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  1 / 4598 MEDLINE  
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[PMID]:29219598
[Au] Autor:Brahmachari S; Gunn KH; Giuntoli RD; Mondragón A; Marko JF
[Ad] Endereço:Department of Physics and Astronomy, and Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA.
[Ti] Título:Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices.
[So] Source:Phys Rev Lett;119(18):188103, 2017 Nov 03.
[Is] ISSN:1079-7114
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:We study the statistical-mechanical properties of intertwined double-helical DNAs (DNA braids). In magnetic tweezers experiments, we find that torsionally stressed stretched braids supercoil via an abrupt buckling transition, which is associated with the nucleation of a braid end loop, and that the buckled braid is characterized by a proliferation of multiple domains. Differences between the mechanics of DNA braids and supercoiled single DNAs can be understood as an effect of the increased bulkiness in the structure of the former. The experimental results are in accord with the predictions of a statistical-mechanical model.
[Mh] Termos MeSH primário: DNA Super-Helicoidal/química
Conformação de Ácido Nucleico
[Mh] Termos MeSH secundário: DNA/química
Magnetismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Superhelical); 9007-49-2 (DNA)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180207
[Lr] Data última revisão:
180207
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171209
[St] Status:MEDLINE
[do] DOI:10.1103/PhysRevLett.119.188103


  2 / 4598 MEDLINE  
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[PMID]:28973473
[Au] Autor:Benedetti F; Racko D; Dorier J; Burnier Y; Stasiak A
[Ad] Endereço:Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
[Ti] Título:Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe.
[So] Source:Nucleic Acids Res;45(17):9850-9859, 2017 Sep 29.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The question of how self-interacting chromatin domains in interphase chromosomes are structured and generated dominates current discussions on eukaryotic chromosomes. Numerical simulations using standard polymer models have been helpful in testing the validity of various models of chromosome organization. Experimental contact maps can be compared with simulated contact maps and thus verify how good is the model. With increasing resolution of experimental contact maps, it became apparent though that active processes need to be introduced into models to recapitulate the experimental data. Since transcribing RNA polymerases are very strong molecular motors that induce axial rotation of transcribed DNA, we present here models that include such rotational motors. We also include into our models swivels and sites for intersegmental passages that account for action of DNA topoisomerases releasing torsional stress. Using these elements in our models, we show that transcription-induced supercoiling generated in the regions with divergent-transcription and supercoiling relaxation occurring between these regions are sufficient to explain formation of self-interacting chromatin domains in chromosomes of fission yeast (S. pombe).
[Mh] Termos MeSH primário: DNA Topoisomerases/química
DNA Fúngico/química
DNA Super-Helicoidal/química
RNA Polimerases Dirigidas por DNA/química
Schizosaccharomyces/genética
Transcrição Genética
[Mh] Termos MeSH secundário: Fenômenos Biomecânicos
Cromatina/química
Cromatina/metabolismo
Cromossomos Fúngicos/química
Cromossomos Fúngicos/metabolismo
DNA Topoisomerases/genética
DNA Topoisomerases/metabolismo
DNA Fúngico/genética
DNA Fúngico/metabolismo
DNA Super-Helicoidal/genética
DNA Super-Helicoidal/metabolismo
RNA Polimerases Dirigidas por DNA/genética
RNA Polimerases Dirigidas por DNA/metabolismo
Regulação Fúngica da Expressão Gênica
Simulação de Dinâmica Molecular
Rotação
Schizosaccharomyces/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromatin); 0 (DNA, Fungal); 0 (DNA, Superhelical); EC 2.7.7.6 (DNA-Directed RNA Polymerases); EC 5.99.1.- (DNA Topoisomerases)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171017
[Lr] Data última revisão:
171017
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171004
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx716


  3 / 4598 MEDLINE  
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[PMID]:28934496
[Au] Autor:Ashley RE; Dittmore A; McPherson SA; Turnbough CL; Neuman KC; Osheroff N
[Ad] Endereço:Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.
[Ti] Título:Activities of gyrase and topoisomerase IV on positively supercoiled DNA.
[So] Source:Nucleic Acids Res;45(16):9611-9624, 2017 Sep 19.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Although bacterial gyrase and topoisomerase IV have critical interactions with positively supercoiled DNA, little is known about the actions of these enzymes on overwound substrates. Therefore, the abilities of Bacillus anthracis and Escherichia coli gyrase and topoisomerase IV to relax and cleave positively supercoiled DNA were analyzed. Gyrase removed positive supercoils ∼10-fold more rapidly and more processively than it introduced negative supercoils into relaxed DNA. In time-resolved single-molecule measurements, gyrase relaxed overwound DNA with burst rates of ∼100 supercoils per second (average burst size was 6.2 supercoils). Efficient positive supercoil removal required the GyrA-box, which is necessary for DNA wrapping. Topoisomerase IV also was able to distinguish DNA geometry during strand passage and relaxed positively supercoiled substrates ∼3-fold faster than negatively supercoiled molecules. Gyrase maintained lower levels of cleavage complexes with positively supercoiled (compared with negatively supercoiled) DNA, whereas topoisomerase IV generated similar levels with both substrates. Results indicate that gyrase is better suited than topoisomerase IV to safely remove positive supercoils that accumulate ahead of replication forks. They also suggest that the wrapping mechanism of gyrase may have evolved to promote rapid removal of positive supercoils, rather than induction of negative supercoils.
[Mh] Termos MeSH primário: DNA Girase/metabolismo
DNA Topoisomerase IV/metabolismo
DNA Super-Helicoidal/química
DNA Super-Helicoidal/metabolismo
[Mh] Termos MeSH secundário: Bacillus anthracis/enzimologia
DNA Girase/química
DNA Topoisomerase IV/química
Proteínas de Escherichia coli/química
Proteínas de Escherichia coli/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Superhelical); 0 (Escherichia coli Proteins); EC 5.99.1.- (DNA Topoisomerase IV); EC 5.99.1.3 (DNA Gyrase)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171024
[Lr] Data última revisão:
171024
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170922
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx649


  4 / 4598 MEDLINE  
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[PMID]:28921956
[Au] Autor:Ashley RE; Blower TR; Berger JM; Osheroff N
[Ti] Título:Recognition of DNA Supercoil Geometry by Mycobacterium tuberculosis Gyrase.
[So] Source:Biochemistry;56(40):5440-5448, 2017 Oct 10.
[Is] ISSN:1520-4995
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Mycobacterium tuberculosis encodes only a single type II topoisomerase, gyrase. As a result, this enzyme likely carries out the cellular functions normally performed by canonical gyrase and topoisomerase IV, both in front of and behind the replication fork. In addition, it is the sole target for quinolone antibacterials in this species. Because quinolone-induced DNA strand breaks generated on positively supercoiled DNA ahead of replication forks and transcription complexes are most likely to result in permanent genomic damage, the actions of M. tuberculosis gyrase on positively supercoiled DNA were investigated. Results indicate that the enzyme acts rapidly on overwound DNA and removes positive supercoils much faster than it introduces negative supercoils into relaxed DNA. Canonical gyrase and topoisomerase IV distinguish supercoil handedness differently during the DNA cleavage reaction: while gyrase maintains lower levels of cleavage complexes on overwound DNA, topoisomerase IV maintains similar levels of cleavage complexes on both over- and underwound substrates. M. tuberculosis gyrase maintained lower levels of cleavage complexes on positively supercoiled DNA in the absence and presence of quinolone-based drugs. By retaining this important feature of canonical gyrase, the dual function M. tuberculosis type II enzyme remains a safe enzyme to act in front of replication forks and transcription complexes. Finally, the N-terminal gate region of the enzyme appears to be necessary to distinguish supercoil handedness during DNA cleavage, suggesting that the capture of the transport segment may influence how gyrase maintains cleavage complexes on substrates with different topological states.
[Mh] Termos MeSH primário: DNA Girase/metabolismo
DNA Super-Helicoidal/química
DNA Super-Helicoidal/metabolismo
Mycobacterium tuberculosis/enzimologia
[Mh] Termos MeSH secundário: Clivagem do DNA
DNA Girase/química
Ligação Proteica
Domínios Proteicos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Superhelical); EC 5.99.1.3 (DNA Gyrase)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171019
[Lr] Data última revisão:
171019
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170919
[St] Status:MEDLINE
[do] DOI:10.1021/acs.biochem.7b00681


  5 / 4598 MEDLINE  
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[PMID]:28887044
[Au] Autor:Liu Y; Berrido AM; Hua ZC; Tse-Dinh YC; Leng F
[Ad] Endereço:Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States; Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, United States; School of Life Sciences, Nanjing University, Nanjing 210023, Jiangsu Province, PR China.
[Ti] Título:Biochemical and biophysical properties of positively supercoiled DNA.
[So] Source:Biophys Chem;230:68-73, 2017 Nov.
[Is] ISSN:1873-4200
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:In this paper we successfully developed a procedure to generate the (+) supercoiled (sc) plasmid DNA template pZXX6 in the milligram range. With the availability of the (+) sc DNA, we are able to characterize and compare certain biochemical and biophysical properties of (+) sc, (-) sc, and relaxed (rx) DNA molecules using different techniques, such as UV melting, circular dichroism, and fluorescence spectrometry. Our results show that (+) sc, (-) sc, and rx DNA templates can only be partially melted due to the fact that these DNA templates are closed circular DNA molecules and the two DNA strands cannot be completely separated upon denaturation at high temperatures. We also find that the fluorescence intensity of a DNA-binding dye SYTO12 upon binding to the (-) sc DNA is significantly higher than that of its binding to the (+) sc DNA. This unique property may be used to differentiate the (-) sc DNA from the (+) sc DNA. Additionally, we demonstrate that E. coli topoisomerase I cannot relax the (+) sc DNA. In contrast, E. coli DNA gyrase can efficiently convert the (+) sc DNA to the (-) sc DNA. Furthermore, our dialysis competition assays show that DNA intercalators prefer binding to the (-) sc DNA.
[Mh] Termos MeSH primário: DNA Super-Helicoidal/química
[Mh] Termos MeSH secundário: Dicroísmo Circular
DNA Girase/metabolismo
DNA Topoisomerases Tipo I/metabolismo
DNA Super-Helicoidal/metabolismo
Eletroforese em Gel de Ágar
Escherichia coli/metabolismo
Corantes Fluorescentes/química
Corantes Fluorescentes/metabolismo
Substâncias Intercalantes/química
Substâncias Intercalantes/metabolismo
Desnaturação de Ácido Nucleico/efeitos da radiação
Plasmídeos/genética
Plasmídeos/metabolismo
Espectrometria de Fluorescência
Raios Ultravioleta
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Superhelical); 0 (Fluorescent Dyes); 0 (Intercalating Agents); EC 5.99.1.2 (DNA Topoisomerases, Type I); EC 5.99.1.3 (DNA Gyrase)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171030
[Lr] Data última revisão:
171030
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170910
[St] Status:MEDLINE


  6 / 4598 MEDLINE  
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[PMID]:28842485
[Au] Autor:Kumar R; Nurse P; Bahng S; Lee CM; Marians KJ
[Ad] Endereço:From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065.
[Ti] Título:The MukB-topoisomerase IV interaction is required for proper chromosome compaction.
[So] Source:J Biol Chem;292(41):16921-16932, 2017 Oct 13.
[Is] ISSN:1083-351X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The bacterial condensin MukB and the cellular decatenating enzyme topoisomerase IV interact. This interaction stimulates intramolecular reactions catalyzed by topoisomerase IV, supercoiled DNA relaxation, and DNA knotting but not intermolecular reactions such as decatenation of linked DNAs. We have demonstrated previously that MukB condenses DNA by sequestering negative supercoils and stabilizing topologically isolated loops in the DNA. We show here that the MukB-topoisomerase IV interaction stabilizes MukB on DNA, increasing the extent of DNA condensation without increasing the amount of MukB bound to the DNA. This effect does not require the catalytic activity of topoisomerase IV. Cells carrying a mutant allele that encodes a protein that does not interact with topoisomerase IV exhibit severe nucleoid decompaction leading to chromosome segregation defects. These findings suggest that the MukB-topoisomerase IV complex may provide a scaffold for DNA condensation.
[Mh] Termos MeSH primário: Proteínas Cromossômicas não Histona/química
Cromossomos Bacterianos/química
DNA Topoisomerase IV/química
DNA Bacteriano/química
DNA Super-Helicoidal/química
Proteínas de Escherichia coli/química
Escherichia coli/química
Complexos Multiproteicos/química
[Mh] Termos MeSH secundário: Proteínas Cromossômicas não Histona/genética
Proteínas Cromossômicas não Histona/metabolismo
Cromossomos Bacterianos/genética
Cromossomos Bacterianos/metabolismo
DNA Topoisomerase IV/genética
DNA Topoisomerase IV/metabolismo
DNA Bacteriano/genética
DNA Bacteriano/metabolismo
DNA Super-Helicoidal/genética
DNA Super-Helicoidal/metabolismo
Escherichia coli/genética
Escherichia coli/metabolismo
Proteínas de Escherichia coli/genética
Proteínas de Escherichia coli/metabolismo
Complexos Multiproteicos/genética
Complexos Multiproteicos/metabolismo
Mutação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromosomal Proteins, Non-Histone); 0 (DNA, Bacterial); 0 (DNA, Superhelical); 0 (Escherichia coli Proteins); 0 (MukB protein, E coli); 0 (Multiprotein Complexes); EC 5.99.1.- (DNA Topoisomerase IV)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171019
[Lr] Data última revisão:
171019
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170827
[St] Status:MEDLINE
[do] DOI:10.1074/jbc.M117.803346


  7 / 4598 MEDLINE  
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[PMID]:28842486
[Au] Autor:Kumar R; Grosbart M; Nurse P; Bahng S; Wyman CL; Marians KJ
[Ad] Endereço:From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065 and.
[Ti] Título:The bacterial condensin MukB compacts DNA by sequestering supercoils and stabilizing topologically isolated loops.
[So] Source:J Biol Chem;292(41):16904-16920, 2017 Oct 13.
[Is] ISSN:1083-351X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:MukB is a structural maintenance of chromosome-like protein required for DNA condensation. The complete condensin is a large tripartite complex of MukB, the kleisin, MukF, and an accessory protein, MukE. As found previously, MukB DNA condensation is a stepwise process. We have defined these steps topologically. They proceed first via the formation of negative supercoils that are sequestered by the protein followed by hinge-hinge interactions between MukB dimers that stabilize topologically isolated loops in the DNA. MukB itself is sufficient to mediate both of these topological alterations; neither ATP nor MukEF is required. We show that the MukB hinge region binds DNA and that this region of the protein is involved in sequestration of supercoils. Cells carrying mutations in the MukB hinge that reduce DNA condensation exhibit nucleoid decondensation .
[Mh] Termos MeSH primário: Proteínas Cromossômicas não Histona/química
DNA Bacteriano/química
DNA Super-Helicoidal/química
Proteínas de Escherichia coli/química
Escherichia coli/química
Multimerização Proteica
[Mh] Termos MeSH secundário: Proteínas Cromossômicas não Histona/genética
Proteínas Cromossômicas não Histona/metabolismo
DNA Bacteriano/genética
DNA Bacteriano/metabolismo
DNA Super-Helicoidal/genética
DNA Super-Helicoidal/metabolismo
Escherichia coli/genética
Escherichia coli/metabolismo
Proteínas de Escherichia coli/genética
Proteínas de Escherichia coli/metabolismo
Mutação
Proteínas Repressoras/química
Proteínas Repressoras/genética
Proteínas Repressoras/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromosomal Proteins, Non-Histone); 0 (DNA, Bacterial); 0 (DNA, Superhelical); 0 (Escherichia coli Proteins); 0 (MukB protein, E coli); 0 (Repressor Proteins); 0 (mukE protein, E coli); 0 (mukF protein, E coli)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171019
[Lr] Data última revisão:
171019
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170827
[St] Status:MEDLINE
[do] DOI:10.1074/jbc.M117.803312


  8 / 4598 MEDLINE  
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[PMID]:28756025
[Au] Autor:Li D; Lv B; Wang Q; Liu Y; Zhuge Q
[Ad] Endereço:Key Lab of Forest Genetics and Biotechnology, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China. Electronic address: dwli@njfu.edu.cn.
[Ti] Título:Direct observation of positive supercoils introduced by reverse gyrase through atomic force microscopy.
[So] Source:Bioorg Med Chem Lett;27(17):4086-4090, 2017 09 01.
[Is] ISSN:1464-3405
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Reverse gyrase is a hyperthermophilic enzyme that can introduce positive supercoiling in substrate DNA. It is showed in our studies that positive DNA supercoils were induced in both pBR322 vector and an artificially synthesized mini-plasmid DNA by reverse gyrase. The left-handed structures adopted by positively supercoiled DNA molecules could be identified from their right-handed topoisomers through atomic force microscopic examination. Additional structural comparisons revealed that positively supercoiled DNA molecule AFM images exhibited increased contour lengths. Moreover, enzymatic assays showed that the positively supercoiled DNA could not be cleaved by T7 endonuclease. Together, this suggests that the overwound structure of positive supercoils could prevent genomic duplex DNA from randomly forming single-stranded DNA regions and intra-stranded secondary structures.
[Mh] Termos MeSH primário: DNA Topoisomerases Tipo I/metabolismo
DNA Super-Helicoidal/biossíntese
[Mh] Termos MeSH secundário: DNA Topoisomerases Tipo I/química
DNA Super-Helicoidal/química
Microscopia de Força Atômica
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Superhelical); EC 5.99.1.- (DNA reverse gyrase); EC 5.99.1.2 (DNA Topoisomerases, Type I)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:171125
[Lr] Data última revisão:
171125
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170731
[St] Status:MEDLINE


  9 / 4598 MEDLINE  
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[PMID]:28696257
[Au] Autor:Zhi X; Dages S; Dages K; Liu Y; Hua ZC; Makemson J; Leng F
[Ad] Endereço:From the Biomolecular Sciences Institute and.
[Ti] Título:Transient and dynamic DNA supercoiling potently stimulates the promoter in .
[So] Source:J Biol Chem;292(35):14566-14575, 2017 Sep 01.
[Is] ISSN:1083-351X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The inactive prokaryotic promoter (P ) contains a single A-to-G point mutation in the -10 region of the leucine operon promoter, which causes leucine auxotrophy. This promoter can be activated by (-) DNA supercoiling in strains. However, whether this activation arises from global, permanent, or transient, dynamic supercoiling is still not fully understood. In this article, using a newly established system carrying a pair of divergently coupled promoters, an IPTG-inducible promoter and P that control the expression of and (the firefly luciferase gene), respectively, we demonstrate that transient, dynamic (-) DNA supercoiling provided by divergent transcription in both wild-type and strains can potently activate P We found that this activation depended on the promoter strength and the length of RNA transcripts, which are functional characteristics of transcription-coupled DNA supercoiling (TCDS) precisely predicted by the twin-supercoiled domain model of transcription in which a (+) supercoiled domain is produced ahead of the RNA polymerase and a (-) supercoiled domain behind it. We also demonstrate that TCDS can be generated on topologically open DNA molecules, linear DNA molecules, in , suggesting that topological boundaries or barriers are not required for the production of TCDS This work demonstrates that transient, dynamic TCDS by RNA polymerases is a major chromosome remodeling force in and greatly influences the nearby, coupled promoters/transcription.
[Mh] Termos MeSH primário: DNA Bacteriano/metabolismo
DNA Super-Helicoidal/metabolismo
Escherichia coli/metabolismo
Regulação Bacteriana da Expressão Gênica
Mutação Puntual
Regiões Promotoras Genéticas
Ativação Transcricional
[Mh] Termos MeSH secundário: Montagem e Desmontagem da Cromatina
DNA Bacteriano/química
DNA Circular
DNA Recombinante/química
DNA Recombinante/metabolismo
DNA Super-Helicoidal/química
RNA Polimerases Dirigidas por DNA/genética
RNA Polimerases Dirigidas por DNA/metabolismo
Escherichia coli/genética
Escherichia coli/crescimento & desenvolvimento
Deleção de Genes
Cinética
Leucina/metabolismo
Luciferases de Vaga-Lume/genética
Luciferases de Vaga-Lume/metabolismo
Óperon
Plasmídeos/genética
Plasmídeos/metabolismo
Proteínas Recombinantes/genética
Proteínas Recombinantes/metabolismo
Especificidade da Espécie
Transcrição Genética
Proteínas Virais/genética
Proteínas Virais/metabolismo
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Bacterial); 0 (DNA, Circular); 0 (DNA, Recombinant); 0 (DNA, Superhelical); 0 (Recombinant Proteins); 0 (Viral Proteins); EC 1.13.12.7 (Luciferases, Firefly); EC 2.7.7.- (bacteriophage T7 RNA polymerase); EC 2.7.7.6 (DNA-Directed RNA Polymerases); GMW67QNF9C (Leucine)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170926
[Lr] Data última revisão:
170926
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170712
[St] Status:MEDLINE
[do] DOI:10.1074/jbc.M117.794628


  10 / 4598 MEDLINE  
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[PMID]:28586463
[Au] Autor:van den Berg AA; Depken M
[Ad] Endereço:Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
[Ti] Título:Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genes.
[So] Source:Nucleic Acids Res;45(13):7623-7632, 2017 Jul 27.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:During eukaryotic transcription, RNA polymerase (RNAP) translocates along DNA molecules covered with nucleosomes and other DNA binding proteins. Though the interactions between a single nucleosome and RNAP are by now fairly well understood, this understanding has not been synthesized into a description of transcription on crowded genes, where multiple RNAP transcribe through nucleosomes while preserving the nucleosome coverage. We here take a deductive modeling approach to establish the consequences of RNAP-nucleosome interactions for transcription in crowded environments. We show that under physiologically crowded conditions, the interactions of RNAP with nucleosomes induce a strong kinetic attraction between RNAP molecules, causing them to self-organize into stable and moving pelotons. The peloton formation quantitatively explains the observed nucleosome and RNAP depletion close to the initiation site on heavily transcribed genes. Pelotons further translate into short-timescale transcriptional bursts at termination, resulting in burst characteristics consistent with instances of bursty transcription observed in vivo. To facilitate experimental testing of our proposed mechanism, we present several analytic relations that make testable quantitative predictions.
[Mh] Termos MeSH primário: RNA Polimerases Dirigidas por DNA/metabolismo
Modelos Genéticos
Nucleossomos/genética
Nucleossomos/metabolismo
Transcrição Genética
[Mh] Termos MeSH secundário: Animais
DNA Super-Helicoidal/genética
DNA Super-Helicoidal/metabolismo
Seres Humanos
Saccharomyces cerevisiae/genética
Saccharomyces cerevisiae/metabolismo
Processos Estocásticos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Superhelical); 0 (Nucleosomes); EC 2.7.7.6 (DNA-Directed RNA Polymerases)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171011
[Lr] Data última revisão:
171011
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170607
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx513



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