메뉴 건너뛰기




Volumn 111, Issue 1, 2014, Pages 349-354

Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors

Author keywords

J factor; Promoter enhancer; TPM

Indexed keywords

BACTERIAL DNA; LAMBDA CI REPRESSOR PROTEIN; REPRESSOR PROTEIN; TISSUE FACTOR PATHWAY INHIBITOR; UNCLASSIFIED DRUG;

EID: 84891933858     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1317817111     Document Type: Article
Times cited : (44)

References (39)
  • 1
    • 0022447855 scopus 로고
    • Gene regulation by proteins acting nearby and at a distance
    • Ptashne M (1986) Gene regulation by proteins acting nearby and at a distance. Nature 322(6081): 697-701.
    • (1986) Nature , vol.322 , Issue.6081 , pp. 697-701
    • Ptashne, M.1
  • 2
    • 0026522733 scopus 로고
    • DNA looping
    • Matthews KS (1992) DNA looping. Microbiol Rev 56(1): 123-136.
    • (1992) Microbiol Rev , vol.56 , Issue.1 , pp. 123-136
    • Matthews, K.S.1
  • 3
    • 77149139820 scopus 로고    scopus 로고
    • Enhancers: The abundance and function of regulatory sequences beyond promoters
    • Bulger M, Groudine M (2010) Enhancers: The abundance and function of regulatory sequences beyond promoters. Dev Biol 339(2): 250-257.
    • (2010) Dev Biol , vol.339 , Issue.2 , pp. 250-257
    • Bulger, M.1    Groudine, M.2
  • 4
    • 84876838711 scopus 로고    scopus 로고
    • The hierarchy of the 3D genome
    • Gibcus JH, Dekker J (2013) The hierarchy of the 3D genome. Mol Cell 49(5): 773-782.
    • (2013) Mol Cell , vol.49 , Issue.5 , pp. 773-782
    • Gibcus, J.H.1    Dekker, J.2
  • 5
    • 0035668536 scopus 로고    scopus 로고
    • Makingcontactsona nucleic acidpolymer
    • Rippe K (2001)Makingcontactsona nucleic acidpolymer. Trends BiochemSci 26(12): 733-740.
    • (2001) Trends BiochemSci , vol.26 , Issue.12 , pp. 733-740
    • Rippe, K.1
  • 6
    • 0042622638 scopus 로고    scopus 로고
    • DNA looping and physical constraints on transcription regulation
    • Vilar JM, Leibler S (2003) DNA looping and physical constraints on transcription regulation. J Mol Biol 331(5): 981-989.
    • (2003) J Mol Biol , vol.331 , Issue.5 , pp. 981-989
    • Vilar, J.M.1    Leibler, S.2
  • 7
    • 1042278041 scopus 로고    scopus 로고
    • Cooperativity in long-range gene regulation by the lambda CI repressor
    • Dodd IB, et al. (2004) Cooperativity in long-range gene regulation by the lambda CI repressor. Genes Dev 18(3): 344-354.
    • (2004) Genes Dev , vol.18 , Issue.3 , pp. 344-354
    • Dodd, I.B.1
  • 8
    • 34547852967 scopus 로고    scopus 로고
    • Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping
    • Zhang Y, McEwen AE, Crothers DM, Levene SD (2006) Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping. PLoS ONE 1:e136.
    • (2006) PLoS ONE , vol.1
    • Zhang, Y.1    McEwen, A.E.2    Crothers, D.M.3    Levene, S.D.4
  • 9
    • 66249118030 scopus 로고    scopus 로고
    • Concentration and length dependence of DNA looping in transcriptional regulation
    • Han L, et al. (2009) Concentration and length dependence of DNA looping in transcriptional regulation. PLoS ONE 4(5):e5621.
    • (2009) PLoS ONE , vol.4 , Issue.5
    • Han, L.1
  • 10
    • 84863969022 scopus 로고    scopus 로고
    • Galactose repressor mediated intersegmental chromosomal connections in Escherichia coli
    • Qian Z, Dimitriadis EK, Edgar R, Eswaramoorthy P, Adhya S (2012) Galactose repressor mediated intersegmental chromosomal connections in Escherichia coli. Proc Natl Acad Sci USA 109(28): 11336-11341.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.28 , pp. 11336-11341
    • Qian, Z.1    Dimitriadis, E.K.2    Edgar, R.3    Eswaramoorthy, P.4    Adhya, S.5
  • 11
    • 84880242640 scopus 로고    scopus 로고
    • Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription
    • Cagliero C, Grand RS, Jones MB, Jin DJ, O'Sullivan JM (2013) Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription. Nucleic Acids Res 41(12): 6058-6071.
    • (2013) Nucleic Acids Res , vol.41 , Issue.12 , pp. 6058-6071
    • Cagliero, C.1    Grand, R.S.2    Jones, M.B.3    Jin, D.J.4    O'Sullivan, J.M.5
  • 12
    • 0033485539 scopus 로고    scopus 로고
    • Quantitative comparison of DNA looping in vitro and in vivo: Chromatin increases effective DNA flexibility at short distances
    • Ringrose L, Chabanis S, Angrand PO, Woodroofe C, Stewart AF (1999) Quantitative comparison of DNA looping in vitro and in vivo: Chromatin increases effective DNA flexibility at short distances. EMBO J 18(23): 6630-6641.
    • (1999) EMBO J , vol.18 , Issue.23 , pp. 6630-6641
    • Ringrose, L.1    Chabanis, S.2    Angrand, P.O.3    Woodroofe, C.4    Stewart, A.F.5
  • 13
    • 18444412915 scopus 로고    scopus 로고
    • Measuring chromosome dynamics on different time scales using resolvases with varying half-lives
    • Stein RA, Deng S, Higgins NP (2005) Measuring chromosome dynamics on different time scales using resolvases with varying half-lives. Mol Microbiol 56(4): 1049-1061.
    • (2005) Mol Microbiol , vol.56 , Issue.4 , pp. 1049-1061
    • Stein, R.A.1    Deng, S.2    Higgins, N.P.3
  • 14
    • 0001191247 scopus 로고
    • DNA flexibility studied by covalent closure of short fragments into circles
    • Shore D, Langowski J, Baldwin RL (1981) DNA flexibility studied by covalent closure of short fragments into circles. Proc Natl Acad Sci USA 78(8): 4833-4837.
    • (1981) Proc Natl Acad Sci USA , vol.78 , Issue.8 , pp. 4833-4837
    • Shore, D.1    Langowski, J.2    Baldwin, R.L.3
  • 15
    • 84867327654 scopus 로고    scopus 로고
    • Measurements of DNA-loop formation via Cre-mediated recombination
    • Shoura MJ, et al. (2012) Measurements of DNA-loop formation via Cre-mediated recombination. Nucleic Acids Res 40(15): 7452-7464.
    • (2012) Nucleic Acids Res , vol.40 , Issue.15 , pp. 7452-7464
    • Shoura, M.J.1
  • 16
    • 0023665179 scopus 로고
    • Influence of sequence and distance between two operators on interaction with the lac repressor
    • Hsieh WT, Whitson PA, Matthews KS, Wells RD (1987) Influence of sequence and distance between two operators on interaction with the lac repressor. J Biol Chem 262(30): 14583-14591.
    • (1987) J Biol Chem , vol.262 , Issue.30 , pp. 14583-14591
    • Hsieh, W.T.1    Whitson, P.A.2    Matthews, K.S.3    Wells, R.D.4
  • 17
    • 66249111861 scopus 로고    scopus 로고
    • Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor
    • Zurla C, et al. (2009) Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor. Nucleic Acids Res 37(9): 2789-2795.
    • (2009) Nucleic Acids Res , vol.37 , Issue.9 , pp. 2789-2795
    • Zurla, C.1
  • 18
    • 0022529619 scopus 로고
    • Upstream operators enhance repression of the lac promoter
    • Mossing MC, Record MT, Jr. (1986) Upstream operators enhance repression of the lac promoter. Science 233(4766): 889-892.
    • (1986) Science , vol.233 , Issue.4766 , pp. 889-892
    • Mossing, M.C.1    Record Jr., M.T.2
  • 19
    • 15744393452 scopus 로고    scopus 로고
    • DNA looping in gene regulation: From the assembly of macromolecular complexes to the control of transcriptional noise
    • Vilar JM, Saiz L (2005) DNA looping in gene regulation: From the assembly of macromolecular complexes to the control of transcriptional noise. CurrOpinGenet Dev 15(2): 136-144.
    • (2005) CurrOpinGenet Dev , vol.15 , Issue.2 , pp. 136-144
    • Vilar, J.M.1    Saiz, L.2
  • 20
    • 84879335479 scopus 로고    scopus 로고
    • Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. Coli cells
    • Hensel Z, Weng X, Lagda AC, Xiao J (2013) Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells. PLoS Biol 11(6):e1001591.
    • (2013) PLoS Biol , vol.11 , Issue.6
    • Hensel, Z.1    Weng, X.2    Lagda, A.C.3    Xiao, J.4
  • 21
    • 0029975889 scopus 로고    scopus 로고
    • Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator
    • Müller J, Oehler S, Müller-Hill B (1996) Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator. J Mol Biol 257(1): 21-29.
    • (1996) J Mol Biol , vol.257 , Issue.1 , pp. 21-29
    • Müller, J.1    Oehler, S.2    Müller-Hill, B.3
  • 22
    • 0028365289 scopus 로고
    • Quality and position of the three lac operators of E. Coli define efficiency of repression
    • Oehler S, Amouyal M, Kolkhof P, von Wilcken-Bergmann B, Müller-Hill B (1994) Quality and position of the three lac operators of E. coli define efficiency of repression. EMBO J 13(14): 3348-3355.
    • (1994) EMBO J , vol.13 , Issue.14 , pp. 3348-3355
    • Oehler, S.1    Amouyal, M.2    Kolkhof, P.3    Von Wilcken-Bergmann, B.4    Müller-Hill, B.5
  • 23
    • 84874247898 scopus 로고    scopus 로고
    • Enhancer-like long-range transcriptional activation by λ CI-mediated DNA looping
    • Cui L, Murchland I, Shearwin KE, Dodd IB (2013) Enhancer-like long-range transcriptional activation by λ CI-mediated DNA looping. Proc Natl Acad Sci USA 110(8): 2922-2927.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.8 , pp. 2922-2927
    • Cui, L.1    Murchland, I.2    Shearwin, K.E.3    Dodd, I.B.4
  • 24
    • 80053596134 scopus 로고    scopus 로고
    • Mechanism of transcriptional repression at a bacterial promoter by analysis of singlemolecules
    • Sanchez A,OsborneML, Friedman LJ, Kondev J, Gelles J (2011)Mechanism of transcriptional repression at a bacterial promoter by analysis of singlemolecules. EMBOJ 30(19): 3940-3946.
    • (2011) EMBOJ , vol.30 , Issue.19 , pp. 3940-3946
    • Sanchez, A.1    Osborne, M.L.2    Friedman, L.J.3    Kondev, J.4    Gelles, J.5
  • 25
    • 79959994529 scopus 로고    scopus 로고
    • Quantitative dissection of the simple repression inputoutput function
    • Garcia HG, Phillips R (2011) Quantitative dissection of the simple repression inputoutput function. Proc Natl Acad Sci USA 108(29): 12173-12178.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.29 , pp. 12173-12178
    • Garcia, H.G.1    Phillips, R.2
  • 26
    • 84870573112 scopus 로고    scopus 로고
    • Sequence dependence of transcription factormediated DNA looping
    • Johnson S, Lindén M, Phillips R (2012) Sequence dependence of transcription factormediated DNA looping. Nucleic Acids Res 40(16): 7728-7738.
    • (2012) Nucleic Acids Res , vol.40 , Issue.16 , pp. 7728-7738
    • Johnson, S.1    Lindén, M.2    Phillips, R.3
  • 27
    • 0035890132 scopus 로고    scopus 로고
    • Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny
    • Dodd IB, Perkins AJ, Tsemitsidis D, Egan JB (2001) Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny. Genes Dev 15(22): 3013-3022.
    • (2001) Genes Dev , vol.15 , Issue.22 , pp. 3013-3022
    • Dodd, I.B.1    Perkins, A.J.2    Tsemitsidis, D.3    Egan, J.B.4
  • 28
    • 0030660412 scopus 로고    scopus 로고
    • Linkage between operator binding and dimer to octamer self-assembly of bacteriophage lambda cI repressor
    • Rusinova E, Ross JB, Laue TM, Sowers LC, Senear DF (1997) Linkage between operator binding and dimer to octamer self-assembly of bacteriophage lambda cI repressor. Biochemistry 36(42): 12994-13003.
    • (1997) Biochemistry , vol.36 , Issue.42 , pp. 12994-13003
    • Rusinova, E.1    Ross, J.B.2    Laue, T.M.3    Sowers, L.C.4    Senear, D.F.5
  • 29
    • 0027278788 scopus 로고
    • The primary self-assembly reaction of bacteriophage lambda cI repressor dimers is to octamer
    • Senear DF, et al. (1993) The primary self-assembly reaction of bacteriophage lambda cI repressor dimers is to octamer. Biochemistry 32(24): 6179-6189.
    • (1993) Biochemistry , vol.32 , Issue.24 , pp. 6179-6189
    • Senear, D.F.1
  • 30
    • 0346750971 scopus 로고    scopus 로고
    • Single-molecule studies of DNA architectural changes induced by regulatory proteins
    • Finzi L, Dunlap D (2003) Single-molecule studies of DNA architectural changes induced by regulatory proteins. Methods Enzymol 370: 369-378.
    • (2003) Methods Enzymol , vol.370 , pp. 369-378
    • Finzi, L.1    Dunlap, D.2
  • 31
    • 33748780364 scopus 로고    scopus 로고
    • Tethered particle motion as a diagnostic of DNA tether length
    • Nelson PC, et al. (2006) Tethered particle motion as a diagnostic of DNA tether length. J Phys Chem B 110(34): 17260-17267.
    • (2006) J Phys Chem B , vol.110 , Issue.34 , pp. 17260-17267
    • Nelson, P.C.1
  • 33
    • 34547642985 scopus 로고    scopus 로고
    • Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli
    • Becker NA, Kahn JD, Maher LJ, 3rd (2007) Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli. Nucleic Acids Res 35(12): 3988-4000.
    • (2007) Nucleic Acids Res , vol.35 , Issue.12 , pp. 3988-4000
    • Becker, N.A.1    Kahn, J.D.2    Maher III, L.J.3
  • 34
    • 50249126024 scopus 로고    scopus 로고
    • Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations
    • Czapla L, Swigon D, Olson WK (2008) Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations. J Mol Biol 382(2): 353-370.
    • (2008) J Mol Biol , vol.382 , Issue.2 , pp. 353-370
    • Czapla, L.1    Swigon, D.2    Olson, W.K.3
  • 35
    • 76949089832 scopus 로고    scopus 로고
    • Bacterial nucleoid-associated proteins, nucleoid structure and gene expression
    • Dillon SC, Dorman CJ (2010) Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 8(3): 185-195.
    • (2010) Nat Rev Microbiol , vol.8 , Issue.3 , pp. 185-195
    • Dillon, S.C.1    Dorman, C.J.2
  • 36
    • 84875385003 scopus 로고    scopus 로고
    • Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations
    • Olson WK, Grosner MA, Czapla L, Swigon D (2013) Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations. Biochem Soc Trans 41(2): 559-564.
    • (2013) Biochem Soc Trans , vol.41 , Issue.2 , pp. 559-564
    • Olson, W.K.1    Grosner, M.A.2    Czapla, L.3    Swigon, D.4
  • 37
    • 0033580635 scopus 로고    scopus 로고
    • Thermodynamic analysis of unfolding and dissociation in lactose repressor protein
    • Barry JK, Matthews KS (1999) Thermodynamic analysis of unfolding and dissociation in lactose repressor protein. Biochemistry 38(20): 6520-6528.
    • (1999) Biochemistry , vol.38 , Issue.20 , pp. 6520-6528
    • Barry, J.K.1    Matthews, K.S.2
  • 38
    • 0035140806 scopus 로고    scopus 로고
    • High local protein concentrations at promoters: Strategies in prokaryotic and eukaryotic cells
    • Dröge P, Müller-Hill B (2001) High local protein concentrations at promoters: Strategies in prokaryotic and eukaryotic cells. Bioessays 23(2): 179-183.
    • (2001) Bioessays , vol.23 , Issue.2 , pp. 179-183
    • Dröge, P.1    Müller-Hill, B.2
  • 39
    • 84884645140 scopus 로고    scopus 로고
    • One-step cloning and chromosomal integration of DNA
    • St-Pierre F, et al. (2013) One-step cloning and chromosomal integration of DNA. ACS Synth Biol 2(9): 537-541.
    • (2013) ACS Synth Biol , vol.2 , Issue.9 , pp. 537-541
    • St-Pierre, F.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.