Intrinsic DNA bends: an organizer of local chromatin structure for transcription

Ohyama, Takashi

doi:10.1002/bies.1100

Cited by 53 publications

(43 citation statements)

References 87 publications

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“…Both cis-acting regulatory sequences near ori and proteins acting in trans appear to have an important function in controlling replication (4,5,14,29,45,50,61). Bent DNA may facilitate interaction between cis-DNA elements and trans-acting factors by organizing local chromatin infrastructure (44). Our data are consistent with the reported role that chromatin structure and nucleosome destabilization play in DNA replication (1,19).…”

Section: Containing the Sequences 5ј-(a/t)(a/t)a‫3-ء‬ј And 5ј-(a/t)(gsupporting

confidence: 87%

Relationship among Location of T-Antigen-Induced DNA Distortion, Auxiliary Sequences, and DNA Replication Efficiency

Okuley

Call

Mitchell

et al. 2003

J Virol

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T-antigen-induced DNA distortion was studied in a series of simian virus 40 (SV40) plasmid constructs whose relative replication efficiency ranges from 0.2 to 36. Bending was detected in the wild-type SV40 regulatory region consisting of three copies of the GC-rich 21-bp repeat but not in constructs with only one or two copies of the 21-bp repeat. In a construct with enhanced replication efficiency, bending occurred in a 69-bp cellular sequence located upstream of a single copy of the 21-bp repeat. Bending occurred both upstream of ori and in the three 21-bp repeats located downstream of ori in a construct with reduced replication efficiency. In a construct with no 21-bp repeats, DNA distortion occurred downstream of ori. The results indicate that SV40 DNA replication is enhanced when the structure of the regulatory region allows the DNA to form a bent structure upstream of the initial movement of the replication fork.Simian virus 40 (SV40) DNA replication has been widely used as a model to study DNA replication in eukaryotes (reviewed in references 7 and 19); the events before the initiation of replication are particularly interesting. SV40 has a welldefined origin of replication (2,10,22,43), and the initiation of replication depends on a single viral protein, T antigen (T-ag) (3,16,36,59). Except for T-ag, all proteins required for DNA replication are supplied by the host cell, and with the development of an in vitro SV40 replication system, their identity and function have been well characterized (35, 65; reviewed in references 7, 30, and 53). The SV40 core ori is a 64-bp region (20,27,43,54) that consists of three functional domains (13, 36, 45): a 17-bp adenine/thymine-rich (AT) region, a central 27-bp palindrome (PEN), and an early palindrome (EP).Located proximal to the AT tract are the promoter and enhancer elements of the SV40 regulatory region. The bidirectional promoter element for SV40 transcription consists of three 21-bp tandem repeats, each containing two copies of the conserved 5Ј-GGGCGG-3Ј (GC box) sequence. The GC boxes are binding sites for the transcription factor Sp1 (16,24,26). The enhancer contains two 72-bp repeats, each with multiple binding sites for transcription factors, including those belonging to the AP family (31).T-ag binds as a trimer to T-ag binding site I (38) located on the early transcription side of ori. The presence of site I facilitates T-ag-dependent unwinding of the DNA (28) and increases the frequency of initiation of DNA replication (25). T-ag binding site II, located at the PEN region in ori, is essential for the initiation of replication (15,17,20,43,46). T-ag forms double hexameric lobes that surround the PEN region (12, 37), and the helicase activity of the hexamers unwinds the DNA bidirectionally (11, 63). T-ag binding also occurs at site III located within the three 21-bp GC-rich repeats on the late transcription side of ori (23,38,60).T-ag binding to ori and flanking sequences induces structural distortions of the region. Both dimethyl sulfate protection and p...

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Section: Containing the Sequences 5ј-(a/t)(a/t)a‫3-ء‬ј And 5ј-(a/t)(gsupporting

confidence: 87%

Relationship among Location of T-Antigen-Induced DNA Distortion, Auxiliary Sequences, and DNA Replication Efficiency

Okuley

Call

Mitchell

et al. 2003

J Virol

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“…A high hierarchical level of gene regulation is represented by changes in the DNA conformation, such as DNA supercoiling or the presence of intrinsically curved DNA (14,33). In studies with mutants it has been shown that the maximal abundance of proteins in a set of 88 proteins investigated occurred at supercoiling levels below that of the wild type, and others were most abundant with elevated levels of negative superhelices (46).…”

Section: Discussionmentioning

confidence: 99%

Global Expression of Prophage Genes in Escherichia coli O157:H7 Strain EDL933 in Response to Norfloxacin

Herold

Siebert²,

Huber³

et al. 2005

Antimicrob Agents Chemother

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We investigated the influence of a low concentration of the gyrase inhibitor norfloxacin on the transcriptome of enterohemorrhagic Escherichia coli O157:H7 strain EDL933. For this purpose, we used a commercial DNA microarray containing oligonucleotides specific for E. coli O157:H7 strains EDL933 and RIMD0509952 and E. coli K-12 strain MG1655. Under the conditions applied, 5,963 spots (94% of all spots) could be analyzed. Among these, 118 spots (P < 0.05) indicated transcriptional upregulation and 122 spots (P < 0.05) indicated transcriptional downregulation of the E. coli genes present on the array. Eighty-five upregulated EDL933 genes were phage borne. Fifty-two of them could be ascribed to the Shiga toxin-encoding phages (Stx phages) BP-933W and CP-933V; the other 33 genes belonged to non-Stx prophage elements in the EDL933 genome. Genes present in the BP-933W prophage genome were induced most strongly up to 158-fold in the case of stxA 2 upon induction with norfloxacin. Twenty-two additional upregulated genes appeared to be E. coli O157:H7 strain RIMD0509952-specific phage elements, and the remaining 11 genes were related mainly to recombination and stress functions. Downregulation was indicated predominantly for genes responsible for bacterial primary metabolism, such as energy production, cell division, and amino acid biosynthesis. Interestingly, some genes present in the locus of enterocyte effacement appeared to be downregulated. The results of the study have shown that a low concentration of norfloxacin has profound effects on the transcriptome of E. coli O157:H7.

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“…This suggests that DNA curvature is important in many basic genetic processes (for reviews, see refs. [9][10][11][12]. In bacterial promoters, curved DNA structures have a range of functions: facilitating RNA polymerase binding to the promoter, promoting the transition from closed to open promoter complexes, and enhancing binding of transcription factors.…”

Section: Introductionmentioning

confidence: 99%

Chromatin structure formed on a eukaryotic promoter activated by a left-handed superhelical bent DNA of 180 bp

Sumida

Sonobe

Ohyama

2007

Journal of Advanced Science

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We have shown previously that a left-handed curved DNA segment of 180 bp (T20) can activate eukaryotic transcription. Here, the local chromatin structure around the promoter was investigated in a HeLa cell line HLB10/T20 harboring the T20-containing reporter and in its control cell line HLB10 in which T20 was deleted from the same reporter locus. An analysis of translational positioning of nucleosomes indicated that the nucleosome density in the region spanning from about -500 to +200 relative to the transcription start site (+1) was lower in HLB10/T20 cells than in HLB10 cells. The results of the chromatin analyses also indicated that the histone core may slide within the T20 region, and the ability of T20 to capture and reposition histones may increase the accessibility of both the TATA box and other cis-DNA elements. These effects seem to be responsible for facilitation of transcription by T20.

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Intrinsic DNA bends: an organizer of local chromatin structure for transcription

Cited by 53 publications

References 87 publications

Relationship among Location of T-Antigen-Induced DNA Distortion, Auxiliary Sequences, and DNA Replication Efficiency

Relationship among Location of T-Antigen-Induced DNA Distortion, Auxiliary Sequences, and DNA Replication Efficiency

Global Expression of Prophage Genes in Escherichia coli O157:H7 Strain EDL933 in Response to Norfloxacin

Chromatin structure formed on a eukaryotic promoter activated by a left-handed superhelical bent DNA of 180 bp

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