DNA Sequence Organization in Chromatosomes

Muyldermans, Serge; Travers, Andrew

doi:10.1006/jmbi.1994.1044

Cited by 49 publications

(37 citation statements)

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“…These provide a data-intensive framework to evaluate models for sequence-based nucleosome positioning. Many previous analyses of smaller nucleosome core data sets have reported a periodicity of k-mer usage within the DNA of the core of the nucleosome (e.g., Satchwell et al 1986;Muyldermans and Travers 1994;Ioshikhes et al 1996;Johnson et al 2006;Albert et al 2007), which is thought to be important in the positioning of nucleosomes due to the ability of certain regularly spaced dinucleotides to more easily facilitate the extreme curvature of the double-stranded DNA around the histone octamer (Luger et al 1997). Consistent with these previous studies, a simple dinucleotide analysis of our core sequence data set reveals an oscillating ∼10-base periodicity of AA/TT with a counter phased ∼10-base periodicity for GC.…”

Section: Global Sequence Characteristics Of Nucleosome Core Segmentsmentioning

confidence: 99%

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

Valouev

Ichikawa²,

Tonthat³

et al. 2008

Genome Res.

538

446

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Using the massively parallel technique of sequencing by oligonucleotide ligation and detection (SOLiD; Applied Biosystems), we have assessed the in vivo positions of more than 44 million putative nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans. These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution. While we observe some degree of reproducible positioning throughout the genome in our mixed stage population of animals, we note that the major chromatin feature in the worm is a diversity of allowed nucleosome positions at the vast majority of individual loci. While absolute positioning of nucleosomes can vary substantially, relative positioning of nucleosomes (in a repeated array structure likely to be maintained at least in part by steric constraints) appears to be a significant property of chromatin structure. The high density of nucleosomal reads enabled a substantial extension of previous analysis describing the usage of individual oligonucleotide sequences along the span of the nucleosome core and linker. We release this data set, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome.[Supplemental material is available online at www.genome.org. SOLiD raw sequencing data from this study have been submitted to the Short Read Archive at NCBI under accession no. SRA001023.]The regulation of genetic information within eukaryotic cells involves a high degree of specificity both in the availability of individual DNA-binding factors in individual cells, and in availability in the genome of DNA sequences that are their potential targets. Modulating the accessibility of individual DNA sequences are many complex interactions, the most prevalent of which are the interactions between histone octamers and DNA in compacted chromosomes. Each histone core interacts with 147 bp of DNA, which coil 1.7 times around the histone octamer (Luger et al. 1997;Davey et al. 2002) to form the basic unit of chromatin structure, the nucleosome. Since the first description over three decades ago (Kornberg 1974), the nucleosome and its role in gene regulation has been the subject of intensive study and speculation.As we have an increasingly detailed functional view of the genome, the tools of high-throughput molecular characterization have been used to begin obtaining a genome-wide description of nucleosome positions (Satchwell et al. 1986;Yuan et al. 2005;Johnson et al. 2006;Albert et al. 2007;Lee et al. 2007;Peckham et al. 2007;Schones et al. 2008;Shivaswamy et al. 2008). These data have in turn been used in attempts to reveal nucleosome positioning signals in DNA sequence (Satchwell et al. 1986;Ioshikhes et al. 1996;Segal et al. 2006;Yuan and Liu 2008). Although of great interest and value, sequence-based predictions of nucleosome position have been limited to date in their accuracy and resolution.In the litera...

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Section: Global Sequence Characteristics Of Nucleosome Core Segmentsmentioning

confidence: 99%

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

Valouev

Ichikawa²,

Tonthat³

et al. 2008

Genome Res.

538

446

View full text Add to dashboard Cite

show abstract

“…Because micrococcal nuclease strongly prefers to cut after AT base pairs (70), the protection seen in these digestion experiments could be the result of sequence preferences of micrococcal nuclease rather than protection by linker histone. Indeed, over 95% of bulk chromatosomal sequences that were cloned and sequenced had AT base pairs at their ends (79). Protection experiments on bulk chromatin are less susceptible to potential problems arising from the sequence preferences of the nuclease.…”

Section: The Chromatosomementioning

confidence: 99%

“…The sequence preference of H1/H5 on the 5S nucleosome is strong enough to make it select one of the two potential binding sites almost exclusively, and this strong preference may also preclude its binding at a possibly more usual site. Interestingly, in a study of bulk chromatosomal sequences, an AGGA sequence was observed near one of the termini of chromatosomal DNA but not the other (79), raising the possibility that this sequence may be involved in binding the globular domain of H1/H5. This sequence does not occur at the same place on the 5S nucleosome.…”

Section: The Chromatosomementioning

confidence: 99%

Histone Structure and the Organization of the Nucleosome

Ramakrishnan

1997

Annu. Rev. Biophys. Biomol. Struct.

162

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“…The length of DNA in the core is conserved, while the "linker" DNA between nucleosomes can vary between species, chromatin regions, and cells. In many situations, an additional set of histones (H1 or H5) associate with linker DNA immediately flanking the core (Muyldermans and Travers 1994;Buttinelli et al 1999).…”

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confidence: 99%

“…While these studies have greatly increased our fundamental understanding of many of the translational and rotational constraints conferred by DNA sequences, they all suffer from the simplicity of the assay, in particular the reconstitution of nucleosomes away from their native nuclear context. Complementary to these are in situ experiments in which chromatin is isolated from cells and then nucleosome positioning and structure are analyzed (Satchwell et al 1986;Muyldermans and Travers 1994;Travers and Muyldermans 1996). Accurate retention and representation of nucleosome positioning has been a long-standing issue in the field, and numerous debates have addressed the questions of whether different isolation and analysis protocols might themselves influence the distributions of observed nucleosome positions.…”

mentioning

confidence: 99%

Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin

Johnson¹,

Tan²,

McCullough³

et al. 2006

Genome Res.

177

158

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Nucleosome positions within the chromatin landscape are known to serve as a major determinant of DNA accessibility to transcription factors and other interacting components. To delineate nucleosomal patterns in a model genetic organism, Caenorhabditis elegans, we have carried out a genome-wide analysis in which DNA fragments corresponding to nucleosome cores were liberated using an enzyme (micrococcal nuclease) with a strong preference for cleavage in non-nucleosomal regions. Sequence analysis of 284,091 putative nucleosome cores obtained in this manner from a mixed-stage population of C. elegans reveals a combined picture of flexibility and constraint in nucleosome positioning. As has previously been observed in studies of individual loci in diverse biological systems, we observe areas in the genome where nucleosomes can adopt a wide variety of positions in a given region, areas with little or no nucleosome coverage, and areas where nucleosomes reproducibly adopt a specific positional pattern. In addition to illuminating numerous aspects of chromatin structure for C. elegans, this analysis provides a reference from which to begin an investigation of relationships between the nucleosomal pattern, chromosomal architecture, and lineage-based gene activity on a genome-wide scale.

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DNA Sequence Organization in Chromatosomes

Cited by 49 publications

References 0 publications

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

Histone Structure and the Organization of the Nucleosome

Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin

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