Measuring RNA polymerase activity genome-wide with high-resolution run-on-based methods

The biogenesis of RNAs is a multi-layered and highly regulated process that involves a diverse set of players acting in an orchestrated manner throughout the transcription cycle. Transcription initiation, elongation and termination factors act on RNA polymerases to modulate their movement along the DNA template in a very precise manner, more complex than previously anticipated. Genome-scale run-on-based methodologies have been developed to study in detail the position of transcriptionally-engaged RNA polymerases. Genomic run-on (GRO), and its many variants and refinements made over the years, are helping the community to address an increasing amount of scientific questions, spanning an increasing range of organisms and systems. In this review, we aim to summarize the most relevant high throughput methodologies developed to study nascent RNA by run-on methods, compare their main features, advantages and limitations, while putting them in context with alternative ways of studying the transcriptional process.