Interactions between RNA polymerase and the "core recognition element" counteract pausing

• Published in: Science (American Association for the Advancement of Science) Vol. 344; no. 6189; pp. 1285 - 1289
• Main Authors: Vvedenskaya, Irina O., Vahedian-Movahed, Hanif, Bird, Jeremy G., Knoblauch, Jared G., Goldman, Seth R., Zhang, Yu, Ebright, Richard H., Nickels, Bryce E.
• Format: Journal Article
• Language: English
• Published: United States American Association for the Advancement of Science 13.06.2014; The American Association for the Advancement of Science
• Subjects: Deoxyribonucleic acid; DNA; DNA-Directed RNA Polymerases - chemistry; DNA-Directed RNA Polymerases - genetics; DNA-Directed RNA Polymerases - metabolism; E coli; Epidemiology; Escherichia coli; Escherichia coli - genetics; Fungal infections; Gene expression; Gene Expression Regulation, Bacterial; Genes; Genome, Bacterial - genetics; Genomes; Genomics; Infectious diseases; Metapopulation ecology; Molecular biology; Nucleotides; Parasite hosts; Pathogens; Phosphoric Monoester Hydrolases - chemistry; Phosphoric Monoester Hydrolases - metabolism; Polymerase; Recognition; Ribonucleic acids; Ribozymes; RNA; RNA polymerase; Scaffolds; Transcription Elongation, Genetic; Transcription Initiation Site; Transcription Initiation, Genetic; Transcripts (Written Records)
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.1253458

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–10 Y–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.