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

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Science  04 Mar 2016:
Vol. 351, Issue 6277, pp. 1090-1093
DOI: 10.1126/science.aad6881

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Choosing where to start transcription

The RNA polymerase enzyme complex binds to the promoter of a gene and separates the two DNA strands. The subsequently formed “transcription bubble” is required for RNA synthesis to begin. How RNA polymerase chooses the exact DNA base at which it will start transcription has been unclear. Winkelman et al. show that a control element upstream of the start site is involved in helping RNA polymerase make this choice in bacteria. Start site selection involves promoter scrunching, where a stationary RNA polymerase unwinds and pulls DNA through the active site, scrunching the DNA of the transcription bubble.

Science, this issue p. 1090


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 410 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.

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