Table 1.

Genome-wide approaches commonly used to detect PPP.

Factor	Principles	References
ChIP-chip and ChIP-seq	Antibodies against Pol II, Pol II S2P, and Pol II S5P as well as various modified histones are used.	[8,14,51,52]
GRO-seq	Nascent RNAs that have incorporated 5-bromouridine 5′-triphosphate are isolated with anti-deoxy bromouridine antibody and sequenced.	[9,10,14]
PRO-seq	Nascent RNAs that have incorporated biotinylated NTP are isolated with streptavidin beads for sequencing	[11]
Short-capped RNA analysis	Short mRNAs (<100 bases) with a 5′ cap are isolated with anti-cap antibody and sequenced.	[12]

Pol II: RNA Polymerase II; Pol II S2P: RNA Polymerase II with phosphorylated serine at the 2^nd position in the carboxy-terminal heptapeptide repeat domain; GRO-seq: Global Run-On sequencing; PRO-seq: Precision Run-On sequencing