Relation of nucleosomes to nucleotide sequences in the rat

Prunell, Ariel; Kornberg, Roger D.

doi:10.1098/rstb.1978.0023

Cited by 13 publications

(2 citation statements)

References 11 publications

(15 reference statements)

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“…To test whether nucleosomes are phased in repressed hsp 70 genes, we used an experimental approach based on a similar idea employed in previous schemes by other groups (12)(13)(14)18). Briefly, nucleosome core particles containing a defined DNA size of 146 base pairs were generated by extensive digestion of nuclei with micrococcal nuclease (24)(25)(26).…”

Section: Resultsmentioning

confidence: 99%

“…Early studies demonstrated that there is no single phase relation between nucleosomes and the bulk of the unique DNA sequences (12,13). While a unique frame of nucleosomes in the a-satellite DNA of African green monkey cells (14) is clearly ruled out by more recent experiments (15), studies with the SV40 and polyoma minichro-mosome suggest that nucleosomes are not arranged in a single phase (16,17) but rather occupy a few defined frames (18).…”

Section: Introductionmentioning

confidence: 99%

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

Levy

Noll

1980

Nucl Acids Res

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Levy

Noll

1980

Nucl Acids Res

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Eukaryotic chromatin

Lilley¹

1981

Topics in Nucleic Acid Structure

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Combined Micrococcal Nuclease and Exonuclease III Digestion Reveals Precise Positions of the Nucleosome Core/Linker Junctions: Implications for High-Resolution Nucleosome Mapping

Nikitina

Wang

Gomberg

et al. 2013

Journal of Molecular Biology

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Micrococcal nuclease (MNase) is extensively used in genome-wide mapping of nucleosomes but its preference for AT-rich DNA leads to errors in establishing precise positions of nucleosomes. Here, we show that the MNase digestion of nucleosomes assembled on a strong nucleosome positioning sequence, Widom's clone 601, releases nucleosome cores whose sizes are strongly affected by the linker DNA sequence. Our experiments produced nucleosomal DNA sizes varying between 147 and 155 bp, with positions of the MNase cuts reflecting positions of the A⋅T pairs rather than the nucleosome core/linker junctions determined by X-ray crystallography. Extent of chromatosomal DNA protection by linker histone H1 also depends on the linker DNA sequence. Remarkably, we found that a combined treatment with MNase and exonuclease III (exoIII) overcomes MNase sequence preference producing nucleosomal DNA trimmed symmetrically and precisely at the core/linker junctions regardless of the underlying DNA sequence. We propose that combined MNase/exoIII digestion can be applied to in situ chromatin for unbiased genome-wide mapping of nucleosome positions that is not influenced by DNA sequences at the core/linker junctions. The same approach can be also used for the precise mapping of the extent of linker DNA protection by H1 and other protein factors associated with nucleosome linkers.

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Relation of nucleosomes to nucleotide sequences in the rat

Abstract: The relation of nucleosomes to nucleotide sequences is random for most single copy sequences in rat liver. This could be due to variation in the DNA content of nucleosomes, and a procedure for detecting such variation is described.

Cited by 13 publications

References 11 publications

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

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

Eukaryotic chromatin

Combined Micrococcal Nuclease and Exonuclease III Digestion Reveals Precise Positions of the Nucleosome Core/Linker Junctions: Implications for High-Resolution Nucleosome Mapping

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