. Author manuscript; available in PMC: 2016 Dec 12.

Published in final edited form as: Nat Protoc. 2016 Feb 4;11(3):413–428. doi: 10.1038/nprot.2016.012

Table 1.

Comparison of non-cross-linking nascent RNA techniques.

	GRO-seq	PRO-seq	NET-seq	3′NT	Human NET-seq	Mammalian NET-seq
Nuclear run on	Yes	Yes	No	No	No	No
RNA fragmentation	Alkaline hydrolysis	Alkaline hydrolysis	Alkaline hydrolysis	Alkaline hydrolysis	Alkaline hydrolysis	MNase digestion
RNA selection	BrU antibody	Biotin-streptavidin	FLAG antibody	5′ cap antibody	No selection	Endogenous Pol II antibody
Pol II modification analyses	No	No	No	No	No	Yes
RNA processing analyses	No	No	No	No	No	Yes (splicing and miRNA processing)
Resolution	30–100 bases	1 base	1 base	1 base	1 base	1 base
Tested species	Human²⁰, mouse²¹, Drosophila²² and Caenorhabditis elegans²³	Human²⁴ and Drosophila⁸	Yeast¹¹ and Bacteria¹²	Drosophila⁹	Human¹⁰	Human¹³

mNET-seq is the only currently available method that allows analysis of both Pol II pausing and co-transcriptional RNA processing at single-nucleotide resolution in a CTD phosphorylation–specific manner.