title: A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting.
abstract: Live-cell imaging has revealed unexpected features of gene expression. Here using improved single-molecule RNA microscopy, we show that synthesis of HIV-1 RNA is achieved by groups of closely spaced polymerases, termed convoys, as opposed to single isolated enzymes. Convoys arise by a Mediator-dependent reinitiation mechanism, which generates a transient but rapid succession of polymerases initiating and escaping the promoter. During elongation, polymerases are spaced by few hundred nucleotides, and physical modelling suggests that DNA torsional stress may maintain polymerase spacing. We additionally observe that the HIV-1 promoter displays stochastic fluctuations on two time scales, which we refer to as multi-scale bursting. Each time scale is regulated independently: Mediator controls minute-scale fluctuation (convoys), while TBP-TATA-box interaction controls sub-hour fluctuations (long permissive/non-permissive periods). A cellular promoter also produces polymerase convoys and displays multi-scale bursting. We propose that slow, TBP-dependent fluctuations are important for phenotypic variability of single cells.
authors.affiliation: Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919, route de Mende, 34293 Montpellier Cedex 5, France.
authors.forename: Katjana
authors.initials: K
authors.lastname: Tantale
authors.affiliation: Unité Imagerie et Modélisation, Département Biologie Cellulaire et Infections, Institut Pasteur and CNRS UMR 3691, 28, rue du Docteur Roux, 75015 Paris, France.
authors.forename: Florian
authors.identifier: 0000-0002-9622-4396
authors.initials: F
authors.lastname: Mueller
authors.affiliation: Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919, route de Mende, 34293 Montpellier Cedex 5, France.
authors.forename: Alja
authors.initials: A
authors.lastname: Kozulic-Pirher
authors.affiliation: Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919, route de Mende, 34293 Montpellier Cedex 5, France.|Laboratoire de Physique Théorique de la Matière Condensée; CNRS UMR 7600, UPMC-Paris 6, Sorbonne Universités, 4 place Jussieu, 75252 Paris Cedex 5, France.
authors.forename: Annick
authors.initials: A
authors.lastname: Lesne
authors.affiliation: Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919, route de Mende, 34293 Montpellier Cedex 5, France.|Laboratoire de Physique Théorique de la Matière Condensée; CNRS UMR 7600, UPMC-Paris 6, Sorbonne Universités, 4 place Jussieu, 75252 Paris Cedex 5, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Victor
authors.affiliation: Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919, route de Mende, 34293 Montpellier Cedex 5, France.
authors.forename: Marie-Cécile
authors.initials: MC
authors.lastname: Robert
authors.affiliation: Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919, route de Mende, 34293 Montpellier Cedex 5, France.
authors.forename: Serena
authors.initials: S
authors.lastname: Capozi
authors.affiliation: Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919, route de Mende, 34293 Montpellier Cedex 5, France.
authors.forename: Racha
authors.initials: R
authors.lastname: Chouaib
authors.affiliation: BioCampus Montpellier, CNRS UMS3426, 141, rue de la Cardonille, 34094 Montpellier Cedex 5, France.
authors.forename: Volker
authors.initials: V
authors.lastname: Bäcker
authors.affiliation: BioCampus Montpellier, CNRS UMS3426, 141, rue de la Cardonille, 34094 Montpellier Cedex 5, France.
authors.forename: Julio
authors.initials: J
authors.lastname: Mateos-Langerak
authors.affiliation: Ecole Normale Supérieure, CNRS UMR 8197 Paris, France.
authors.forename: Xavier
authors.initials: X
authors.lastname: Darzacq
authors.affiliation: Unité Imagerie et Modélisation, Département Biologie Cellulaire et Infections, Institut Pasteur and CNRS UMR 3691, 28, rue du Docteur Roux, 75015 Paris, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Zimmer
authors.affiliation: Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919, route de Mende, 34293 Montpellier Cedex 5, France.
authors.forename: Eugenia
authors.initials: E
authors.lastname: Basyuk
authors.affiliation: Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919, route de Mende, 34293 Montpellier Cedex 5, France.
authors.forename: Edouard
authors.initials: E
authors.lastname: Bertrand
mesh_terms: D001483:Base Sequence; D002470:Cell Survival; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D015696:Gene Products, tat; D015497:HIV-1 / Q000235:genetics; D006367:HeLa Cells; D006801:Humans; D007700:Kinetics; D008954:Models, Biological; D011401:Promoter Regions, Genetic / Q000235:genetics; D012313:RNA / Q000378:metabolism; D000072760:Single Molecule Imaging / Q000379:methods*; D016385:TATA Box / Q000235:genetics; D035181:TATA-Box Binding Protein / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D015696:Gene Products, tat; D035181:TATA-Box Binding Protein; D012313:RNA; D012321:DNA-Directed RNA Polymerases