Identification of Schistosoma mansoni microRNAs

Simões, M.C., Lee, J., Djikeng, A., Cerqueira, G.C., Zerlotini, A., da Silva-Pereira, R.A., Dalby, A.R., LoVerde, P., El-Sayed, N.M. and Oliveira, G. 2011. Identification of Schistosoma mansoni microRNAs. BMC Genomics. 12 (47), pp. 1-17. https://doi.org/10.1186/1471-2164-12-47

TitleIdentification of Schistosoma mansoni microRNAs
AuthorsSimões, M.C., Lee, J., Djikeng, A., Cerqueira, G.C., Zerlotini, A., da Silva-Pereira, R.A., Dalby, A.R., LoVerde, P., El-Sayed, N.M. and Oliveira, G.
Abstract

Background: MicroRNAs (miRNAs) constitute a class of single-stranded RNAs which play a crucial role in regulating development and controlling gene expression by targeting mRNAs and triggering either translation repression or messenger RNA (mRNA) degradation. miRNAs are widespread in eukaryotes and to date over 14,000 miRNAs have been identified by computational and experimental approaches. Several miRNAs are highly conserved across species. In Schistosoma, the full set of miRNAs and their expression patterns during development remain poorly understood. Here we report on the development and implementation of a homology-based detection strategy to search for miRNA genes in Schistosoma mansoni. In addition, we report results on the experimental detection of miRNAs by means of cDNA cloning and sequencing of size-fractionated RNA samples. Results: Homology search using the high-throughput pipeline was performed with all known miRNAs in miRBase. A total of 6,211 mature miRNAs were used as reference sequences and 110 unique S. mansoni sequences were returned by BLASTn analysis. The existing mature miRNAs that produced these hits are reported, as well as the locations of the homologous sequences in the S. mansoni genome. All BLAST hits aligned with at least 95% of the miRNA sequence, resulting in alignment lengths of 19-24 nt. Following several filtering steps, 15 potential miRNA candidates were identified using this approach. By sequencing small RNA cDNA libraries from adult worm pairs, we identified 211 novel miRNA candidates in the S. mansoni genome. Northern blot analysis was used to detect the expression of the 30 most frequent sequenced miRNAs and to compare the expression level of these miRNAs between the lung stage schistosomula and adult worm stages. Expression of 11 novel miRNAs was confirmed by northern blot analysis and some presented a stage-regulated expression pattern. Three miRNAs previously identified from S. japonicum were also present in S. mansoni.

Conclusion: Evidence for the presence of miRNAs in S. mansoni is presented. The number of miRNAs detected by homology-based computational methods in S. mansoni is limited due to the lack of close relatives in the miRNA repository. In spite of this, the computational approach described here can likely be applied to the identification of pre-miRNA hairpins in other organisms. Construction and analysis of a small RNA library led to the experimental identification of 14 novel miRNAs from S. mansoni through a combination of molecular cloning, DNA sequencing and expression studies. Our results significantly expand the set of known miRNAs in multicellular parasites and provide a basis for understanding the structural and functional evolution of miRNAs in these metazoan parasites.

JournalBMC Genomics
Journal citation12 (47), pp. 1-17
ISSN1471-2164
Year2011
PublisherBioMed Central
Digital Object Identifier (DOI)https://doi.org/10.1186/1471-2164-12-47
Publication dates
Published2011
File

Related outputs

microRNA 1307 Is a Potential Target for SARS-CoV-2 Infection: An <i>in Vitro</i> Model
Arisan, Elif Damla, Dart, D. Alwyn, Grant, Guy H., Dalby, A.R., Kancagi, Derya Dilek, Turan, Raife Dilek, Yurtsever, Bulut, Karakus, Gozde Sir, Ovali, Ercument, Lange, Sigrun and Uysal-Onganer, P. 2022. microRNA 1307 Is a Potential Target for SARS-CoV-2 Infection: An <i>in Vitro</i> Model. ACS Omega. 7 (42), pp. 38003-38014. https://doi.org/10.1021/acsomega.2c05245

Bacterial Adaptation to Venom in Snakes and Arachnida
Esmaeilishirazifard, Elham, Usher, Louise, Trim, Carol, Denise, Hubert, Sangal, V., Tyson, G., Barlow, Axel, Redway, Keith F, Taylor, John D, Kremyda-Vlachou, Myrto, Davies, Sam, Loftus, Teresa D, Lock, Mikaella M G, Wright, Kstir, Dalby, Andrew, Snyder, L., Wuster, Wolfgang, Trim, Steve and Moschos, S. 2022. Bacterial Adaptation to Venom in Snakes and Arachnida. Microbiology Spectrum. 10 (3) e02408-21. https://doi.org/10.1128/spectrum.02408-21

Complete analysis of the H5 hemagglutinin and N8 neuraminidase phylogenetic trees reveals that the H5N8 subtype has been produced by multiple reassortment events
Dalby, A.R. 2016. Complete analysis of the H5 hemagglutinin and N8 neuraminidase phylogenetic trees reveals that the H5N8 subtype has been produced by multiple reassortment events. F1000Research . 5, p. 2463 2463. https://doi.org/10.12688/f1000research.9261.1

Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation
Dalby, A.R. and Shamsir, M. 2015. Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation. F1000Research. 4 (589). https://doi.org/10.12688/f1000research.6831.1

The European and Japanese outbreaks of H5N8 derive from a single source population providing evidence for the dispersal along the long distance bird migratory flyways
Dalby, A.R. and Iqbal, M. 2015. The European and Japanese outbreaks of H5N8 derive from a single source population providing evidence for the dispersal along the long distance bird migratory flyways. PeerJ. 3 e934. https://doi.org/10.7717/peerj.934

A global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 influenza hemagglutinin
Dalby, A.R. and Iqbal, M. 2014. A global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 influenza hemagglutinin. PeerJ. 2 e655. https://doi.org/10.7717/peerj.655

The Robustness of Pathway Analysis in Identifying Potential Drug Targets in Non-Small Cell Lung Carcinoma
Dalby, A.R. and Bailey, I. 2014. The Robustness of Pathway Analysis in Identifying Potential Drug Targets in Non-Small Cell Lung Carcinoma. Microarrays. 3 (4), pp. 212-225. https://doi.org/10.3390/microarrays3040212

Analysis of gene expression data from non-small celllung carcinoma cell lines reveals distinct sub-classesfrom those identified at the phenotype level
Dalby, A.R., Emam, I. and Franke, R. 2012. Analysis of gene expression data from non-small celllung carcinoma cell lines reveals distinct sub-classesfrom those identified at the phenotype level. PLoS ONE. 7 (11) e50253. https://doi.org/10.1371/journal.pone.0050253

Developing stochastic models for spatial inference: bacterial chemotaxis
Yu, Y.D., Choi, Y., Teo, Y.Y. and Dalby, A.R. 2010. Developing stochastic models for spatial inference: bacterial chemotaxis. PLoS ONE. 5 (5) e10464. https://doi.org/10.1371/journal.pone.0010464

A comparative proteomic analysis of the simple aminoacid repeat distributions in Plasmodia reveals lineagespecific amino acid selection
Dalby, A.R. 2009. A comparative proteomic analysis of the simple aminoacid repeat distributions in Plasmodia reveals lineagespecific amino acid selection. PLoS ONE. 4 (7) e6231. https://doi.org/10.1371/journal.pone.0006231

Beta-sheet containment by flanking prolines: molecular dynamic simulations of the inhibition of beta-sheet elongation by proline residues in human prion protein.
Shamsir, M.S. and Dalby, A.R. 2007. Beta-sheet containment by flanking prolines: molecular dynamic simulations of the inhibition of beta-sheet elongation by proline residues in human prion protein. Biophysical Journal. 92 (6), pp. P2080-2089. https://doi.org/10.1529/biophysj.106.092320

COPASAAR--a database for proteomic analysis of single amino acid repeats.
Depledge, D.P. and Dalby, A.R. 2005. COPASAAR--a database for proteomic analysis of single amino acid repeats. BMC Bioinformatics. https://doi.org/10.1186/1471-2105-6-196

Predicting the phosphorylation sites using hidden Markov models and machine learning methods.
Senawongse, P., Dalby, A.R. and Yang, Z.R. 2005. Predicting the phosphorylation sites using hidden Markov models and machine learning methods. Journal of Chemical Information and Modeling. 45 (4), pp. 1147-1152. https://doi.org/10.1021/ci050047+

Evaluation of mutual information and genetic programming for feature selection in QSAR.
Venkatraman, V., Dalby, A.R. and Yang, Z.R. 2004. Evaluation of mutual information and genetic programming for feature selection in QSAR. Journal of Chemical Information and Computer Sciences. 44 (5), pp. 1686-1692. https://doi.org/10.1021/ci049933v

Reduced bio basis function neural network for identification of protein phosphorylation sites: comparison with pattern recognition algorithms.
Berry, E.A., Dalby, A.R. and Yang, Z.R. 2004. Reduced bio basis function neural network for identification of protein phosphorylation sites: comparison with pattern recognition algorithms. Computational Biology and Chemistry. 28 (1), pp. 75-85. https://doi.org/10.1016/j.compbiolchem.2003.11.005

Constructing an enzyme-centric view of metabolism.
Horne, A.B., Hodgman, T.C., Spence, H.D. and Dalby, A.R. 2004. Constructing an enzyme-centric view of metabolism. Bioinformatics. 20 (13), pp. 2050-2055. https://doi.org/10.1093/bioinformatics/bth199

Mining HIV protease cleavage data using genetic programming with a sum-product function.
Yang, Z.R., Dalby, A.R. and Qiu, J. 2004. Mining HIV protease cleavage data using genetic programming with a sum-product function. Bioinformatics. 20 (18), pp. 3398-3405. https://doi.org/10.1093/bioinformatics/bth414

The structure of human liver fructose-1,6-bisphosphate aldolase
Dalby, A.R., Tolan, D.R. and Littlechild, J.A. 2002. The structure of human liver fructose-1,6-bisphosphate aldolase. Acta Crystallographica Section D. D57, pp. 1526-1533. https://doi.org/10.1107/s0907444901012719

Structural and functional comparisons between vanadium haloperoxidase and acid phosphatase enzymes.
Littlechild, J., Garcia-Rodriguez, E., Dalby, A.R. and Isupov, M. 2002. Structural and functional comparisons between vanadium haloperoxidase and acid phosphatase enzymes. Journal of Molecular Recognition. 15 (5), pp. 291-296. https://doi.org/10.1002/jmr.590

Crystal structure of dodecameric vanadium-dependent bromoperoxidase from the red algae Corallina officinalis.
Isupov, M.N., Dalby, A.R., Brindley, A.A., Izumi, Y., Tanabe, T., Murshudov, G.N. and Littlechild, J.A. 2000. Crystal structure of dodecameric vanadium-dependent bromoperoxidase from the red algae Corallina officinalis. Journal of Molecular Biology. 299 (4), pp. 1035-1049. https://doi.org/10.1006/jmbi.2000.3806

Crystal structure of human muscle aldolase complexed with fructose 1,6-bisphosphate: mechanistic implications.
Dalby, A.R., Dauter, Z. and Littlechild, J.A. 1999. Crystal structure of human muscle aldolase complexed with fructose 1,6-bisphosphate: mechanistic implications. Protein Science. 8 (2), pp. 291-297. https://doi.org/10.1110/ps.8.2.291

Structure of a phosphoglycerate mutase:3-phosphoglyceric acid complex at 1.7 A.
Crowhurst, G.S., Dalby, A.R., Isupov, M.N., Campbell, J.W. and Littlechild, J.A. 1999. Structure of a phosphoglycerate mutase:3-phosphoglyceric acid complex at 1.7 A. Acta Crystallographica Section D. D55, pp. 1822-1826. https://doi.org/10.1107/s0907444999009944

Preliminary X-ray analysis of a new crystal form of the vanadium-dependent bromoperoxidase from Corallina officinalis.
Brindley, A.A., Dalby, A.R., Isupov, M.N. and Littlechild, J.A. 1998. Preliminary X-ray analysis of a new crystal form of the vanadium-dependent bromoperoxidase from Corallina officinalis. Acta Crystallographica Section D: Structural Biology. D54 (Pt 3), pp. 454-457. https://doi.org/10.1107/s0907444997014558

Studies with type I aldolase to understand fructose intolerance and combat parasitic disease.
Dalby, A.R. and Littlechild, J.A. 1996. Studies with type I aldolase to understand fructose intolerance and combat parasitic disease. Journal of Pharmacy and Pharmacology. 48 (2), pp. 214-217. https://doi.org/10.1111/j.2042-7158.1996.tb07126.x

Permalink - https://westminsterresearch.westminster.ac.uk/item/9004w/identification-of-schistosoma-mansoni-micrornas


Share this

Usage statistics

132 total views
163 total downloads
These values cover views and downloads from WestminsterResearch and are for the period from September 2nd 2018, when this repository was created.