RNA sequencing potent tool for understanding gene expression

Two papers published in the journal Nature show that next generation RNA sequencing technologies can give us a deep insight into transcription and the natural variation in genetic expression.

Previous RNA studies were performed using microarrays, which are only able to delve into a relatively small portion of the genome and can only reveal expression levels by targeting particular parts of each gene.

Using high throughput screening of RNA, RNA-Seq, the researchers were able to measure expression levels across the entire length of the transcript.

In one paper, Joseph K. Pickrell and colleagues sequenced RNA from 69 cell lines derived from unrelated Nigerian individuals for whom extensive genotype information is known from the HapMap project. In the second paper, Emmanouil T. Dermitzakis and colleagues characterise the messenger RNA (mRNA) of 60 Caucasian individuals.

The researchers created a map of the transcriptional landscape by pooling the data from all the individuals in the respective studies. In doing so, they found previously undiscovered protein-coding regions and identified over 1,000 genes at which genetic variation influences overall expression levels.

They also found that polymorphisms, SNPs, that affect gene expression are often found close to the gene itself, particularly near the transcription start site.

These studies represent only the tip of the iceberg of our understanding of RNA and the epigenome, which appears to play a major role in evolution.

Joseph K. Pickrell et al, 'Understanding mechanisms underlying human gene expression variation with RNA sequencing'. DOI: 10.1038/nature08872

Stephen B. Montgomery et al, 'Transcriptome genetics using second generation sequencing in a Caucasian population', DOI: 10.1038/nature08903

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