title: RNA polymerase II senses obstruction in the DNA minor groove via a conserved sensor motif.
abstract: RNA polymerase II (pol II) encounters numerous barriers during transcription elongation, including DNA strand breaks, DNA lesions, and nucleosomes. Pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA with programmable sequence specificity and high affinity. Previous studies suggest that Py-Im polyamides can prevent transcription factor binding, as well as interfere with pol II transcription elongation. However, the mechanism of pol II inhibition by Py-Im polyamides is unclear. Here we investigate the mechanism of how these minor-groove binders affect pol II transcription elongation. In the presence of site-specifically bound Py-Im polyamides, we find that the pol II elongation complex becomes arrested immediately upstream of the targeted DNA sequence, and is not rescued by transcription factor IIS, which is in contrast to pol II blockage by a nucleosome barrier. Further analysis reveals that two conserved pol II residues in the Switch 1 region contribute to pol II stalling. Our study suggests this motif in pol II can sense the structural changes of the DNA minor groove and can be considered a "minor groove sensor." Prolonged interference of transcription elongation by sequence-specific minor groove binders may present opportunities to target transcription addiction for cancer therapy.
authors: Department of Cellular and Molecular Medicine, School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093.
authors: Liang
authors: L
authors: Xu
authors: Department of Cellular and Molecular Medicine, School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093.
authors: Wei
authors: W
authors: Wang
authors: Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702.
authors: Deanna
authors: D
authors: Gotte
authors: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125.
authors: Fei
authors: F
authors: Yang
authors: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125.
authors: Alissa A
authors: AA
authors: Hare
authors: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125.
authors: Timothy R
authors: TR
authors: Welch
authors: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125.
authors: Benjamin C
authors: BC
authors: Li
authors: Department of Cellular and Molecular Medicine, School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093.
authors: Ji Hyun
authors: JH
authors: Shin
authors: Department of Cellular and Molecular Medicine, School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093.
authors: Jenny
authors: J
authors: Chong
authors: Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702; strathej@mail.nih.gov dervan@caltech.edu dongwang@ucsd.edu.
authors: Jeffrey N
authors: JN
authors: Strathern
authors: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 strathej@mail.nih.gov dervan@caltech.edu dongwang@ucsd.edu.
authors: Peter B
authors: PB
authors: Dervan
authors: Department of Cellular and Molecular Medicine, School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093; strathej@mail.nih.gov dervan@caltech.edu dongwang@ucsd.edu.
authors: Dong
authors: D
authors: Wang
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D007093:Imidazoles / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009757:Nylons / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D011485:Protein Binding / Q000187:drug effects; D000072417:Protein Domains; D011758:Pyrroles / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D012319:RNA Polymerase II / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D014158:Transcription, Genetic / Q000187:drug effects / Q000235:genetics*
chemical_list: D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; D029701:Saccharomyces cerevisiae Proteins; C029899:imidazole; D004247:DNA; D012319:RNA Polymerase II; C511736:RPB1 protein, S cerevisiae
keywords: DNA; Py-Im polyamide; minor groove; transcription inhibition