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

Research paper by Jared T JT Winkelman, Irina O IO Vvedenskaya, Yuanchao Y Zhang, Yu Y Zhang, Jeremy G JG Bird, Deanne M DM Taylor, Richard L RL Gourse, Richard H RH Ebright, Bryce E BE Nickels

Indexed on: 05 Mar '16Published on: 05 Mar '16Published in: Science



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.