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Background  Many studies of the eukaryotic transcription mechanism and its regulation rely on  in vitro  assays. Conventional RNA polymerase II transcription assays are based on radioactive labelling of the newly synthesized RNA. Due to the inefficient  in vitro  transcription, the detection of the RNA involving purification and gel electrophoresis is laborious and not always quantitative.    Results  Herein, we describe a new, non-radioactive, robust and reproducible eukaryotic  in vitro  transcription assay that has been established in our laboratory. Upon transcription, the newly synthesized RNA is directly detected and quantified using the QuantiGene assay. Alternatively, the RNA can be purified and a primer extension followed by PCR detection or qPCR quantification can be performed. When applied to assess the activity of RNA polymerase II inhibitors, this new method allowed an accurate estimation of their relative potency.    Conclusions  Our novel assay provides a non-radioactive alternative to a standard  in vitro  transcription assay that allows for sensitive detection and precise quantification of the newly transcribed, unlabelled RNA and is particularly useful for quantification of strong transcriptional inhibitors like α-amanitin. Moreover, the method can be easily adapted to quantify the reaction yield and the transcription efficiency of other eukaryotic  in vitro  systems, thus providing a complementary tool for the field of transcriptional research.

A novel, non-radioactive eukaryotic in vitro transcription assay for sensitive quantification of RNA polymerase II activity