title: Interactions between RNA polymerase and the "core recognition element" counteract pausing.
abstract: 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.
authors.affiliation: Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Irina O
authors.initials: IO
authors.lastname: Vvedenskaya
authors.affiliation: Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Hanif
authors.initials: H
authors.lastname: Vahedian-Movahed
authors.affiliation: Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA. Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Jeremy G
authors.initials: JG
authors.lastname: Bird
authors.affiliation: Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Jared G
authors.initials: JG
authors.lastname: Knoblauch
authors.affiliation: Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Seth R
authors.initials: SR
authors.lastname: Goldman
authors.affiliation: Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA. bnickels@waksman.rutgers.edu ebright@waksman.rutgers.edu.
authors.forename: Richard H
authors.initials: RH
authors.lastname: Ebright
authors.affiliation: Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA. bnickels@waksman.rutgers.edu ebright@waksman.rutgers.edu.
authors.forename: Bryce E
authors.initials: BE
authors.lastname: Nickels
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial / Q000235:genetics; D010744:Phosphoric Monoester Hydrolases / Q000737:chemistry / Q000378:metabolism; D061805:Transcription Elongation, Genetic; D024363:Transcription Initiation Site; D061785:Transcription Initiation, Genetic
chemical_list: D012321:DNA-Directed RNA Polymerases; D010744:Phosphoric Monoester Hydrolases; C024329:3-deoxy-manno-octulosonate-8-phosphatase