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
SIROCCO Symposium at the 4th ESF Conference on Functional Genomics and Disease
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The session will be chaired by Gunter Meister (Martinsried), and the speakers will be Thomas Meyer (Berlin), Jørgen Kjems (Aarhus) and Eric Miska (Cambridge).
Latest News
UEA Animal Small RNA Toolkit
A toolkit for analyzing large-scale animal small RNA datasets.
Tools available include
- Sequence file pre-processing: Sequence adaptor removal and conversion to FASTA format
- Filter tool: Filter sequences in large-scale data sets
- miRProf: Expression profiles of known miRNAs from large scale sRNA data sets
- miRCat: Identification of miRNA sequences in large-scale sRNA data sets
- SiLoCo: Identification and comparison of sRNA-producing loci in large-scale data sets
- SiLoMa: Generate graphical maps of individual sRNA loci.
- RNA folding/annotation: For highlighting sRNA locations on a folded RNA sequence.
A FASTA Maker – SOFT to FASTA file conversion utility released
Many toolkits (for example the UEA Small Plant and Animal toolkit) require data to be provided in FASTA format. However sequence data sets from GEO often come in the SOFT format, and hence need to be converted before they can be used by many of the tools used in the bioinformatic sphere.
Sirocco have today released A FASTA Maker – a Java based tool to help perform these SOFT to FASTA file conversions in an easy to use GUI.
This utility operates in two modes – it can either transform local SOFT files containing sequence data into FASTA data or, given an accession number, can fetch a dataset from GEO. It also allows the creation of a ZIP version of the newly created FASTA file and a choice or redundant or non-redundant FASTA formats.
Click here to read more about and use the A FASTA Maker tool.
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
Clark AM, Goldstein LD, Tevlin M, Tavaré S, Shaham S, Miska EA. The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans. Nucleic Acids Res. 2010 Feb 21. [Epub ahead of print]
Csorba T, Lózsa R, Hutvágner G, Burgyán J. Polerovirus protein P0 prevents the assembly of small RNA containing RISC complexes and leads to degradation of ARGONAUTE1. Plant J. 2010 Feb 1. [Epub ahead of print]
Amendola E, Sanges R, Galvan A, Dathan N, Manenti G, Ferrandino G, Alvino FM, Di Palma T, Scarfò M, Zannini M, Dragani T, De Felice M, Di Lauro R. A Locus on Mouse Chromosome 2 Is Involved in Susceptibility to Congenital Hypothyroidism and Contains an Essential Gene Expressed in Thyroid. Endocrinology. 2010 Feb 16. [Epub ahead of print]
Havecker ER, Wallbridge LM, Hardcastle TJ, Bush MS, Kelly KA, Dunn RM, Schwach F, Doonan JH, Baulcombe DC. The Arabidopsis RNA-Directed DNA Methylation Argonautes Functionally Diverge Based on Their Expression and Interaction with Target Loci. Plant Cell. 2010 Feb 19. [Epub ahead of print]
Fulci V, Scappucci G, Sebastiani GD, Giannitti C, Franceschini D, Meloni F, Colombo T, Citarella F, Barnaba V, Minisola G, Galeazzi M, Macino G miR-223 is overexpressed in T-lymphocytes of patients affected by rheumatoid arthritis. Hum Immunol. 2010 Feb;71(2):206-11. Epub 2009 Nov 18.