The Utility of Shallow RNA-Seq for Documenting Differential Gene Expression in Genes with High and Low Levels of Expression

rna-seqThe sequencing depth necessary for documenting differential gene expression using RNA-Seq has been little explored outside of model systems. In particular, the depth required to analyze large-scale patterns of differential transcription factor expression is not known. The goal of the present study is to explore the effectiveness of shallow (relatively low read depth) RNA-Seq. Researchers at the University of California Davis focused on two tissues in the honey bee: the sting gland and the digestive tract. The sting gland is an experimentally well-understood tissue that we use to benchmark the utility of this approach. They used the digestive tract to test the results obtained with the sting gland, and to conduct RNA-Seq between tissue types. Using a list of experimentally verified genes conferring tissue-specific functions in the sting gland, they show that relatively little read depth is necessary to identify them. They argue that this result should be broadly applicable, since genes important for tissue-specific functions often have robust expression patterns, and because they obtained similar results in their analysis of the digestive tract. Furthermore, the researchers demonstrate that the differential expression of transcription factors, which are transcribed at low levels compared to other genes, can nevertheless often be determined using shallow RNA-Seq. Overall, they found over 150 differentially expressed transcription factors in their tissues at a read depth of only 12 million. This work shows the utility of low-depth sequencing for identifying genes important for tissue-specific functions. It also verifies the often-held belief that transcription factors show low levels of expression, while demonstrating that, in spite of this, they are frequently amenable to shallow RNA-Seq. These findings should be of benefit to researchers using RNA-Seq in many different biological systems.


Atallah J, Plachetzki DC, Jasper WC, Johnson BR (2013) The Utility of Shallow RNA-Seq for Documenting Differential Gene Expression in Genes with High and Low Levels of Expression. PLoS ONE 8(12): e84160. [article]