Periodicity of strong nucleosome positioning sites around the chicken adult beta-globin gene may encode regularly spaced chromatin.

Davey, Colin S.; Pennings, Sari; Meersseman, Geert; Wess, Tim J; Allan, James

doi:10.1073/pnas.92.24.11210

Cited by 34 publications

(49 citation statements)

References 32 publications

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“…However, a cleavage pattern consistent with a more complex chromatin structure was observed (not shown), and nucleosome positions could not be determined. Therefore, the monomer extension method (61) for identifying nucleosome positions was used, which was developed to resolve arrays of overlapping positions in complex reconstituted chromatin structures, without ambiguity (10,11). This method requires purified chromatin; it is unlikely to be effective with nuclei because of the large excess of nucleosomes from the rest of the genome.…”

Section: Resultsmentioning

confidence: 99%

Remodeling of YeastCUP1Chromatin Involves Activator-Dependent Repositioning of Nucleosomes over the Entire Gene and Flanking Sequences

Shen

LeBlanc

Alfieri

et al. 2001

Molecular and Cellular Biology

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The yeast CUP1 gene is activated by the copper-dependent binding of the transcriptional activator, Ace1p. An episome containing transcriptionally active or inactive CUP1 was purified in its native chromatin structure from yeast cells. The amount of RNA polymerase II on CUP1 in the purified episomes correlated with its transcriptional activity in vivo. Chromatin structures were examined by using the monomer extension technique to map translational positions of nucleosomes. The chromatin structure of an episome containing inactive CUP1 isolated from ace1⌬ cells is organized into clusters of overlapping nucleosome positions separated by linkers. Novel nucleosome positions that include the linkers are occupied in the presence of Ace1p. Repositioning was observed over the entire CUP1 gene and its flanking regions, possibly over the entire episome. Mutation of the TATA boxes to prevent transcription did not prevent repositioning, implicating a chromatin remodeling activity recruited by Ace1p. These observations provide direct evidence in vivo for the nucleosome sliding mechanism proposed for remodeling complexes in vitro and indicate that remodeling is not restricted to the promoter but occurs over a chromatin domain including CUP1 and its flanking sequences.

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Section: Resultsmentioning

confidence: 99%

Remodeling of YeastCUP1Chromatin Involves Activator-Dependent Repositioning of Nucleosomes over the Entire Gene and Flanking Sequences

Shen

LeBlanc

Alfieri

et al. 2001

Molecular and Cellular Biology

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“…Mapping of Nucleosome Positions on Reconstituted TAC DNA by Monomer Extension-The positions adopted by nucleosomes reconstituted on the entire TAC sequence were mapped using the monomer extension method, which is ideal for long range mapping and can resolve arrays of overlapping positions in complex chromatin structures, without ambiguity (20,27,32,33).…”

Section: Resultsmentioning

confidence: 99%

DNA Sequence Plays a Major Role in Determining Nucleosome Positions in Yeast CUP1 Chromatin

Shen

Clark

2001

Journal of Biological Chemistry

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The role of DNA sequence in determining nucleosome positions in vivo was investigated by comparing the positions adopted by nucleosomes reconstituted on a yeast plasmid in vitro using purified core histones with those in native chromatin containing the same DNA, described previously. Nucleosomes were reconstituted on a 2.5 kilobase pair DNA sequence containing the yeast TRP1ARS1 plasmid with CUP1 as an insert (TAC-DNA). Multiple, alternative, overlapping nucleosome positions were mapped on TAC-DNA. For the 58 positioned nucleosomes identified, the relative positioning strengths and the stabilities to salt and temperature were determined. These positions were, with a few exceptions, identical to those observed in native, remodeled TAC chromatin containing an activated CUP1 gene. Only some of these positions are utilized in native, unremodeled chromatin. These observations suggest that DNA sequence is likely to play a very important role in positioning nucleosomes in vivo. We suggest that events occurring in yeast CUP1 chromatin determine which positions are occupied in vivo and when they are occupied.Eukaryotic DNA is packaged into chromatin, the basic structural repeat unit of which is the nucleosome. The nucleosome core contains 147 bp 1 of DNA wrapped in about 1.75 superhelical turns around a central octamer composed of two each of the four core histones H2A, H2B, H3, and H4. Its structure has been solved at high resolution by x-ray crystallography (1). In recent years, it has become clear that the nucleosome is not just a means of packaging large amounts of DNA into the nucleus but is also involved in regulation of gene expression (2, 3). The latter role stems from the fact that sequence-specific DNAbinding proteins often cannot recognize their sites when they are tightly wrapped in a nucleosome. The solution to this problem apparently resides in the activities of the many different chromatin remodeling and histone acetylase complexes recently identified. These facilitate the disruption or displacement of nucleosomes, allowing factors to bind, transcription complexes to form, and RNA polymerase II to initiate transcription.One of the most interesting aspects of nucleosome structure is that the histone octamer does not bind to DNA randomly but exhibits preferences for some sequences over others, a phenomenon referred to as nucleosome positioning (4, 5). Positioning is actually determined by the central H3-H4 tetramer (6). The translational position of a nucleosome is defined by the 147-bp DNA sequence it occupies (see Ref. 7 for a detailed analysis). The affinity of the histone octamer for a particular 147-bp DNA sequence defines its positioning strength. Strongly positioned nucleosomes are those that contain sequences that bind the octamer much more tightly than neighboring sequences. There are many examples of these, the most well known being the 5 S RNA gene (8). There is a great deal of evidence for the importance of positioned nucleosomes in gene regulation (4). In budding yeast, the best studied example ...

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“…The globin sequence (shaded) is numbered with respect to the cap site of the gene. The ovals depict the four major positions adopted by histone octamers reconstituted onto this DNA (the nomenclature (5, 6, 7) is in accordance with Davey et al, 1995). The location of each CpG dinucleotide is given by the 32 short vertical bars.…”

Section: Resultsmentioning

confidence: 99%

“…For example, histone octamers reconstituted onto the promoter of the chicken adult b-globin gene, adopt characteristic translational positions with respect to the underlying DNA (Yenidunya et al, 1994;Davey et al, 1995). By modulating the accessibility of promoter elements, these nucleosomes may participate in the developmental regulation of the gene Buckle et al, 1991).…”

Section: Introductionmentioning

confidence: 99%

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CpG methylation remodels chromatin structure in vitro

Davey

Pennings

Allan

1997

Journal of Molecular Biology

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Periodicity of strong nucleosome positioning sites around the chicken adult beta-globin gene may encode regularly spaced chromatin.

Cited by 34 publications

References 32 publications

Remodeling of YeastCUP1Chromatin Involves Activator-Dependent Repositioning of Nucleosomes over the Entire Gene and Flanking Sequences

Remodeling of YeastCUP1Chromatin Involves Activator-Dependent Repositioning of Nucleosomes over the Entire Gene and Flanking Sequences

DNA Sequence Plays a Major Role in Determining Nucleosome Positions in Yeast CUP1 Chromatin

CpG methylation remodels chromatin structure in vitro

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