Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel
Alan D Winter
0
William Weir
0
Martin Hunt
2
Matthew Berriman
2
John S Gilleard
1
Eileen Devaney
0
Collette Britton
0
0
Institute of Infection, Immunity and Inflammation; College of Medical, Veterinary and Life Sciences; University of Glasgow
,
Garscube Estate, Bearsden Road, Glasgow, G61 1QH
,
UK
1
Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary
,
Calgary, Alberta, T2N 4N1
,
Canada
2
Wellcome Trust Sanger Institute
,
Hinxton, Cambridge, CB10 1SA
,
UK
Background: MicroRNAs (miRNAs) play key roles in regulating post-transcriptional gene expression and are essential for development in the free-living nematode Caenorhabditis elegans and in higher organisms. Whether microRNAs are involved in regulating developmental programs of parasitic nematodes is currently unknown. Here we describe the the miRNA repertoire of two important parasitic nematodes as an essential first step in addressing this question. Results: The small RNAs from larval and adult stages of two parasitic species, Brugia pahangi and Haemonchus contortus, were identified using deep-sequencing and bioinformatic approaches. Comparative analysis to known miRNA sequences reveals that the majority of these miRNAs are novel. Some novel miRNAs are abundantly expressed and display developmental regulation, suggesting important functional roles. Despite the lack of conservation in the miRNA repertoire, genomic positioning of certain miRNAs within or close to specific coding genes is remarkably conserved across diverse species, indicating selection for these associations. Endogenous smallinterfering RNAs and Piwi-interacting (pi)RNAs, which regulate gene and transposon expression, were also identified. piRNAs are expressed in adult stage H. contortus, supporting a conserved role in germline maintenance in some parasitic nematodes. Conclusions: This in-depth comparative analysis of nematode miRNAs reveals the high level of divergence across species and identifies novel sequences potentially involved in development. Expression of novel miRNAs may reflect adaptations to different environments and lifestyles. Our findings provide a detailed foundation for further study of the evolution and function of miRNAs within nematodes and for identifying potential targets for intervention.
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Background
microRNAs (miRNAs) are small, non-coding RNAs that
play key roles in regulating gene expression in animals,
plants and viruses. The processing of miRNAs from long
primary transcripts to their mature functional form by
Drosha and Dicer RNase III enzymes has been reviewed
recently [1]. The mature ~22-nucleotide single-stranded
molecule is incorporated into an RNA-induced silencing
complex (RISC), directing it to mRNA targets resulting
in their translational repression or destabilisation [2]. In
animals, miRNA target sites most often show partial
sequence complementarity and, although best
characterised in 3UTRs, can occur anywhere in the gene [3,4].
Accumulating evidence suggests that the majority of
mRNAs may be targets of miRNA regulation [5],
providing an increased level of complexity to global gene
control.
miRNAs show temporally controlled and cell-specific
patterns of expression [6-8], with the first level of regulation
being transcriptional. However, the importance of
posttranscriptional regulation is becoming increasingly
apparent [9]. In mammals, miRNAs have been shown to regulate
diverse and important processes such as B-cell
differentiation [10], adipocyte differentiation [11], cardiogenesis [12],
insulin secretion [13], antiviral defence [14], and the
development of cancer [15,16].
Genetic analysis in the free-living nematode
Caenorhabditis elegans led to the discovery of the first
miRNA, lin-4, which controls hypodermal cell fate
decisions during early larval development [17,18].
Similarly, C. elegans let-7 and the related miRNAs, mir-48,
mir-84 and mir-241, also function to regulate the
timing of developmental events [19,20]. A cell-specific role
has been defined for C. elegans lys-6 and mir-273,
which act sequentially to control the laterality of
chemosensory neurons [21,22]. However, in most cases,
mutation of other C. elegans miRNAs, either
individually [23] or by combined mutation of related sequences
[24], results in no observable effect on development or
viability. Exceptions are the early lethality phenotypes
resulting from both the combined loss of
mir-35-mir42 [24] and of mir-51-mir-56, [24,25], as well as the
movement and body size defect resulting from
combined mutation of mir-58, -80, -81 and -82 [24].
Importantly, miRNAs which are unrelated in sequence may
function in concert as demonstrated by the phenotypes
of individual miRNA mutants, which are revealed only
in genetic backgrounds where miRNA levels are
globally reduced [26]. Additionally, function may only
become apparent after detailed analysis, as
demonstrated for C. elegans mir-1, which regulates synaptic
signalling (...truncated)