Multiple phases of nucleosomes in the hsp 70 genes of Drosophila melanogaster

Levy, Allan H.; Noll, Markus

doi:10.1093/nar/8.24.6059

Cited by 29 publications

(7 citation statements)

References 34 publications

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“…Since the core particle is a distinctive structure and is associated with a rather defined length of DNA (146-148 bp), it has been used in such experiments [cf. Levy & Noll (1979)]. Figure 5 shows the results of a Taql (site at'-1-54 bp) cleavage of core particle DNA, probed with (=*40 bp) of RI G, which will lie within the first nucleosome on the 35S coding sequence, whether it begins at +5 or +30 bp.…”

Section: Resultsmentioning

confidence: 99%

Protected region upstream and limited nucleosomal positioning downstream of the transcription initiation region of yeast 35S ribosomal gene

Lohr¹

1983

Biochemistry

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To locate nucleosome positions around the transcription initiation site of 35S rDNA in yeast, single and double cleavage site data for staphylococcal nuclease and single cleavage site data for DNase I were obtained by methods involving some modifications of the usual indirect end-labeling procedure. Results show that immediately upstream of the initiation site there is an approximately 225 base pair (bp) stretch of chromatin which is quite resistant to nuclease digestion. The nucleosomal domain begins on the coding sequences, at the downstream end of the resistant region, with the major locus 30 bp and a minor locus 5 bp downstream of the initiation site in growing cells. The location of the major locus is corroborated by analysis within the coding sequences, although results within the gene are less convincing because of a strong similarity of chromatin and naked DNA digestion profiles. The staphylococcal nuclease cleavage maps were tested by their ability to reproduce chromatin digest profiles and to explain the presence or absence, depending on which parts of the region were used as probes, of specific bands within the pattern. The site of the major upstream locus of the nucleosomal domain differs in growing and stationary cells. This shift changes the accessibility of approximately 25 bp of DNA and may be associated with the expression of these genes.

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Section: Resultsmentioning

confidence: 99%

Protected region upstream and limited nucleosomal positioning downstream of the transcription initiation region of yeast 35S ribosomal gene

Lohr¹

1983

Biochemistry

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“…lim 1+L (3] These expressions for w(g,n) and s(g) can be used to calculate the probability of any particular distribution of beads and bare sites. Consider the distribution on a DNA molecule of length z.…”

Section: Theorymentioning

confidence: 99%

Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism

1988

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Expressions are derived for distributions of nucleosomes in chromatin. Nucleosomes are placed on DNA at the densities found in bulk chromatin, and their locations are allowed to vary at random. No further assumptions are required to simulate the periodic patterns of digestion obtained with various nucleases. The introduction of a boundary constraint, due for example to sequence-specific protein binding, results in an array of regularly spaced nucleosomes at nonrandom locations, similar to the arrays reported for some genes and other chromosomal regions.

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“…phased. There have been many reports recently that nucleosomes are indeed phased; for example, in tRNA genes in chicken chromatin (8), in 5S genes in Xenopus (9) and Drosophila (10), in heat shock genes in Drosophila (11), and in satellite DNA in rat (12). The locations of the nucleosomes have been mapped to the nucleotide in the histone genes of Drosophila (13).…”

Section: Introductionmentioning

confidence: 99%

High sequence specificity of micrococcal nuclease

1981

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The substrate specificity of micrococcal nuclease (EC 3.1.4.7.) has been studied. The enzyme recognises features of nucleotide composition, nucleotide sequence and tertiary structure of DNA. Kinetic analysis indicates that the rate of cleavage is 30 times greater at the 5' side of A or T than at G or C. Digestion of end-labelled linear DNA molecules of known sequence revealed that only a limited number of sites are cut, generating a highly specific pattern of fragments. The frequency of cleavage at each site has been determined and it may reflect the poor base overlap in the 5' T-A 3' stack as well as the length of contiguous A and T residues. The same sequence preferences are found when DNA is assembled into nucleosomes. Deoxyribonuclease 1 (EC 3.1.4.5.) recognises many of the same sequence features. Micrococcal nuclease also mimics nuclease S1 selectively cleaving an inverted repeat in supercoiled pBR322. The value of micrococcal nuclease as a "non-specific" enzymatic probe for studying nucleosome phasing is questioned.

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Multiple phases of nucleosomes in the hsp 70 genes of Drosophila melanogaster

Abstract: The arrangement of the nucleosomes with respect to the DNA sequence has been examined in the genes coding for the major heat shock protein (hsp 70) in Drosophila. In the repressed state of the genes, the nucleosomes are precisely phased in at least three frames.

Cited by 29 publications

References 34 publications

Protected region upstream and limited nucleosomal positioning downstream of the transcription initiation region of yeast 35S ribosomal gene

Protected region upstream and limited nucleosomal positioning downstream of the transcription initiation region of yeast 35S ribosomal gene

Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism

High sequence specificity of micrococcal nuclease

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