The regulation and control of SINE transcription is likely a key process to preserve the physiology and homeostasis of specific tissues and organs. This implies that the analysisof SINE expression is relevant to understand the mechanisms by which these elements affect cell functioning. SINE transcription can be measured by several available methods.
In vitro techniques, such as in vitro transcription or retrotransposition colony formation assays, are useful for the dissection of general regulatory pathways involving a specifi c family of SINEs. However, these methods do not give enough mechanistic insight if we are interested in studying the transcription of specific SINE instances along the genome or in detecting novel SINE amplification events during development. Quantitative real-time PCR protocols can be designed to perform these specific analyses; however, NGS tools need to be applied for whole genome analysis of SINEs-derived transcription, where information involving millions of sequence reads need to be processed. Although a great effort has been invested in recent years to develop these techniques, there are still important limitations that make difficult the application of NGS to the study of retrotransposon expression. Particularly relevant are the reduced length and the repetitive nature of SINE elements, two properties that jeopardize the identification and functional validation of single SINE instances regulating cell functions.
Schematic representation of the importance of transcription of SINE elements to biological processes
Here, researchers from the Champalimaud Center for the Unkown, Portugal propose and discuss several methods to overcome these constraints using an RNA-seq analytic protocol specifically designed for SINE detection.