Nascent RNA analyses: tracking transcription and its regulation

The programmes that direct an organism’s development and maintenance are encoded in its genome. Decoding of this information begins with regulated transcription of genomic DNA into RNA. Although transcription and its control can be tracked indirectly by measuring stable RNAs, it is only by directly measuring nascent RNAs that the immediate regulatory changes in response to developmental, environmental, disease and metabolic signals are revealed. Multiple complementary methods have been developed to quantitatively track nascent transcription genome-wide at nucleotide resolution, all of which have contributed novel insights into the mechanisms of gene regulation and transcription-coupled RNA processing. Here we critically evaluate the array of strategies used for investigating nascent transcription and discuss the recent conceptual advances they have provided. This Review provides an overview of different approaches for measuring nascent RNA synthesis. It discusses the complementary strengths of these different methods and how they have contributed to a mechanistic understanding of transcription regulation.