The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages

Next Generation Sequencing (NGS) strategies, like RNA-Seq, have revealed the transcription of a wide variety of long non-coding RNAs (lncRNAs) in the genomes of several organisms. In the present work we assessed the lncRNAs complement of Schistosoma mansoni, the blood fluke that causes schistosomias...

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Published in:Scientific reports 2017-09, Vol.7 (1), p.10508-10508, Article 10508
Main Authors: Vasconcelos, Elton J R, daSilva, Lucas F, Pires, David S, Lavezzo, Guilherme M, Pereira, Adriana S A, Amaral, Murilo S, Verjovski-Almeida, Sergio
Format: Article
Language:English
Subjects:
Animals
Antisense RNA
Computational Biology - methods
Computer applications
Epigenesis, Genetic
Epigenetics
Evolutionary conservation
Gene Expression Profiling
Genome, Fungal
Genomes
Genomics - methods
Isoforms
Life Cycle Stages
Parasites
Parasitic diseases
Pc gene
Ribonucleic acid
RNA
RNA, Helminth
RNA, Long Noncoding
Schistosoma mansoni
Schistosoma mansoni - genetics
Schistosoma mansoni - growth & development
Schistosomiasis
Schistosomiasis mansoni - parasitology
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Summary:Next Generation Sequencing (NGS) strategies, like RNA-Seq, have revealed the transcription of a wide variety of long non-coding RNAs (lncRNAs) in the genomes of several organisms. In the present work we assessed the lncRNAs complement of Schistosoma mansoni, the blood fluke that causes schistosomiasis, ranked among the most prevalent parasitic diseases worldwide. We focused on the long intergenic/intervening ncRNAs (lincRNAs), hidden within the large amount of information obtained through RNA-Seq in S. mansoni (88 libraries). Our computational pipeline identified 7029 canonically-spliced putative lincRNA genes on 2596 genomic loci (at an average 2.7 isoforms per lincRNA locus), as well as 402 spliced lncRNAs that are antisense to protein-coding (PC) genes. Hundreds of lincRNAs showed traits for being functional, such as the presence of epigenetic marks at their transcription start sites, evolutionary conservation among other schistosome species and differential expression across five different life-cycle stages of the parasite. Real-time qPCR has confirmed the differential life-cycle stage expression of a set of selected lincRNAs. We have built PC gene and lincRNA co-expression networks, unraveling key biological processes where lincRNAs might be involved during parasite development. This is the first report of a large-scale identification and structural annotation of lncRNAs in the S. mansoni genome.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-017-10853-6