CPD Damage Recognition by Transcribing RNA Polymerase II

Cells use transcription-coupled repair (TCR) to efficiently eliminate DNA lesions such as ultraviolet light–induced cyclobutane pyrimidine dimers (CPDs). Here we present the structure-based mechanism for the first step in eukaryotic TCR, CPD-induced stalling of RNA polymerase (Pol) II. A CPD in the transcribed strand slowly passes a translocation barrier and enters the polymerase active site. The CPD 5′-thymine then directs uridine misincorporation into messenger RNA, which blocks translocation. Artificial replacement of the uridine by adenosine enables CPD bypass; thus, Pol II stalling requires CPD-directed misincorporation. In the stalled complex, the lesion is inaccessible, and the polymerase conformation is unchanged. This is consistent with nonallosteric recruitment of repair factors and excision of a lesion-containing DNA fragment in the presence of Pol II.

[1]  N. Savery,et al.  Structural Basis for Bacterial Transcription-Coupled DNA Repair , 2006, Cell.

[2]  J. Egly,et al.  Initiation of DNA repair mediated by a stalled RNA polymerase IIO , 2006, The EMBO journal.

[3]  P. Doetsch,et al.  RNA polymerase encounters with DNA damage: transcription-coupled repair or transcriptional mutagenesis? , 2006, Chemical reviews.

[4]  E. Nogales,et al.  Recognition of RNA polymerase II and transcription bubbles by XPG, CSB, and TFIIH: insights for transcription-coupled repair and Cockayne Syndrome. , 2005, Molecular cell.

[5]  P. Cramer,et al.  Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. , 2004, Molecular cell.

[6]  D. Bushnell,et al.  Structural Basis of Transcription Nucleotide Selection by Rotation in the RNA Polymerase II Active Center , 2004, Cell.

[7]  H. Handa,et al.  Blockage of RNA polymerase II at a cyclobutane pyrimidine dimer and 6-4 photoproduct. , 2004, Biochemical and biophysical research communications.

[8]  S. Doublié,et al.  Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7 , 2004, Nature Structural &Molecular Biology.

[9]  J. Egly,et al.  Fate of RNA Polymerase II Stalled at a Cisplatin Lesion* , 2004, Journal of Biological Chemistry.

[10]  R. Woodgate,et al.  Replication of a cis–syn thymine dimer at atomic resolution , 2003, Nature.

[11]  J. Hoeijmakers,et al.  Divide and conquer: nucleotide excision repair battles cancer and ageing. , 2003, Current opinion in cell biology.

[12]  J. Svejstrup.  Rescue of arrested RNA polymerase II complexes , 2003, Journal of Cell Science.

[13]  L. Prakash,et al.  Yeast RAD26, a Homolog of the Human CSB Gene, Functions Independently of Nucleotide Excision Repair and Base Excision Repair in Promoting Transcription through Damaged Bases , 2002, Molecular and Cellular Biology.

[14]  H. Erdjument-Bromage,et al.  A Rad26–Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage , 2002, Nature.

[15]  P. Cramer,et al.  Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution , 2001, Science.

[16]  L. Prakash,et al.  Nucleotide excision repair in yeast. , 2000, Mutation research.

[17]  D. Reines,et al.  Transcription elongation factor SII , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[18]  M. Kashlev,et al.  The 8-Nucleotide-long RNA:DNA Hybrid Is a Primary Stability Determinant of the RNA Polymerase II Elongation Complex* , 2000, The Journal of Biological Chemistry.

[19]  P. Hanawalt,et al.  Nucleotide Sequence Context Effect of a Cyclobutane Pyrimidine Dimer upon RNA Polymerase II Transcription* , 1997, The Journal of Biological Chemistry.

[20]  A. Sancar,et al.  Cockayne syndrome group B protein enhances elongation by RNA polymerase II. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[21]  P. van de Putte,et al.  Transcription elongation factor S-II is not required for transcription-coupled repair in yeast , 1997, Molecular and General Genetics MGG.

[22]  A. Sancar,et al.  Model for XPC-independent Transcription-coupled Repair of Pyrimidine Dimers in Humans* , 1997, The Journal of Biological Chemistry.

[23]  D. Reinberg,et al.  RNA polymerase II stalled at a thymine dimer: footprint and effect on excision repair. , 1997, Nucleic acids research.

[24]  A. Sancar,et al.  Human Transcription-Repair Coupling Factor CSB/ERCC6 Is a DNA-stimulated ATPase but Is Not a Helicase and Does Not Disrupt the Ternary Transcription Complex of Stalled RNA Polymerase II* , 1997, The Journal of Biological Chemistry.

[25]  A. Sancar.  DNA excision repair. , 1996, Annual review of biochemistry.

[26]  R. Wood,et al.  Mammalian DNA nucleotide excision repair reconstituted with purified protein components , 1995, Cell.

[27]  P. Hanawalt,et al.  Transcript cleavage by RNA polymerase II arrested by a cyclobutane pyrimidine dimer in the DNA template. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[28]  P. Hanawalt,et al.  Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene , 1987, Cell.