The ultrafast Genome Sequencer 20 system from Roche Applied Science, a business area of Roche Diagnostics, finds its application in ever-increasing fields of life science research
Recently some new publications reported on the sequencing of small non coding RNAs (scnRNAs).
Due to the fact that, compared to the current procedure to sequence sncRNA, sample preparation is considerably facilitated and due to the ultra high throughput provided, the GS20 system is perfectly suited for this application.
Henderson et al studied the role of the four Arabidopsis thaliana Dicer-like genes (DCL1-DCL4) in small RNA processing, gene silencing, and DNA methylation patterning.
They used the Genome Sequencer 20 to sequence RNAs from a dcl2 dcl3 dcl4 triple mutant and found markedly reduced tasiRNA and siRNA production.
Their conclusion was that DCL1, which is also the major enzyme for processing miRNAs, has a previously unknown role in the production of small RNAs from endogenous inverted repeats.
DCL2, DCL3 and DCL4 were functionaly redundand in production of siRNA and tasiRNA and in the establishment and maintenance of DNA methylation.
The studies also suggest that asymmetric DNA methylation can be maintained by pathways that do not require siRNAs.
In their publication, Angelique Girard et al used the system in order to characterise a new class of small RNAs, called piRNAs, in mouse testis.
More than 87,000 reads were generated with the Genome Sequencer 20 System, around 53,000 of which would be classified as candidate piRNAs.
The researchers found that a germline-specific class of small RNAs binds mammalian Piwi proteins.
During a search for candidate mammalian factors for transcriptional gene silencing (TGS), Nelson Lau et al generated 99,753 and 105,793 raw sequencing reads with the Genome Sequencer 20 system.
They purified a complex that contains small RNAs and Riwi, the rat homolog to human Piwi, from rat testes.
The RNAs, frequently 29 to 30 nucleotides in length, are called Piwi-interacting RNAs (piRNAs), 94% of which map to 100 defined (<100kb) genomic regions.
Since 2005, a new approach is available on the sequencing market, setting new standards in velocitiy and cost-effectiveness.
The Genome Sequencer 20 System, is based on 454 Sequencing technology, developed by the US company 454 Life Sciences, and can perform sequencing runs up to 60 times faster than conventional commercially available platforms.
For preparation of a whole genome, only one single preparation step, without extensive robots for colony picking and handling of the microtiter plates, is needed.
One single instrument can produce dozens of megabases of sequence data within a few hours, thanks to parallel-processing, the latest imaging techniques and unique data analysis.
The resulting substantial reductions in both time and costs will offer the prospect of new applications for sequencing in the fields of whole genome sequencing, transcriptome and gene regulation studies, or amplicon analysis, eg, as basis for the detection of somatic mutations in cancer samples.
