Non-coding RNAs in schistosomes: an unexplored world

Oliveira, Kátia C.; Carvalho, Mariana; Maracaja-Coutinho, Vinícius; Kitajima, João Paulo; Verjovski-Almeida, Sérgio

doi:10.1590/s0001-37652011000200026

Cited by 30 publications

(43 citation statements)

References 123 publications

(84 reference statements)

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“…A survey of the available S. mansoni EST sequences (Oliveira et al, 2011) concluded that 10.3% (21,107 sequences) match the genome but have no protein coding potential and are therefore possible ncRNAs. This in turn suggests that the parasite may use a range of ncRNAs in transcriptional and translational regulation.…”

Section: Micro-rnasmentioning

confidence: 99%

“…This in turn suggests that the parasite may use a range of ncRNAs in transcriptional and translational regulation. Moreover, the presence of proteins involved in miRNA processing (Drosha, Dicer, and Argonaute) (reviewed in Oliveira et al, 2011) supports a role for miRNA regulation of development and differentiation of schistosomes and explains the effectiveness of RNAi and siRNA knockdown of transcription in the parasite (Boyle et al, 2003). miRNAs were first identified in S. japonicum (Xue et al, 2008; Huang et al, 2009) in two separate studies that demonstrated the existence of a limited number of miRNA that are conserved in other organisms including humans and several hundred novel miRNAs.…”

Section: Micro-rnasmentioning

confidence: 99%

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Epigenetic control of gene function in schistosomes: a source of therapeutic targets?

et al. 2014

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The discovery of the epigenetic regulation of gene expression has revolutionized both our understanding of how genomes function and approaches to the therapy of numerous pathologies. Schistosomes are metazoan parasites and as such utilize most, if not all the epigenetic mechanisms in play in their vertebrate hosts: histone variants, histone tail modifications, non-coding RNA and, perhaps, DNA methylation. Moreover, we are acquiring an increasing understanding of the ways in which these mechanisms come into play during the complex schistosome developmental program. In turn, interest in the actors involved in epigenetic mechanisms, particularly the enzymes that carry out epigenetic modifications of histones or nucleic acid, as therapeutic targets has been stimulated by the finding that their inhibitors exert profound effects, not only on survival, but also on the reproductive function of Schistosoma mansoni. Here, we review our current knowledge, and what we can infer, about the role of epigenetic mechanisms in schistosome development, differentiation and survival. We will consider which epigenetic actors can be targeted for drug discovery and what strategies can be employed to develop potent, selective inhibitors as drugs to cure schistosomiasis.

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Section: Micro-rnasmentioning

confidence: 99%

Section: Micro-rnasmentioning

confidence: 99%

Epigenetic control of gene function in schistosomes: a source of therapeutic targets?

et al. 2014

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“…The interest of the scientific community in miRNA research is evident in the overwhelming number of biological databases available for this particular class of noncoding RNAs (Paschoal et al, 2012). This is especially due to the role of miRNAs as key regulators of important biological processes in different organisms (Oliveira et al, 2011) as well as their use as possible therapeutics and biomarkers (Saunders and Lim, 2009). According to the Noncoding RNA Databases Resource, http://www.ncrnadatabases.org/ (Paschoal et al, 2012), 51% of the indexed noncoding RNA databases (70 of 137, version 2.0) are specific for this particular class.…”

Section: Introductionmentioning

confidence: 99%

miRQuest: integration of tools on a Web server for microRNA research

et al. 2016

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ABSTRACT. This report describes the miRQuest -a novel middleware available in a Web server that allows the end user to do the miRNA research in a user-friendly way. It is known that there are many prediction tools for microRNA (miRNA) identification that use different programming languages and methods to realize this task. It is difficult to understand each tool and apply it to diverse datasets and organisms available for miRNA analysis. miRQuest can easily be used by biologists and researchers with limited experience with bioinformatics. We built it using the middleware architecture on a Web platform for miRNA research that performs two main functions: i) integration of different miRNA prediction tools for miRNA identification in a user-friendly environment; and ii) comparison of these prediction tools. In both cases, the user provides sequences (in FASTA format) as an input set for the analysis and comparisons. All the tools were selected on the basis of a survey of the literature on the available tools for miRNA prediction. As results, three different cases of use of the tools are also described, where one is the miRNA identification analysis in 30 different species. Finally, miRQuest seems to be a novel and useful tool; and it is freely available for both benchmarking and miRNA identification at

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“…All of the authors have reviewed knowledge in the specific area of their work and have contributed novel results and/or novel perspectives on their subjects of study. Evidence of non-coding RNA expression in S. mansoni is reviewed by Oliveira et al (2011). This is an example of analysis that has only been possible because of the combined availability of the parasite genome sequence (Berriman et al 2009) and of large scale transcriptome data which was pioneered by Franco et al (1997) and considerably extended by Verjovski-Almeida et al (2003).…”

mentioning

confidence: 99%

“…This is an example of analysis that has only been possible because of the combined availability of the parasite genome sequence (Berriman et al 2009) and of large scale transcriptome data which was pioneered by Franco et al (1997) and considerably extended by Verjovski-Almeida et al (2003). Among other topics, these authors map all publicly available ESTs to the genome sequence, thus identifying those long (> 200 nt) non-coding RNAs transcribed from the opposite strand of protein-coding genes and provide microarray data on the differential expression of long non-coding RNAs in different life cycle stages of the parasite (Oliveira et al 2011). …”

mentioning

confidence: 99%

E Schistosoma mansoni at the molecular and cellular biology of helminth parasites VI meeting

Verjovski-Almeida

2011

An. Acad. Bras. Ciênc.

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Molecular information about eukaryotes has increased exponentially in the last decade. Sequencing of genomes and transcriptomes of model eukaryotic organisms has been followed by efforts in many groups to obtain equivalent information on helminth parasites. Large-scale molecular information is opening a door to understanding the intricate molecular and cellular biology of complex eukaryote parasites and raising the expectations to the ability of interfering with parasite-host interactions. Recognizing the need to increase the exchange of ideas in the area of helminth parasites, the international scientific community has gathered around a specialized meeting as early as 1997, when the first "Parasitic Helminths from Genomes to Vaccines" meeting took place in Edinburgh, UK, organized by Malcolm Kennedy from the University of Glasgow, and by Mark Blaxter and Rick Maizels, from the University of Edinburgh. A second meeting took place in Edinburgh in 1999, under the same title.In 2002 the event was renamed "Molecular and Cellular Biology of Helminth Parasites III" and it has been moved to the isle of Hydra, in Greece, where all subsequent events of the series have taken place. On September 5-10, 2010 the "Molecular and Cellular Biology of Helminth Parasites VI" meeting was organized by Kleoniki Gounaris and Murray Selkirk from the Imperial College, UK, and by Rick Maizels, from the University of Edinburgh. The meeting has an attendance limited to approximately 150 scientists, and the 2010 event comprised one keynote lecture, another 52 oral presentations with discussions in the mornings and evenings, and two poster sessions at night. We have invited several of the speakers who presented their work on Schistosoma mansoni to contribute articles to the Anais da Academia Brasileira de Ciências.In this volume, there are five contributions on S. mansoni. All of the authors have reviewed knowledge in the specific area of their work and have contributed novel results and/or novel perspectives on their subjects of study. Evidence of non-coding RNA expression in S. mansoni is reviewed by Oliveira et al. (2011). This is an example of analysis that has only been possible because of the combined availability of the parasite genome sequence (Berriman et al. 2009) and of large scale transcriptome data which was pioneered by Franco et al. (1997) and considerably extended by Verjovski-Almeida et al. (2003). Among other topics, these authors map all publicly available ESTs to the genome sequence, thus identifying those long (> 200 nt) non-coding RNAs transcribed from the opposite strand of protein-coding genes and provide microarray data on the differential expression of long non-coding RNAs in different life cycle stages of the parasite (Oliveira et al. 2011).Serpins or serine protease inhibitors are a structurally conserved family of macromolecular inhibitors found in virtually all biological systems. Quezada and McKerrow (2011) give here another very interesting example as to how the completion and annotation of the genomes of S. m...

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Non-coding RNAs in schistosomes: an unexplored world

Cited by 30 publications

References 123 publications

Epigenetic control of gene function in schistosomes: a source of therapeutic targets?

Epigenetic control of gene function in schistosomes: a source of therapeutic targets?

miRQuest: integration of tools on a Web server for microRNA research

E Schistosoma mansoni at the molecular and cellular biology of helminth parasites VI meeting

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