Perspectives on transcriptomics in animal physiology studies

Reductionist approaches in physiology and biochemistry are essential for understanding how animals cope and adapt to their environments. Transcriptomics is no longer restricted to a select few, and accessibility and affordability continue to facilitate its rapid growth as a science. More than 6000 publications (a conservative estimate) over the past decade quantify the response of the transcriptome to a wide breadth of questions in animal physiology. Transcriptomes have been quantified under conditions of hypoxia, climate change, salinity, drought, environmental pollution, and ultraviolet radiation among others; these studies have greatly improved understanding of the molecular machinery required for organismal adaptation. These "snapshots in time" however are never complete as the transcriptome is exquisitely sensitive to an individual's current physiologic state. Animal physiologists new to the field must recognize limitations of transcriptome technologies and consider experimental designs that strengthen physiologic interpretation. Current estimates suggest that a sample size of 6 or more are required for RNA-seq experiments in order to capture the majority of differentially expressed genes confidently. "Outside-the-box" approaches for statistical analyses of data derived from RNA-seq should be explored, as studies continue to point out that high false discoveries rates are pervasive with RNA-seq studies, reminiscent of the early days of microarrays. Incorporating biological variability, rather than reducing it (i.e. pooling strategies), into experimental designs is essential. Moreover, real-time PCR must not be viewed as a "validation step" to justify low samples sizes, but rather an orthogonal method to strengthen biological interpretation. The use of proper experimental controls in transcriptomics studies (i.e. spike-in controls and technical replication) are recommended and there is a pressing need for inter-laboratory tests (round robin experiments) to quantify repeatability and to identify sources of transcriptome variation within the context of animal physiology. Testing the reproducibility of transcriptome experiments in light of physiology in non-model organisms would be a significant contribution to the community. Single cell transcriptomics and multiplexing barcoding strategies such as decode-seq are poised to further advance the reductionist view of animal physiology; researchers are encouraged to consult literature herein and elsewhere for guidance on best practices and limitations of transcriptome technologies when studying the physiology of animals.