Mapping of RNA polymerase on mammalian genes in cells and nuclei

J Mirkovitch and JE Darnell

Rockefeller University, New York, New York 10021.

The assembly of an RNA polymerase II initiation complex at a promoter is associated with the melting of the DNA template to allow the polymerase to read the DNA sequence and synthesize the corresponding RNA. Using the specific single-stranded modifying reagent KMnO4 and a new genomic sequencing technique, we have explored the melted regions of specific genes in genomic DNA of whole cells or of isolated nuclei. We have demonstrated for the first time in vivo the melting in the promoter proximal transcribed region that is associated with the presence of RNA polymerase II complexes. An interferon-inducible gene, ISG-54, exhibited KMnO4 sensitivity over approximately 300 nucleotides downstream of the RNA initiation site in interferon-treated cells when the gene was actively transcribed but not in untreated cells where the gene was not transcribed. The extent of KMnO4 modification was proportional to transcription levels. The KMnO4 sensitivity was retained when nuclei were isolated from induced cells but was lost if the engaged polymerases were further allowed to elongate the nascent RNA chains ("run-on"). The sensitivity to KMnO4 in isolated nuclei was retained if the run-on incubation was performed in the presence of alpha-amanitin, which blocks progress of engaged polymerases. A similar analysis identified an open sequence of only approximately 30 bases just downstream of the start site of the transthyretin (TTR) gene in nuclei isolated from mouse liver, a tissue where TTR is actively transcribed. This abrupt boundary of KMnO4 sensitivity, which was removed completely by allowing engaged polymerases to elongate RNA chains, suggests that most polymerases transcribing this gene paused at about position +20. The possibility of mapping at the nucleotide level the position of actively transcribing RNA polymerases in whole cells or isolated nuclei opens new prospects in the study of transcription initiation and elongation.

Volume 3, Issue 10, pp. 1085-1094, 10/01/1992
Copyright © 1992 by The American Society for Cell Biology

This article has been cited by other articles:

				M. Ghosh, G. Liu, G. Randall, J. Bevington, and M. Leffak Transcription Factor Binding and Induced Transcription Alter Chromosomal c-myc Replicator Activity Mol. Cell. Biol., December 1, 2004; 24(23): 10193 - 10207. [Abstract] [Full Text] [PDF]

				H. Barrios, R. Grande, L. Olvera, and E. Morett In vivo genomic footprinting analysis reveals that the complex Bradyrhizobium japonicum fixRnifA promoter region is differently occupied by two distinct RNA polymerase holoenzymes PNAS, February 3, 1998; 95(3): 1014 - 1019. [Abstract] [Full Text] [PDF]

				J. Darnell Jr, I. Kerr, and G. Stark Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins Science, June 3, 1994; 264(5164): 1415 - 1421. [Abstract] [PDF]