Chromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence

Simpson, Robert T.; Künzler, Peter

doi:10.1093/nar/6.4.1387

Cited by 209 publications

(115 citation statements)

References 31 publications

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“…The difference in rates of release of 3H and 14C observed in Fig. 2A (51)(52)(53). These results differ slightly from previous studies which indicated that, in a different buffer, rDNA and bulk DNA in isolated nuclei were digested at the same rate by staphylococcal nuclease (10).…”

Section: Resultscontrasting

confidence: 82%

DNase I sensitivity of ribosomal genes in isolated nucleosome core particles

Giri¹,

Gorovsky²

1980

Nucl Acids Res

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The level of chromatin structure at which DNase I recognizes conformationial differences between inert and activated genes has been investigated. Bulk and ribosomal DNA's of Tetrahymena pyriformis were differentially labeled in vivo with [14C]-and [5H]-thymidineI respectively, utilizing a defined starvation-refeeding protocol. The H-labeled ribosomal genes were shown to be preferentially digested by DNase I in isolated nuclei. Staphylococcal nuclease digested the ribosomal genes more slowly than bulk DNA, probably owing to the higher GC content of rDNA. DNase I and staphylococcal nuclease digestions of purified nucleosomes and of nucleosome core particles isolated from dual-labeled, starved-refed nuclei were indistinguishable from those of intact nuclei. We conclude from these studies that DNase I recognizes an alteration in the internal nucleosome core structure of activated ribosomal genes.

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Section: Resultscontrasting

confidence: 82%

DNase I sensitivity of ribosomal genes in isolated nucleosome core particles

Giri¹,

Gorovsky²

1980

Nucl Acids Res

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“…The bendability of (AT)n repeats is in fact well known from experiment [12]. Also, protein-induced bending at TATA sequences seems to be especially pronounced [13][14][15][16][17]. The lowest bendability value, on the other hand, is associated with poly(dA) motifs, which is also in agreement with experimental data, obtained by nucleosome studies [9,17] and X-ray crystallography [20,21].…”

Section: Asymmetric Bendability Reflects Propensity To Curvaturesupporting

confidence: 85%

Distribution of bending propensity in DNA sequences

Gabrielian¹,

Simoncsits²,

Pongor³

1996

FEBS Letters

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Local bending propensity and curvature of DNA can he characterized using a vector description of DNA bendability, based on a set of parameters derived from deoxyribonuclease I (DNase I) cleavage experiments. Two characteristics -arithmetic and vector averages of bendability -were successfully used to predict experimentally known bendable, rigid and curved segments in DNA. A characteristic distribution of bendability is conserved in evolutionarily related kinetoplast sequences. An analysis of the M. genitalium and H. influenzae genomes as well as fragments of human and yeast genomes shows, on the other hand, that highly curved segments -similar to artificially designed curved oligonucleotides -are extremely rare in natural DNA.bendable segments [2]. Bendability plots were drawn by first dividing a DNA sequence into overlapping trinucleotides, then assigning a bendability value given in Table 1 to the center of each trinucleotide. (In this way the first and last nucleotides will have no values so a sequence of 32 residues will have 30 values.) Average bendability and helical asymmetry (see below at Eq. 1) were calculated for segments of 32 bp, i.e. approximately three helical turns. The calculated profiles do not significantly depend on this window length. Random sequences were generated by random shuffling the sequence of entire genomes. The shuffled sequences were then divided into overlapping segments of 32 residues for the calculation of the values given in Table 1 which are averages and standard deviations calculated from 10 runs of randomization. Results and discussion

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“…It has been known for some time that in vitro nucleosomes have a high preference for certain DNA sequences (11)(12)(13)(14) and tend to avoid other sequences (15)(16)(17)(18)(19)(20)(21)(22). For instance, Kaplan et al (23) concluded from genome-scale nucleosome mapping that intrinsic nucleosome sequence preferences have a dominant role in determining nucleosome organization in vivo.…”

mentioning

confidence: 99%

Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy

Heijden

Vugt

Logie

et al. 2012

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

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Nucleosome positioning dictates eukaryotic DNA compaction and access. To predict nucleosome positions in a statistical mechanics model, we exploited the knowledge that nucleosomes favor DNA sequences with specific periodically occurring dinucleotides. Our model is the first to capture both dyad position within a few base pairs, and free binding energy within 2 kBT, for all the known nucleosome positioning sequences. By applying Percus’s equation to the derived energy landscape, we isolate sequence effects on genome-wide nucleosome occupancy from other factors that may influence nucleosome positioning. For both in vitro and in vivo systems, three parameters suffice to predict nucleosome occupancy with correlation coefficients of respectively 0.74 and 0.66. As predicted, we find the largest deviations in vivo around transcription start sites. This relatively simple algorithm can be used to guide future studies on the influence of DNA sequence on chromatin organization.

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Chromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence

Cited by 209 publications

References 31 publications

DNase I sensitivity of ribosomal genes in isolated nucleosome core particles

DNase I sensitivity of ribosomal genes in isolated nucleosome core particles

Distribution of bending propensity in DNA sequences

Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy

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