight lncRNAs showed remarkably differential expression both in vivo (duck individuals) and in vitro (duck embryo fibroblast cells, DEF cells) after infected with H5N1 viruses, implying they might play important roles in response to influenza A virus infection.ConclusionsThis study presented an example to annotate lncRNA in new species based on model species using transcriptome data. These data and analysis provide information for duck lncRNAs’ function in immune response to influenza A virus.
Highlights
Long non-coding RNAs are important component of mammalian genomes, where their numbers are even larger than that of protein-coding genes
Compared to chicken being destroyed by influenza A virus, Lu et al BMC Genomics (2019) 20:36 ducks are tolerant to most subtypes of H5N1 viruses [12]
We found that most Long non-coding RNAs (lncRNAs) transcripts are > 200 nucleotides in length, have more than one exon, and the length of open reading frame (ORF) are < 100 amino acids (AA) (Additional file 1: Figure S1); (2) build a strict platform to identify putative lncRNA transcripts larger than 200 nt and having ORFs shorter than 100 AA according to the features of lncRNA in five model organisms (Fig. 1) [19]; (3) the putative lncRNA is aligned to known protein sequences using
Summary
Long non-coding RNAs (lncRNAs) are important component of mammalian genomes, where their numbers are even larger than that of protein-coding genes. Mammalian lncRNAs were reported to play critical roles in immune response to influenza A virus infections. Such observation inspired us to identify lncRNAs related to immune response to influenza A virus in duck, which is the most important natural host of influenza A viruses. Transcriptome analysis has revealed that 80% of eukaryotic (such as human [1] and mouse [2]) genomes are transcribed, but 1–2% of the genome encodes proteins [3], suggesting that a large number of transcripts were non-coding RNAs (ncRNAs). RIG-I (Retinoic Acid Inducible Gene I), one of the important intracellular viral RNA detector, is absent in chicken but play a critical role in immune response to H5N1 virus infections, partly contributing to the stark difference in influenza pathology between ducks and chickens [13]. LncRNAs were only characterized on few birds (i.e. chicken and zebra finch) [17, 18] and their functions in anti-influenza immune response in birds are not clear
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
