A Theoretical Model for the Prediction of Sequence-Dependent Nucleosome Thermodynamic Stability

Anselmi, Claudio; Bocchinfuso, Gianfranco; Santis, P. De; Savino, M.; Scipioni, Anita

doi:10.1016/s0006-3495(00)76319-3

Cited by 102 publications

(114 citation statements)

References 60 publications

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“…The surveys of Olson and coworkers of the cumulative x-ray data on ds-oligonucleotides (42) and dsoligonucleotide-protein complexes (43) led to two sets of sequence-dependent flexibility. As already pointed out by Anselmi et al (44) and Crothers (33), significant divergences and contradictions exist among these different sets of values. The possibility of generating a set of parameters that are able to predict the local DNA flexibility still has to be considered an open problem.…”

Section: Curvature Along the Chain And Sequence-dependent Differentialmentioning

confidence: 78%

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Mapping the intrinsic curvature and flexibility along the DNA chain

Zuccheri

Scipioni

Cavaliere

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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The energy of DNA deformation plays a crucial and active role in its packaging and its function in the cell. Considerable effort has gone into developing methodologies capable of evaluating the local sequence-directed curvature and flexibility of a DNA chain. These studies thus far have focused on DNA constructs expressly tailored either with anomalous flexibility or curvature tracts. Here we demonstrate that these two structural properties can be mapped also along the chain of a “natural” DNA with any sequence on the basis of its scanning force microscope (SFM) images. To know the orientation of the sequence of the investigated DNA molecules in their SFM images, we prepared a palindromic dimer of the long DNA molecule under study. The palindromic symmetry also acted as an internal gauge of the statistical significance of the analysis carried out on the SFM images of the dimer molecules. It was found that although the curvature modulus is not efficient in separating static and dynamic contributions to the curvature of the population of molecules, the curvature taken with its direction (its sign in two dimensions) permits the direct separation of the intrinsic curvature from the flexibility contributions. The sequence-dependent flexibility seems to vary monotonically with the chain's intrinsic curvature; the chain rigidity was found to modulate as its local thermodynamic stability and does not correlate with the dinucleotide chain rigidities evaluation made from x-ray data by other authors.

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Section: Curvature Along the Chain And Sequence-dependent Differentialmentioning

confidence: 78%

“…Very recently, Anselmi et al connected the flexibility of a DNA tract to its double-helix thermodynamic stability (44). They represented the chain stability by the ratio of the dinucleotide melting temperatures (in thermodynamic scale), averaged over the tract considered, relative to that of the standard: ͗T͞T*͘ (44).…”

mentioning

confidence: 99%

Mapping the intrinsic curvature and flexibility along the DNA chain

Zuccheri

Scipioni

Cavaliere

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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“…There were suggestions that the sequence dependence of DNA bending rigidity correlates to the free energy of stacking between adjacent base pairs, ΔG st (4,8). We compared our results with the data on the sequence dependence of ΔG st obtained recently (43,44).…”

Section: Discussionmentioning

confidence: 84%

“…However, the sequence dependence of DNA bending rigidity is vital for many aspects of DNAprotein interaction, and is particularly important for understanding how nucleosomes position along DNA molecules (4,5). Despite its importance, the problem has formerly remained unsolved, although a few research groups have tried various approaches (6)(7)(8). The data that are generally considered most reliable were obtained from statistical analysis of DNA-protein crystal structures (9,10).…”

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confidence: 99%

Sequence dependence of DNA bending rigidity

Geggier

Vologodskii

2010

Proc. Natl. Acad. Sci. U.S.A.

203

247

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For many aspects of DNA-protein interaction, it is vital to know how DNA bending rigidity (or persistence length, a) depends on its sequence. We addressed this problem using the method based on cyclization of short DNA fragments, which allows very accurate determination of a. Our approach was based on assigning specific values of a to each of 10 distinct dinucleotide steps. We prepared DNA fragments, each about 200 bp in length, with various quasiperiodic sequences, measured their cyclization efficiencies (j factors), and fitted the data by the theoretical equation to obtain the values of a for each fragment. From these data, we obtained a set of a for the dinucleotide steps. To test this set, we used it to design DNA sequences that should correspond to very low and very high values of a, prepared the corresponding fragments, and determined their values of a experimentally. The measured and calculated values of a were very close to one another, confirming that we have found the correct solution to this long-standing problem. The same experimental data also allowed us to determine the sequence dependence of DNA helical repeat.DNA elasticity | DNA persistence length T he value of DNA persistence length, a, closely related to the bending rigidity of the double helix, is very important for quantitative analysis of many aspects of DNA functioning. Many different methods were applied over the last decades to determine this value and its dependence on ionic conditions (1). These studies showed that under near physiological ionic conditions the value of a is close to 50 nm (1-3). They also showed that, in a good approximation, the value of a does not depend on DNA sequence, because many studies that use different DNA molecules gave very close values of a. However, the sequence dependence of DNA bending rigidity is vital for many aspects of DNAprotein interaction, and is particularly important for understanding how nucleosomes position along DNA molecules (4, 5). Despite its importance, the problem has formerly remained unsolved, although a few research groups have tried various approaches (6-8). The data that are generally considered most reliable were obtained from statistical analysis of DNA-protein crystal structures (9, 10). The large volume of available structural data allowed this group of researchers to present a very detailed picture of the sequence dependence of DNA conformational properties. This analysis, however, is based on the assumption that variations of the DNA bend angles in the crystals correspond to the amplitudes of thermal fluctuations of these angles in solution. It is hard to justify this assumption.The major obstacle in determining the sequence dependence of a is the necessity of highly accurate measurements of a for different sequences. The majority of methods applied for the measurements of a do not provide the necessary level of accuracy. The only known method that allows one to measure a with the required accuracy is based on cyclization of short DNA fragments by DNA ligase (2,3,11,12). It i...

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“…In alternative, the approach we previously proposed evaluates the minimum free energy to transform a free DNA tract into the nucleosomal shape preserving the maximum of intrinsic features of the sequence [69,70]. A mathematical formulation based on the Parseval equality, which allows the integration of quadratic differences of two functions in terms of the sum of the differences between the related Fourier transform amplitudes, was adopted [71].…”

Section: Accepted M Manuscriptmentioning

confidence: 99%

Predicting nucleosome positioning in genomes: Physical and bioinformatic approaches

Scipioni

Santis

2011

Biophysical Chemistry

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In eukaryotic genomes, nucleosomes are responsible for packaging DNA and controlling gene expression. For this reason, an increasing interest is arising on computational methods capable of predicting the nucleosome positioning along genomes. In this review we describe and compare bioinformatic and physical approaches adopted to predict nucleosome occupancy along genomes. Computational analyses attempt at decoding the experimental nucleosome maps of genomes in terms of certain dinucleotide step periodicity observed along DNA. Such investigations show that highly significant information about the occurrence of a nucleosome along DNA is intrinsic in certain features of the sequence suggesting that DNA of eukaryotic genomes encodes nucleosome organization. Besides the bioinformatic approaches, physical models were proposed based on the sequence dependent conformational features of the DNA chain, which govern the free energy needed to transform recurrent DNA tracts along the genome into the nucleosomal shape. Graphical abstractHighlights > Theoretical models for predicting nucleosome positioning along genomes are reviewed. > Bioinformatics and physical approaches are compared and discussed. > Mechanical properties of DNA rule thermodynamic stability of nucleosomes. > Nucleosomes are regularly spaced along genomes as required for chromatin fibers. KeywordsThermodynamic stability of nucleosomes; nucleosome code; nucleosome distribution along genomes; bioinformatic approaches for the prediction of nucleosome occupancy; physical models predicting nucleosome occupancy.

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A Theoretical Model for the Prediction of Sequence-Dependent Nucleosome Thermodynamic Stability

Cited by 102 publications

References 60 publications

Mapping the intrinsic curvature and flexibility along the DNA chain

Mapping the intrinsic curvature and flexibility along the DNA chain

Sequence dependence of DNA bending rigidity

Predicting nucleosome positioning in genomes: Physical and bioinformatic approaches

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