Effects of Histone Acetylation on Chromatin Topology In Vivo

Lutter, Leonard C.; Judis, Luann; Paretti, Robert F.

doi:10.1128/mcb.12.11.5004-5014.1992

Cited by 10 publications

(7 citation statements)

References 59 publications

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“…Measurement of linking number difference (Δ L ) has been described previously [e.g. ( − ), reviewed in ()]. Briefly, the polymerase-induced linking number difference is the difference between the mean linking number of the polymerase−bound circle following ligation ( L +RP ) and that of the circle ligated in the absence of polymerase ( L - RP ), i.e., Δ L = L +RP − L - RP .…”

Section: Methodsmentioning

confidence: 99%

DNA Bubble Formation in Transcription Initiation

et al. 2008

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The properties of the DNA bubble in the transcription open complex have been characterized by topological analysis of DNA circles containing the lac UV5 promoter or the PR promoter from bacteriophage lambda. Topological analysis is particularly well suited to this purpose since it quantifies the changes in DNA duplex geometry caused by bubble formation as well as by superhelical DNA wrapping. The duplex unwinding that results from bubble formation is detected as a reduction in topological linking number of the DNA circle, and the precision of this measurement has been enhanced in the current study through the use of 8 or 10 promoter copies per circle. Several lines of evidence indicate that the linking number change induced by open complex formation is essentially all due to bubble generation, with very little derived from superhelical wrapping. Accordingly, the linking number change of -1.17 measured for the lac UV5 promoter indicates that the size of the lac UV5 bubble is about 12.3 base pairs, while the change of -0.98 measured for the lambda PR promoter indicates that the lambda PR bubble is 10.3 base pairs. It was also found that the presence or absence of magnesium ion had little effect on the value of the linking number change, a result that resolves the uncertainty associated with use of chemical probes to study the effect of magnesium on bubble size. Finally, the magnitude of linking number change increases progressively when the 3' end of a transcript is extended to +2 and +3 in an abortive initiation complex. This indicates that the transcription bubble expands at its leading edge in the abortive complex, results that confirm and extend the proposal of a DNA "scrunching" mechanism at the onset of transcription. These results are relevant to several models for the structure of DNA in the functional open complex in solution, and provide an important complement to the structural information available from recent crystal structures.

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Section: Methodsmentioning

confidence: 99%

DNA Bubble Formation in Transcription Initiation

et al. 2008

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“…Acetylated histones wrap DNA less tightly in mononucleosomes which may result in a decrease in the amount of DNA superhelical writhe constrained by the nucleosome (101-103; but see ref. 104). These changes might be due to the fact that the acetylated N-terminal histone tails bind DNA with reduced affinity (99,105) and are more mobile with respect to the DNA surface than unmodified tails (29).…”

Section: Structural and Functional Consequences Of Acetylation Of The...mentioning

confidence: 99%

Chromatin disruption and modification

Wolffe¹,

Hayes

1999

Nucleic Acids Research

501

322

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Chromatin disruption and modification are associated with transcriptional regulation by diverse coactivators and corepressors. Here we discuss the possible structural basis and functional consequences of the observed alterations in chromatin associated with transcriptional activation and repression. Recent advances in defining the roles of individual histones and their domains in the assembly and maintenance of regulatory architectures provide a framework for understanding how chromatin remodelling machines, histone acetyltransferases and deacetylases function.

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“…Hyperacetylation of the core histones alone has only minor consequences for the topological constraint of DNA within nucleosomes (Norton et al ., 1989; Bauer et al ., 1994). The TR‐RXR‐mediated targeted disruption of chromatin (Wong et al ., 1997a) leads to a much more severe loss of topological constraint than would be anticipated from histone acetylation alone (Norton et al ., 1989; Lutter et al ., 1992). This would indicate that histone acetylation might not be involved in the disruption process or might just be one component of the overall chromatin rearrangement (Wong et al ., 1997a).…”

Section: Introductionmentioning

confidence: 99%

Distinct requirements for chromatin assembly in transcriptional repression by thyroid hormone receptor and histone deacetylase

Wong¹,

et al. 1998

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contributed equally to this work Histone deacetylase and chromatin assembly contribute to the control of transcription of the Xenopus TRβA gene promoter by the heterodimer of Xenopus thyroid hormone receptor and 9-cis retinoic acid receptor (TR-RXR). Addition of the histone deacetylase inhibitor Trichostatin A (TSA) relieves repression of transcription due to chromatin assembly following microinjection of templates into Xenopus oocyte nuclei, and eliminates regulation of transcription by TR-RXR. Expression of Xenopus RPD3p, the catalytic subunit of histone deacetylase, represses the TRβA promoter, but only after efficient assembly of the template into nucleosomes. In contrast, the unliganded TR-RXR represses templates only partially assembled into nucleosomes; addition of TSA also relieves this transcriptional repression. This result indicates the distinct requirements for chromatin assembly in mediating transcriptional repression by the deacetylase alone, compared with those needed in the presence of unliganded TR-RXR. In addition, whereas hormonebound TR-RXR targets chromatin disruption as assayed through changes in minichromosome topology and loss of a regular nucleosomal ladder on micrococcal nuclease digestion, addition of TSA relieves transcriptional repression but does not disrupt chromatin. Thus, TR-RXR can facilitate transcriptional repression in the absence of hormone through mechanisms in addition to recruitment of deacetylase, and disrupts chromatin structure through mechanisms in addition to the inhibition or release of deacetylase.

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Effects of Histone Acetylation on Chromatin Topology In Vivo

Cited by 10 publications

References 59 publications

DNA Bubble Formation in Transcription Initiation

DNA Bubble Formation in Transcription Initiation

Chromatin disruption and modification

Distinct requirements for chromatin assembly in transcriptional repression by thyroid hormone receptor and histone deacetylase

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