Nuclear run-on

A nuclear run-on assay is conducted to identify the genes that are being transcribed at a certain time point.

[3] Alternative microarray methods have recently been developed, mainly PolII RIP-chip: RNA immunoprecipitation of RNA polymerase II with phosphorylated C-terminal domain directed antibodies and hybridization on a microarray slide or chip (the word chip in the name stems from "ChIP-chip" where a special Affymetrix GeneChip was required).

These assays are known as GRO-Seq and provide an incredibly detailed view of genes engaged in transcription with quantitative levels of expression.

Cells or nuclei are incubated with BrUTP in the presence of sarkosyl, which prevents the attachment of RNA polymerase to the DNA.

Therefore only RNA polymerase that are already on the DNA before the addition of sarkosyl will produce new transcripts that will be labeled with BrU.