title: Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection.
abstract: In bacterial transcription initiation, RNA polymerase (RNAP) selects a transcription start site (TSS) at variable distances downstream of core promoter elements. Using next-generation sequencing and unnatural amino acid-mediated protein-DNA cross-linking, we have determined, for a library of 4(10) promoter sequences, the TSS, the RNAP leading-edge position, and the RNAP trailing-edge position. We find that a promoter element upstream of the TSS, the "discriminator," participates in TSS selection, and that, as the TSS changes, the RNAP leading-edge position changes, but the RNAP trailing-edge position does not change. Changes in the RNAP leading-edge position, but not the RNAP trailing-edge position, are a defining hallmark of the "DNA scrunching" that occurs concurrent with RNA synthesis in initial transcription. We propose that TSS selection involves DNA scrunching prior to RNA synthesis.
authors.affiliation: Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA. Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53705, USA.
authors.forename: Jared T
authors.initials: JT
authors.lastname: Winkelman
authors.affiliation: Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Irina O
authors.initials: IO
authors.lastname: Vvedenskaya
authors.affiliation: Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors.forename: Yuanchao
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Jeremy G
authors.initials: JG
authors.lastname: Bird
authors.affiliation: Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. Department of Obstetrics, Gynecology and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA.
authors.forename: Deanne M
authors.initials: DM
authors.lastname: Taylor
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53705, USA.
authors.forename: Richard L
authors.initials: RL
authors.lastname: Gourse
authors.affiliation: Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA. bnickels@waksman.rutgers.edu ebright@waksman.rutgers.edu.
authors.forename: Richard H
authors.initials: RH
authors.lastname: Ebright
authors.affiliation: Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA. bnickels@waksman.rutgers.edu ebright@waksman.rutgers.edu.
authors.forename: Bryce E
authors.initials: BE
authors.lastname: Nickels
mesh_terms: D001419:Bacteria / Q000235:genetics*; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry / Q000235:genetics; D015723:Gene Library; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000096:biosynthesis*; D024363:Transcription Initiation Site; D061785:Transcription Initiation, Genetic
chemical_list: D012333:RNA, Messenger; D004247:DNA