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- Title
Discovery of long non-coding RNAs in the liver fluke, Fasciola hepatica.
- Authors
McVeigh, Paul; McCammick, Erin; Robb, Emily; Brophy, Peter; Morphew, Russell M.; Marks, Nikki J.; Maule, Aaron G.
- Abstract
Long non-coding (lnc)RNAs are a class of eukaryotic RNA that do not code for protein and are linked with transcriptional regulation, amongst a myriad of other functions. Using a custom in silico pipeline we have identified 6,436 putative lncRNA transcripts in the liver fluke parasite, Fasciola hepatica, none of which are conserved with those previously described from Schistosoma mansoni. F. hepatica lncRNAs were distinct from F. hepatica mRNAs in transcript length, coding probability, exon/intron composition, expression patterns, and genome distribution. RNA-Seq and digital droplet PCR measurements demonstrated developmentally regulated expression of lncRNAs between intra-mammalian life stages; a similar proportion of lncRNAs (14.2%) and mRNAs (12.8%) were differentially expressed (p<0.001), supporting a functional role for lncRNAs in F. hepatica life stages. While most lncRNAs (81%) were intergenic, we identified some that overlapped protein coding loci in antisense (13%) or intronic (6%) configurations. We found no unequivocal evidence for correlated developmental expression within positionally correlated lncRNA:mRNA pairs, but global co-expression analysis identified five lncRNA that were inversely co-regulated with 89 mRNAs, including a large number of functionally essential proteases. The presence of micro (mi)RNA binding sites in 3135 lncRNAs indicates the potential for miRNA-based post-transcriptional regulation of lncRNA, and/or their function as competing endogenous (ce)RNAs. The same annotation pipeline identified 24,141 putative lncRNAs in F. gigantica. This first description of lncRNAs in F. hepatica provides an avenue to future functional and comparative genomics studies that will provide a new perspective on a poorly understood aspect of parasite biology. Author summary: With increased understanding of genomes and transcriptomes it has become clear that not all RNAs code for protein, in contrast to the Central Dogma of molecular biology. Nevertheless, many such "non-coding" RNAs have functions in their own right. For example, long non-coding (lnc)RNAs comprise a large proportion of the human genome and control expression of some human protein coding genes. In parasites, lncRNAs remain understudied and poorly understood. This paper provides the first description of the lncRNA complement of the liver fluke, Fasciola hepatica. We show that lncRNA expression changes as parasites develop, in a similar manner to protein-coding mRNA, suggesting important roles in parasite growth and development. Some lncRNAs show correlated developmental expression with mRNAs coding for important parasite proteins, suggesting that they may interact, suggesting regulatory functions for fluke lncRNAs. A larger subset of lncRNA may interact with micro (mi)RNAs, another type of non-coding RNA that are important regulators of gene expression in eukaryotes. These interactions are, again, important additions to our understanding of fluke lncRNA biology. Our ultimate goal is to discover ways to inhibit these interactions that could be used for new medicines for fluke infections which are a global scourge on the farming industry.
- Subjects
LINCRNA; FASCIOLA hepatica; LIVER flukes; GENE expression; MOLECULAR biology
- Publication
PLoS Neglected Tropical Diseases, 2023, Vol 17, Issue 9, p1
- ISSN
1935-2727
- Publication type
Article
- DOI
10.1371/journal.pntd.0011663