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Characterisation of the complete miRNA and siRNA profile in our three model plants

These projects have now become possible because recently developed high throughput sequencing technologies have made it possible to determine millions of separate siRNA or miRNA sequences for low cost. We are using this approach to determine which regions of the three model system genomes are transcribed into precursors of siRNA and miRNAs. We can also use this technology to compare siRNA and miRNA profiles of plants subjected to different treatments or in different mutants. There are many thousands of loci with the potential to generate siRNAs and miRNAs in Arabidopsis and Chlamydomonas.

The analysis of these large sequence databases requires expertise in computational biology and considerable computational input. For that reason we are establishing a computational biology group in the Plant Science Department in Cambridge who will work with us on these and other projects including systems modelling.

This is a view from the Arabidopsis genome browser showing the alignment of siRNA and miRNA sequences with 200 kilobase pairs of the genome sequence. Each small arrow represents one siRNA or miRNA sequence and the blue boxes are long RNAs including messenger RNA. The siRNAs and miRNAs clearly align to specific regions of the genome that we refer to as siRNA or miRNA loci. A computational challenge is to develop ways to define these loci, to compare their representation in different datasets and to classify them in terms of their corresponding genomic features.