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Genome Sequencer 20 Used for Genome-wide Discovery of Small RNAs
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The Genome Sequencer 20 System from Roche Applied Science, a business area of Roche Diagnostics, finds its application in fields of life science research.
Recently some 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 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 characterize a class of small RNAs, called piRNAs, in mouse testis.
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 C. 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 (<100 kb) genomic regions.
