Interactions between RNA polymerase and the “core recognition element” counteract pausing

Science  13 Jun 2014:
Vol. 344, Issue 6189, pp. 1285-1289
DOI: 10.1126/science.1253458

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Pausing for control of gene expression

Pausing during gene transcription can play a critical role in gene regulation. Vvedenskaya et al. mapped pause sites across the whole genome in actively growing Escherichia coli (see the Perspective by Roberts). Thousands of undocumented pause sites were identified across well-transcribed genes, allowing the definition of a consensus pause sequence that is dependent on specific interactions of RNA polymerase with the DNA template and nascent RNA transcript.

Science, this issue p. 1285; see also p. 1226


Transcription elongation is interrupted by sequences that inhibit nucleotide addition and cause RNA polymerase (RNAP) to pause. Here, by use of native elongating transcript sequencing (NET-seq) and a variant of NET-seq that enables analysis of mutant RNAP derivatives in merodiploid cells (mNET-seq), we analyze transcriptional pausing genome-wide in vivo in Escherichia coli. We identify a consensus pause-inducing sequence element, G–10Y–1G+1 (where –1 corresponds to the position of the RNA 3′ end). We demonstrate that sequence-specific interactions between RNAP core enzyme and a core recognition element (CRE) that stabilize transcription initiation complexes also occur in transcription elongation complexes and facilitate pause read-through by stabilizing RNAP in a posttranslocated register. Our findings identify key sequence determinants of transcriptional pausing and establish that RNAP-CRE interactions modulate pausing.

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