By Doug Macron
SIROCCO, a European consortium of RNAi and microRNA researchers focused on RNA silencing, this month announced that it is seeking new partners that either have expertise in computational analysis and modeling or can help translate some of the effort's early discoveries for diagnostic and clinical applications.
"There is [already bioinformatics] expertise within the consortium … and various partners have bioinformatics groups … but no particular group at the moment has the availability to handle the whole consortium's" needs, Aileen Hogan, the SIROCCO project manager, told RNAi News this week. "We thought it would be advantageous to have [a] bioinformatics hub" to address this shortcoming.
At the same time, while certain SIROCCO members have been investigating the biotechnological applications of the consortium's work, this work has been limited, and the organization "would like to take this further to see if [the discoveries can be] developed into therapies and into diagnostics," she noted.
SIROCCO is structuring its search for up to three new members as a competitive call, and is accepting applications until Nov. 12. A final decision is expected to be made before the end of the year, Hogan said.
SIROCCO has earmarked €1 million ($1.48 million) to fund the work of the new members over the consortium's remaining two years.
Looking to fill the bioinformatics gap, SIROCCO is searching for a new participant who can "collaborate with other [consortium] partners in the development of computational methods for the analysis of small RNA datasets produced by high-throughput sequencing and will collaborate with existing partners in the construction of a bioinformatics platform for analysis of data by groups that do not have bioinformatics expertise," it said.
Specifically, the new member will handle tasks associated with the identification of the genomic loci responsible for the production of sRNAs, sequence motifs, structures in transcribed RNA, and "other genomic features associated with these loci," SIROCCO said. "Further analysis of these datasets will be aimed at developing methods for predicting sRNA targets including miRNA targets [associated with] development and … diseased states."
The partner will also be required to develop computational methods that allow sRNA datasets to be "integrated with transcript and epigenetic profiling in development and disease states," the consortium said. "This task will incorporate modeling approaches to the understanding of complex systems in which small silencing RNA molecules have a regulatory or modulatory role."
A key goal here, SIROCCO noted, would be the predictive modeling of sRNA networks, and the identification of regulatory nodes in these networks and how they interact with other cellular control mechanisms.
Lastly, the new partner "will be pivotal in centralizing the bioinformatics and computational modeling functions across the consortium," SIROCCO added. As such, experience with large datasets and modeling of complex biological systems is a requirement, as is the ability to work on systems and datasets from any organism amenable to genome-wide analysis and computational-modeling approaches. The new consortium member should also be able to develop computational tools for the analysis of animal sRNAs including miRNAs.
"It is expected that the new computational biology partner will work with experimentalist members of the consortium to analyze large datasets of mRNAs, sRNAs, and … epigenetic modifications," SIROCCO said. "The analysis will take into account the quantitative representation, as well as the presence [or] absence, of components of the various datasets. … It is expected that the new partner will play an important role in formulating new hypotheses and models that will be tested in the future rounds of experimentation."
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On the biomedical front, the search for a new SIROCCO member is driven by the need to "transfer knowledge produced in the first two years of the project to … diagnostic/clinical applications," the organization said.
The new partner would work to define rules for sRNA efficiency and specificity, as well as develop sRNA delivery methods and improved gene-silencing technologies in model or experimental systems, according to SIROCCO. At the same time, the partner would help evaluate the diagnostic potential of sRNAs or variation in sRNA target sites.
This effort has so far been driven by consortium members studying sRNA biogenesis and targeting. The new member would help to "translate discoveries from this work package into the development of sRNA-based pharmaceuticals and diagnostic tools," SIROCCO said.
"Efficient use of sRNAs as pharmaceuticals depends on methods for their efficient delivery into cells and animals," it added. Therefore, the consortium expects that a new member would carry out research into the delivery of sRNAs or their precursor molecules into animal models or experimental systems.
"The research may also involve the use of such delivery systems to investigate sRNA targeting," the consortium noted.
Additional information on the competitive call can be found here.
SIROCCO, short for Silencing RNAs: Organizers and Coordinators of Complexity in Eukaryotic Organisms, was established in January 2007 with €11.8 million ($17.5 million) in funding from the European Union (see RNAi News, 4/26/2007). It is set to run until the end of 2010.
The consortium’s primary goals are to “characterize the full complement” of miRNAs and siRNAs in animals and plants using bioinformatics, genomics, biochemistry, cell biology, and genetics.
The group's researchers study miRNA and siRNA profiles "that are associated with development, disease, and phenotypic divergence within populations," according to SIROCCO. Consortium deliverables include "databases of silencing RNA sequence and function in several organisms, new technologies for detection and manipulation of these RNAs, and information that will allow small RNA profiles to be used as molecular markers and diagnostic tools.
"SIROCCO will analyze the components of the small RNA silencing systems in order to identify potential targets for disease therapy and to improve the specificity with which therapeutic agents are used," the consortium said.
Earlier this year, SIROCCO publicly released a suite of bioinformatics tools developed by its members for analyzing the vast amounts of sequencing data generated by the initiative, as well as a web-based application for designing artificial miRNAs (see RNAi News, 2/26/2009).
The complete list of tools available through SIROCCO can be found here.