Mapping RNA exit channel on transcribing RNA polymerase II by FRET analysis.
A simple genetic tag-based labeling method that permits specific attachment of a fluorescence probe near the C terminus of virtually any subunit of a protein complex is implemented. Its immediate application to yeast RNA polymerase II (pol II) enables us to test various hypotheses of RNA exit channel by using fluorescence resonance energy transfer (FRET) analysis. The donor dye is labeled on a site near subunit Rpb3 or Rpb4, and the acceptor dye is attached to the 5' end of RNA transcript in the pol II elongation complex. Both in-gel and single-molecule FRET analysis show that the growing RNA is leading toward Rpb4, not Rpb3, supporting the notion that RNA exits through the proposed channel 1. Distance constraints derived from our FRET results, in conjunction with triangulation, reveal the exit track of RNA transcript on core pol II by identifying amino acids in the vicinity of the 5' end of RNA and show that the extending RNA forms contacts with the Rpb7 subunit. The significance of RNA exit route in promoter escape and that in cotranscriptional mRNA processing is discussed.
Chen
Chin-Yu
CY
Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.
Chang
Chia-Chi
CC
Yen
Chi-Fu
CF
Chiu
Michael T-K
MT
Chang
Wei-Hau
WH
D031541:Fluorescence Resonance Energy Transfer; D005456:Fluorescent Dyes; D015336:Molecular Probe Techniques; D012319:RNA Polymerase II / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D014158:Transcription, Genetic
D005456:Fluorescent Dyes; D029701:Saccharomyces cerevisiae Proteins; D012319:RNA Polymerase II; C423309:RPB4 protein, S cerevisiae; C470553:RPB7 protein, S cerevisiae