Nucleosome dynamics. VI. histone tail regulation of tetrasome chiral transition. A relaxation study of tetrasomes on DNA minicircles

Sivolob, Andrei; Lucia, Filomena De; Alilat, Mohamed; Prunell, Ariel

doi:10.1006/jmbi.1999.3302

Cited by 36 publications

(44 citation statements)

References 34 publications

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“…(a) Lk ¼ 31 topoisomers of 360 bp and 362 bp pBR minicircles were relaxed with 600 units of topoisomerase I/ml in the Mg 2þ -minus buffer (see Materials and Methods) for one hour at the temperatures indicated (T; 8C), deproteinized, ethanol precipitated and electrophoresed in a chloroquine-containing 4% polyacrylamide mini-gel as described. 9 An autoradiogram is shown. (b) The natural logarithm of the topoisomer ratios, as calculated from the radioactivity profiles of the (a) gel (not shown), was plotted as function of the temperature increment DT ¼ T 2 37 8C (see equation (10) in Materials and Methods).…”

Section: Cleavagementioning

confidence: 99%

“…Experimentally, G n (i) was measured by reference to the sO state, and noted as DG n (i) ( Table 2). The model was fitted to the topoisomer relative amounts versus DLk curves as described, 9 to find the values of five parameters at the most: DLk n (i) and DG n (i), with i ¼ 1-3 ( Table 2). K SC (i)/N l was calculated for each state using the explicit solutions theory (see below).…”

Section: Relaxation Of Nucleosomes On Dna Minicirclesmentioning

confidence: 99%

“…9 In this theory, the loop is considered as a segment with specified conditions at the end points (where it contacts the protein surface). The DNA segment is then treated as an unexpansive, homogeneous body obeying the rod theory described by Kirchhoff.…”

Section: Loop Most Probable Conformationsmentioning

confidence: 99%

“…(The theory 5 -7 has been used in this laboratory to simulate tetrasome chiral transition. 8,9 ) The most probable conformations strictly depend on the loop end conditions, and hence on the parameters of the DNA superhelix. Results showed that the free energies of s 2 and s þ states could be affected in opposite directions, as observed experimentally, by modulating the trajectories of entering and exiting DNAs so as to make them more or less divergent when projected onto the superhelix axis.…”

Section: Introductionmentioning

confidence: 99%

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Sequence-dependent Nucleosome Structural and Dynamic Polymorphism. Potential Involvement of Histone H2B N-Terminal Tail Proximal Domain

Sivolob¹,

Lavelle²,

Prunell³

2003

Journal of Molecular Biology

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Section: Cleavagementioning

confidence: 99%

Section: Relaxation Of Nucleosomes On Dna Minicirclesmentioning

confidence: 99%

Section: Loop Most Probable Conformationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Sequence-dependent Nucleosome Structural and Dynamic Polymorphism. Potential Involvement of Histone H2B N-Terminal Tail Proximal Domain

Sivolob¹,

Lavelle²,

Prunell³

2003

Journal of Molecular Biology

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“…by affecting the ability of the H2A/H2B dimer to exchange, which is likely to be involved in at least some traversal events (2). The N-terminal tails could also affect more complex unfolding transitions in the nucleosome, which would facilitate traversal (11,12). Higher order chromatin structure, which could affect the efficiency of transcription through chromatin, can be influenced by the N-terminal tails (13)(14)(15)(16).…”

mentioning

confidence: 99%

Histone N-terminal Tails Interfere with Nucleosome Traversal by RNA Polymerase II

Újvári

Hsieh²,

Luse

et al. 2008

Journal of Biological Chemistry

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We determined the effect of the N-terminal histone tails on nucleosome traversal by yeast and human RNA polymerase II (pol II). Removal of H2A/H2B tails, H3/H4 tails, or all tails increased complete traversal of the nucleosome by human pol II, although the increase varied considerably depending on the template and on which tails were removed. Human pol II achieved >80% traversal of one nucleosomal template lacking the H2A/H2B tails, but even in those reactions, the transcript elongation rate was lower than the rate on pure DNA templates. For yeast pol II, transcription proceeded much farther into the nucleosome in the absence of tails, but complete read-through was not substantially increased by tail removal. Transcription factor IIS provided roughly the same level of read-through stimulation for transcript elongation in the presence or absence of tails. FACT also stimulated elongation on nucleosomal templates, and this effect was similar regardless of the presence of tails. For both polymerases, removal of the H2A/H2B tails reduced pausing throughout the nucleosome, suggesting that histone tails affect a common step at most points during nucleosome traversal. We conclude that histone tails provide a significant part of the nucleosomal barrier to pol II transcript elongation.It has long been appreciated that nucleosomes form a strong blockade to transcript elongation by pol II in vitro (1, 2). It has not been established what role, if any, the N-terminal tails of the histones play in this blockade. The core structure of the nucleosome does not depend on the tails (3-7). However, the tails are strongly positively charged, and they could associate nonspecifically with the DNA, thereby impeding polymerase access to the template (8 -10). The tails could influence traversal in other ways, e.g. by affecting the ability of the H2A/H2B dimer to exchange, which is likely to be involved in at least some traversal events (2). The N-terminal tails could also affect more complex unfolding transitions in the nucleosome, which would facilitate traversal (11, 12). Higher order chromatin structure, which could affect the efficiency of transcription through chromatin, can be influenced by the N-terminal tails (13-16). Covalent modifications of the tails, especially of the H3 tail of promoter-proximal nucleosomes, are well known to be correlated with transcriptional activity in vivo (reviewed in . A recent survey of transcriptionally active human genes revealed that most of these genes contain a high level of RNA polymerase II (pol II) 3 immediately downstream of the transcription start and a strongly positioned nucleosome with a promoter-proximal edge at about position ϩ40 (20). This suggests that the ability of pol II to cross the first nucleosome it encounters after transcript initiation is a major and general control point for gene expression. In light of all of these findings, we decided to explore directly the effect of the histone tails on the ability of pol II to traverse single nucleosomes. As an initial test of the effec...

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Nucleosome dynamics.V. ethidium bromide versus histone tails in modulating ethidium bromide-driven tetrasome chiral transition. A fluorescence study of tetrasomes on DNA minicircles

Sivolob

Prunell

2000

Journal of Molecular Biology

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Nucleosome dynamics. VI. histone tail regulation of tetrasome chiral transition. A relaxation study of tetrasomes on DNA minicircles

Cited by 36 publications

References 34 publications

Sequence-dependent Nucleosome Structural and Dynamic Polymorphism. Potential Involvement of Histone H2B N-Terminal Tail Proximal Domain

Sequence-dependent Nucleosome Structural and Dynamic Polymorphism. Potential Involvement of Histone H2B N-Terminal Tail Proximal Domain

Histone N-terminal Tails Interfere with Nucleosome Traversal by RNA Polymerase II

Nucleosome dynamics.V. ethidium bromide versus histone tails in modulating ethidium bromide-driven tetrasome chiral transition. A fluorescence study of tetrasomes on DNA minicircles

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