Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection

Jared T Winkelman; Irina O Vvedenskaya; Yuanchao Zhang; Yu Zhang; Jeremy G Bird; Deanne M Taylor; Richard L Gourse; Richard H Ebright; Bryce E Nickels

doi:10.1126/science.aad6881

Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection

Science. 2016 Mar 4;351(6277):1090-3. doi: 10.1126/science.aad6881.

Authors

Jared T Winkelman¹, Irina O Vvedenskaya², Yuanchao Zhang³, Yu Zhang⁴, Jeremy G Bird⁵, Deanne M Taylor⁶, Richard L Gourse⁷, Richard H Ebright⁸, Bryce E Nickels⁹

Affiliations

¹ 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.
² Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
³ Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
⁴ Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
⁵ 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.
⁶ 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.
⁷ Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53705, USA.
⁸ 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.
⁹ 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.

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.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Bacteria / genetics*
Crystallography, X-Ray
DNA / chemistry
DNA / genetics
Gene Library
Nucleic Acid Conformation
Promoter Regions, Genetic*
RNA, Messenger / biosynthesis*
Transcription Initiation Site*
Transcription Initiation, Genetic*

Substances

RNA, Messenger
DNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding