Silencing RNAs: organisers and coordinators of complexity in eukaryotic organisms
Welcome to the SIROCCO Project!
RNA silencing is a natural mechanism of gene regulation in cells. Small double-stranded RNA molecules 20-28 nucleotides long trigger the degradation of target RNA or DNA, thereby reducing specific gene expression. There is the potential to create small regulatory RNAs (siRNAs) that can be introduced into cells and silence genes that cause diseases.
The goals of the SIROCCO project are
- to exploit RNA silencing mechanisms in order to improve human and plant health
- to reveal how siRNAs play a role in developmental biology and disease defense
- to provide fundamental insights into the genetic networks that underlie normal and diseased embryonic development and adult growth
Project Announcements
The Third SIROCCO Annual Meeting, held in Hinxton UK, was a great success. View the photo gallery.
Please acknowledge SIROCCO funding in publications with “This work was supported by the European Commission Sixth Framework Programme Integrated Project SIROCCO contract number LSHG-CT-2006-037900″
Latest News
Sirocco Symposia at the 4th ESF Conference on Functional Genomics and Disease
A symposium will be taking place at the Sirocco Symposia at the 4th ESF Conference on Functional Genomics and Disease.
The session will be chaired by Gunter Meister (Martinsried), and the speakers will be Thomas Meyer (Berlin), Jørgen Kjems (Aarhus) and Eric Miska (Cambridge).
Seqbuster offers analysis of deep sequencing data
SeqBuster is a web-based bioinformatic tool offering a custom analysis of deep sequencing data at different levels, with special emphasis on the analysis of miRNA variants or isomiRs.SeqBuster includes a stand-alone version that permits the annotation against any custom database installed in the local machine independently of the web server tool. This offers a pre-analysis that is not restricted to the databases stored in the web server, overcoming the limitations in the storage capacities detected in other web-based bioinformatic tools. The R environment in which the different analysis packages have been developed permits the incorporation and/or modification of different types of analysis, which may be focused not only on small non-coding RNAs, but also on any type of sequence generated in large-scale sequencing strategies. SeqBuster is highly versatile offering a wide range of options both in the pre-analysis for annotation purposes and in the different module analysis for data manipulation.
Click here to access the tool.
SeqBuster is developed by the Genes and Diseases Group at the Centre for Genomic Regulation (Sirocco Partner 14). It has been developed and was presented to the Sirocco at the Sirocco Conference in 2009.
A detailed description of our research program can be found on our About Page.
Partners have access to a Private Partners page including discounts and reporting documents.
There is also a Data and Bioinformatics site available which aggregates the various bioinformatic and resources developed and hosted by the SIROCCO consortium.
Recent Publications
Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JW, Green PJ, Barton GJ, Hutvagner G. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA. 2009 Dec;15(12):2147-60. Epub 2009 Oct 22.
Wollmann H, Weigel D. Small RNAs in flower development. Eur J Cell Biol. 2009 Dec 21. [Epub ahead of print]
Pantano L, Estivill X, Martí E. SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. Nucleic Acids Res. [Epub ahead of print]
Armisen J, Gilchrist MJ, Wilczynska A, Standart N, Miska EA. Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis. Genome Res. 2009 Oct;19(10):1766-75. Epub 2009 Jul 23.
Structure Determinants for Accurate Processing of miR172a in Arabidopsis thaliana. Werner S, Wollmann H, Schneeberger K, Weigel D. Curr Biol. 2009 Dec 14. [Epub ahead of print]