Structural characterization of RNA polymerase II complexes arrested by a cyclobutane pyrimidine dimer in the transcribed strand of template DNA

• Type of Material: Article
• Authors: Silvia Tornaletti, Stanford University; Daniel Reines, Emory University; Philip C. Hanawalt, Stanford University
• Language: English
• Date: 1999-08-20
• Publisher: American Society for Biochemistry and Molecular Biology
• Publication Version: Final Published Version
• Copyright Statement: © 1999 by The American Society for Biochemistry and Molecular Biology, Inc
• Final Published Version (URL): http://dx.doi.org/10.1074/jbc.274.34.24124
• Title of Journal or Parent Work: Journal of Biological Chemistry
• ISSN: 0021-9258
• Volume: 274
• Issue: 34
• Start Page: 24124
• End Page: 24130
• Grant/Funding Information: This work was supported by Grant CA-77712 from the National Cancer Institute, United States Department of Health and Human Services.
• Keywords: Life Sciences & Biomedicine; THYMINE DIMER; CLEAVAGE; TERMINATION; Biochemistry & Molecular Biology; DAMAGE; GENE; EXCISION-REPAIR; TRANSLOCATION; RECOGNITION; ESCHERICHIA-COLI; Science & Technology; ELONGATION COMPLEX
• Research Categories: Chemistry, Biochemistry; Biology, General

Abstract

We have characterized the properties of immunopurified transcription complexes arrested at a specifically located cyclobutane pyrimidine dimer (CPD) using enzymatic probes and an in vitro transcription system with purified RNA polymerase II (RNAP II) and initiation factors. To help understand how RNAP II distinguishes between a natural impediment and a lesion in the DNA to initiate a repair event, we have compared the conformation of RNAP II complexes arrested at a CPD with complexes arrested at a naturally occurring elongation impediment. The footprint of RNAP II arrested at a CPD, using exonuclease III and T4 DNA polymerase's 3'→5' exonuclease, covers ~35 base pairs and is asymmetrically located around the dimer. A similar footprint is observed when RNAP II is arrested at the human histone H3.3 arrest site. Addition of elongation factor SII to RNAP II arrested at a CPD produced shortened transcripts of discrete lengths up to 25 nucleotides shorter than those seen without SII. After addition of photolyase and exposure to visible light, some of the transcripts could be reelongated beyond the dimer, suggesting that SII-mediated transcript cleavage accompanied significant RNAP II backup, thereby providing access of the repair enzyme to the arresting CPD.