title: Synergistic action of RNA polymerases in overcoming the nucleosomal barrier.
abstract: During gene expression, RNA polymerase (RNAP) encounters a major barrier at a nucleosome and yet must access the nucleosomal DNA. Previous in vivo evidence has suggested that multiple RNAPs might increase transcription efficiency through nucleosomes. Here we have quantitatively investigated this hypothesis using Escherichia coli RNAP as a model system by directly monitoring its location on the DNA via a single-molecule DNA-unzipping technique. When an RNAP encountered a nucleosome, it paused with a distinctive 10-base pair periodicity and backtracked by approximately 10-15 base pairs. When two RNAPs elongate in close proximity, the trailing RNAP apparently assists in the leading RNAP's elongation, reducing its backtracking and enhancing its transcription through a nucleosome by a factor of 5. Taken together, our data indicate that histone-DNA interactions dictate RNAP pausing behavior, and alleviation of nucleosome-induced backtracking by multiple polymerases may prove to be a mechanism for overcoming the nucleosomal barrier in vivo.
authors.affiliation: Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: Jin
authors.forename: Lu
authors.initials: L
authors.lastname: Bai
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Johnson
authors.forename: Robert M
authors.initials: RM
authors.lastname: Fulbright
authors.forename: Maria L
authors.initials: ML
authors.lastname: Kireeva
authors.forename: Mikhail
authors.initials: M
authors.lastname: Kashlev
authors.forename: Michelle D
authors.initials: MD
authors.lastname: Wang
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D008954:Models, Biological; D009707:Nucleosomes / Q000378:metabolism*; D012319:RNA Polymerase II / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D006657:Histones; D009707:Nucleosomes; D012319:RNA Polymerase II; D012321:DNA-Directed RNA Polymerases
references.citation: J Biol Chem. 2003 Jun 27;278(26):24189-99
references.pmid: 12692127
references.citation: Trends Biochem Sci. 2000 Aug;25(8):375-80
references.pmid: 10916156
references.citation: J Biol Chem. 2003 Sep 19;278(38):36148-56
references.pmid: 12851391
references.citation: Proc Natl Acad Sci U S A. 1995 Feb 28;92(5):1739-43
references.pmid: 7878051
references.citation: Annu Rev Biochem. 2001;70:81-120
references.pmid: 11395403
references.citation: Mol Cell. 2005 Mar 18;17(6):831-40
references.pmid: 15780939
references.citation: Science. 1998 Oct 30;282(5390):902-7
references.pmid: 9794753
references.citation: Biophys J. 2004 Dec;87(6):3945-53
references.pmid: 15465875
references.citation: Biochemistry. 1997 Oct 7;36(40):12371-82
references.pmid: 9315878
references.citation: Trends Biochem Sci. 2000 Jan;25(1):15-9
references.pmid: 10637607
references.citation: Proc Natl Acad Sci U S A. 1990 Aug;87(15):5724-8
references.pmid: 2377610
references.citation: Mol Cell. 2005 Dec 9;20(5):771-81
references.pmid: 16337600
references.citation: Nat Struct Mol Biol. 2006 Jun;13(6):549-54
references.pmid: 16732285
references.citation: Cell. 1994 Jun 3;77(5):749-59
references.pmid: 8205623
references.citation: Science. 2008 Mar 28;319(5871):1791-2
references.pmid: 18369138
references.citation: Nat Struct Mol Biol. 2009 Feb;16(2):124-9
references.pmid: 19136959
references.citation: Nat Genet. 1995 Feb;9(2):184-90
references.pmid: 7719347
references.citation: Nat Genet. 2004 Aug;36(8):900-5
references.pmid: 15247917
references.citation: J Mol Biol. 2001 Apr 6;307(4):977-85
references.pmid: 11286549
references.citation: Mol Cell Biol. 2003 Mar;23(6):1961-7
references.pmid: 12612070
references.citation: Science. 2003 May 2;300(5620):801-5
references.pmid: 12730602
references.citation: Nat Rev Mol Cell Biol. 2006 Aug;7(8):557-67
references.pmid: 16936696
references.citation: Genes Dev. 1991 Apr;5(4):683-96
references.pmid: 2010092
references.citation: Nature. 2000 Sep 28;407(6803):471-5
references.pmid: 11028991
references.citation: Proc Natl Acad Sci U S A. 1995 May 9;92(10):4596-600
references.pmid: 7538676
references.citation: Cell. 1995 Oct 6;83(1):19-27
references.pmid: 7553869
references.citation: Science. 1998 Jul 17;281(5375):424-8
references.pmid: 9665887
references.citation: Mol Cell. 2009 Jul 31;35(2):191-205
references.pmid: 19647516
references.citation: Biochem Biophys Res Commun. 2007 Jun 29;358(2):666-71
references.pmid: 17498649
references.citation: Nucleic Acids Res. 1998 Feb 15;26(4):1051-5
references.pmid: 9461467
references.citation: Phys Rev Lett. 2007 Feb 9;98(6):068103
references.pmid: 17358986
references.citation: Nature. 2005 Aug 11;436(7052):876-80
references.pmid: 15988478
references.citation: Nat Struct Mol Biol. 2007 Sep;14(9):796-806
references.pmid: 17676063
references.citation: Mol Cell. 2002 Mar;9(3):541-52
references.pmid: 11931762
references.citation: Biophys J. 2002 Aug;83(2):1098-105
references.pmid: 12124289
references.citation: Science. 2003 Aug 22;301(5636):1090-3
references.pmid: 12934006
references.citation: J Mol Biol. 2000 Dec 15;304(5):687-98
references.pmid: 11124018
references.citation: J Biol Chem. 1996 Sep 20;271(38):23495-505
references.pmid: 8798558
references.citation: Mol Cell Biol. 1992 Sep;12(9):4142-52
references.pmid: 1508210
references.citation: J Mol Biol. 1998 Feb 13;276(1):19-42
references.pmid: 9514715
references.citation: Science. 1997 Dec 12;278(5345):1960-3
references.pmid: 9395401
references.citation: Science. 2000 Jul 28;289(5479):619-25
references.pmid: 10915625
references.citation: Mol Cell Biol. 1993 Jun;13(6):3456-63
references.pmid: 8497261
references.citation: EMBO J. 2003 Sep 15;22(18):4719-27
references.pmid: 12970184
references.citation: Mol Cell Biol. 2007 Oct;27(20):6987-95
references.pmid: 17709398
references.citation: J Biol Chem. 2008 Nov 21;283(47):32236-43
references.pmid: 18815126
references.citation: Nat Struct Mol Biol. 2009 Dec;16(12):1272-8
references.pmid: 19935686
references.citation: Science. 2009 Jul 31;325(5940):626-8
references.pmid: 19644123
references.citation: Mol Cell. 2006 Nov 3;24(3):469-79
references.pmid: 17081995
references.citation: Nature. 1997 Sep 18;389(6648):251-60
references.pmid: 9305837
references.citation: Nature. 2007 Apr 12;446(7137):820-3
references.pmid: 17361130
references.citation: J Biol Chem. 1998 Aug 28;273(35):22595-605
references.pmid: 9712888
references.citation: J Mol Biol. 2004 Nov 19;344(2):335-49
references.pmid: 15522289
references.citation: Curr Opin Microbiol. 2001 Apr;4(2):119-25
references.pmid: 11282465
references.citation: Mol Cell. 2005 Apr 1;18(1):97-108
references.pmid: 15808512
references.citation: EMBO J. 1992 Sep;11(9):3307-14
references.pmid: 1505520
references.citation: Nature. 2003 Dec 11;426(6967):684-7
references.pmid: 14634670