Arabidopsis plants flowering.

Matchpoint software solution supporting hairpinRNAi

MatchPoint is a software module developed by CSIRO to support CSIRO’s gene silencing technology.

• 12 June 2008 | Updated 14 October 2011

• Meeting the need
• The technology
• Outcomes

Meeting the need

RNA interference (RNAi), also called gene silencing, is a powerful technology that has been developed by CSIRO Plant Industry over the past 10 years.

The technology uses a hairpin-RNA construct to interfere with the normal delivery of messenger RNA within a cell, and hence to suppress the expression of genetic information. Applications include the discovery of important trait genes, and the development of novel traits in plants.

Researchers at CSIRO Mathematical and Information Sciences have been working with CSIRO Plant Industry to obtain a clearer functional view of the silencing process. One outcome of this collaboration is a software system called MatchPoint, designed to support effective use of the RNAi technology.

The technology

MatchPoint can generate optimum sequences to silence target genes by predicting matches between a given hairpin silencer and a given genome, and scoring points in a quantitative assessment of those matches.

The matching step resembles a search task that arises in the design of very large databases, and is addressed by a highly efficient search procedure that has been developed especially for MatchPoint.

The model’s implementation allows rapid estimation of the impacts to be expected from the application of a given silencer sequence in relation to a given genome.

In addition to its analytical functions, MatchPoint provides algorithms to design silencer sequences directed at a given target gene or genes.

In general the design objective is to maximise impact on the target gene(s) while avoiding collateral damage to other genes by way of cross-silencing. Of the algorithms currently provided, two are specialised for the synthesis techniques in most common use at present, while the third involves constructing arbitrary sequences.

Outcomes

The genomes currently supported by MatchPoint are Arabidopsis thaliana and Oryza sativa (rice). MatchPoint’s model of the silencing process includes a detailed representation of the actions of the currently known processes of gene silencing.

A series of biological experiments is currently being undertaken by CSIRO Plant Industry to test the details of the silencing model and the effectiveness of the design algorithms.

Read more about CSIRO's work in HairpinRNAi and MatchPoint.