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Unlocking the mysteries of a cell

What makes a tomato red? UEA has created software that helped to answer this question through providing the technology for academics to drill down into the tomato's DNA.

Some technological advances unlock potential and enable other research projects to progress and UEA's small RNA Workbench software is one such advance.  By reducing the time it takes to analyse complex sequencing data it unlocks research potential in the biosciences.

RNAs (ribonucleic acids) are universal and essential to all living things so all bacteria, fungi, plants and animals have them. They are linked to cell processes and carry messages from DNA to control the synthesis of proteins.

Small RNAs (sRNA) are small molecules involved in stress response regulation and repressing gene expression in plants and animals. They act as switches, helping regulate the cell in terms of how it responds to its environment. They are fundamental because they tell cells what to do.

The small RNA workbench is a suite of tools for analysing small RNAs. It comprises computational software for bioscientists to analyse sequencing data of small RNAs.

"The software package is based on algorithms developed for the original UEA sRNA Toolkit that will perform a complete analysis of single or multiple-sample small RNA datasets to identify interesting landmarks or other tasks such as profiling small RNA expression patterns in genetic data."
Professor Vince Moulton, Professor in Computational Biology

sRNA’s are central to how plant and animal cells sense and respond to their environment. Sequencing all the DNA and RNA in plants or animals provides scientists with vast sRNA datasets. The workbench gives scientists the tools to analyse gigantic, complicated datasets, to enable them to draw out interesting results and unlock the mysteries of the cell.

At its conception the, free of charge, workbench was one of the first tools in the world tailored to sRNA analysis and it has evolved into a sophisticated package of tools for scientists. There have been over 10,000 downloads to date and a cloud-based version is in production.

The technology can be used for many applications; from understanding how sRNA's affect bee behaviour, to cancer therapies, sRNA response networks and decoding the oat genome.

This project has the potential to provide significant benefits for both the scientific community and industry, as the application will remove entry-level barriers for sRNA analysis, accelerating development in the field of RNA interference. With a direct route to the target audience, the aim is to develop commercial use of the workbench.

So why are tomatos red? UEA researchers Moxon, Jing, Szittya et al found that microRNAs target the genes involved in tomato ripening2.  They state that their study opened "..a new avenue in the field of fleshy fruit biology by raising the possibility that fruit development and ripening may be under miRNA regulation."  This deep sequencing was made possible by the Small RNA Workbench.

Developed from a research collaboration between Prof Vincent Moulton of the School of Computing Sciences and Prof Tamas Dalmay of the School of Biological Sciences at UEA the project was originally funded by the BBSRC ‘BioInformatics and Biological Resources’ fund, set up to establish and enhance resources and tools for the bioscience research community.

References

1.Small RNA Workbench - http://srna-workbench.cmp.uea.ac.uk

2.Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Simon Moxon, Runchun Jing, Gyorgy Szittya, et al.
Genome Res. 2008 18: 1602-1609 originally published online July 24, 2008

 

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Prof Vincent Moulton

Professor in Computational Biology, School of Computing Sciences

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