title: Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics.
abstract: Transcription factors IIS (TFIIS) and IIF (TFIIF) are known to stimulate transcription elongation. Here, we use a single-molecule transcription elongation assay to study the effects of both factors. We find that these transcription factors enhance overall transcription elongation by reducing the lifetime of transcriptional pauses and that TFIIF also decreases the probability of pause entry. Furthermore, we observe that both factors enhance the processivity of RNA polymerase II through the nucleosomal barrier. The effects of TFIIS and TFIIF are quantitatively described using the linear Brownian ratchet kinetic model for transcription elongation and the backtracking model for transcriptional pauses, modified to account for the effects of the transcription factors. Our findings help elucidate the molecular mechanisms by which transcription factors modulate gene expression.
authors.affiliation: Jason L. Choy Laboratory of Single-Molecule Biophysics, California Institute for Quantitative Biosciences, Kavli Energy NanoSciences Institute, Department of Chemistry, Department of Physics, Howard Hughes Medical Institute, and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.
authors.forename: Toyotaka
authors.initials: T
authors.lastname: Ishibashi
authors.forename: Manchuta
authors.initials: M
authors.lastname: Dangkulwanich
authors.forename: Yves
authors.initials: Y
authors.lastname: Coello
authors.forename: Troy A
authors.initials: TA
authors.lastname: Lionberger
authors.forename: Lucyna
authors.initials: L
authors.lastname: Lubkowska
authors.forename: Alfred S
authors.initials: AS
authors.lastname: Ponticelli
authors.forename: Mikhail
authors.initials: M
authors.lastname: Kashlev
authors.forename: Carlos
authors.initials: C
authors.lastname: Bustamante
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli; D005786:Gene Expression Regulation / Q000235:genetics / Q000502:physiology*; D007700:Kinetics; D009010:Monte Carlo Method; D052898:Optical Tweezers; D012333:RNA, Messenger / Q000096:biosynthesis*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000502:physiology*; D061805:Transcription Elongation, Genetic / Q000502:physiology*; D019473:Transcription Factors, TFII / Q000378:metabolism*; D035602:Transcriptional Elongation Factors / Q000378:metabolism*
chemical_list: D012333:RNA, Messenger; D019473:Transcription Factors, TFII; D035602:Transcriptional Elongation Factors; C018648:transcription factor S-II; D012321:DNA-Directed RNA Polymerases; C056604:transcription factor TFIIF
keywords: Pol II; enzyme kinetics; optical tweezers; yeast