Crop Biotech Update

Exploring Transcriptomes through Next-Generation DNA Sequencing Methods

June 27, 2008

Scientists need all the help they can get to spell out the blue print of life encoded by the Gs, As, Ts and Cs of the DNA. Studying an organism’s transcriptome, or the set of all messenger RNAs transcribed by the DNA, will significantly aid gene identification as well as help illuminate the inner workings of the genome. Recently, several papers have been published describing how advances in DNA-sequencing technology can be harnessed to explore transcriptomes in detail. These technologies are summarized in an article published by the journal Nature.

Expressed sequence tag (EST) method and tilling arrays have been successfully used in identifying genes. But these methods are relatively slow and costly. Now, a trio of next-generation sequencing technologies: 454 (from 454 Life Sciences), Solexa (from Illumina) and SOLiD (from ABI), can generate gigabases of sequence in a single experiment. These sequencing systems have revolutionized the study of DNA-binding proteins, genome packaging and organization, and small RNAs.

The systems work differently from traditional sequencing methods: instead of sequencing individual DNA clones, millions of DNA molecules are sequenced in parallel. However, the sequences obtained using these technologies are much shorter. Brenton R. Graveley, who authored the paper pointed out that this is just a minor trade-off considering the massive amount of total sequence generated using these technologies.

The paper is available at