The conformation dependent hydrolysis of DNA by micrococcal nuclease

Wingert, Lavinia M.; Hippel, Peter H. von

doi:10.1016/0005-2787(68)90270-0

Cited by 72 publications

(29 citation statements)

References 15 publications

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“…One feature illustrated by this analysis is modest sequence bias at the sites of micrococcal nuclease cleavage. Previous studies of micrococcal nuclease specificity have suggested preferential cleavage at A/T-rich target sequences (Wingert and Von Hippel 1968). We observe evidence for this, as G/C residues are considerably underrepresented on both residues immediately flanking the site of cleavage (Supplemental Fig.…”

Section: Coli)supporting

confidence: 66%

“…At one extreme of this spectrum are some chemical probes, such as hy- droxyl radical (Tullius and Dombroski 1986) and MPE (Cartwright et al 1983), that show a modest degree of preferential cleavage relative to the nucleosome position, but which have little or no bias in terms of the underlying sequence. At an opposite end of the specificity spectrum are enzymatic probes, such as micrococcal nuclease (Wingert and Von Hippel 1968;Horz and Altenburger 1981) and the apoptotic nuclease DFF40 (Widlak et al 2000), which have some sequence bias, but which show a much stronger respect for nucleosome boundaries in their initial attack on a chromatin template. Some studies have also used pancreatic DNaseI, which is selective for different regions of nucleosomes (Noll 1974a) and has been used particularly successfully to delineate open regions and sites in chromatin (Lutter 1979;Crawford et al 2006).…”

Section: Discussionmentioning

confidence: 99%

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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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Section: Coli)supporting

confidence: 66%

Section: Discussionmentioning

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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“…While this enzyme is universally used to isolate nucleosome core DNA by preferentially digesting linker DNA to liberate the mononucleosome cores, its activity is not without sequence biases (Wingert and Von Hippel 1968;Horz and Altenburger 1981;McGhee and Felsenfeld 1983). These biases can result in the imprecise trimming of nucleosome core DNAs, cutting into the core DNA by a few nucleotides, or leaving behind a few linker DNA nucleotides.…”

Section: General Caveatsmentioning

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.

537

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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“…Depletion of A∶T and enrichment of G∶C-containing dinucleotides in nucleosomal sequences and the discontinuity of dinucleotide frequencies across the nucleosome boundary may be exaggerated by MNase sequence specificity -MNase is well known to preferentially digest A∶T-rich sequences through its exonuclease activity (31,32). To study this possibility, we have partially digested naked DNA from S. cerevisiae and E. coli genomes with MNase, isolated ∼150 bp DNA fragments, and sequenced them.…”

mentioning

confidence: 99%

High-throughput sequencing reveals a simple model of nucleosome energetics

Locke

Tolkunov

Moqtaderi

et al. 2010

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

162

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We use genome-wide nucleosome maps to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of finite-size particles in an arbitrary external potential and arrays of DNA-bound histone octamers. We derive an analytical solution to infer free energies of nucleosome formation directly from nucleosome occupancies measured in high-throughput experiments. The sequence-specific part of free energies is then captured by fitting them to a sum of energies assigned to individual nucleotide motifs. We have developed hierarchical models of increasing complexity and spatial resolution, establishing that nucleosome occupancies can be explained by systematic differences in mono-and dinucleotide content between nucleosomal and linker DNA sequences, with periodic dinucleotide distributions and longer sequence motifs playing a minor role. Furthermore, similar sequence signatures are exhibited by control experiments in which nucleosome-free genomic DNA is either sonicated or digested with micrococcal nuclease, making it possible that current predictions based on high-throughput nucleosomepositioning maps are biased by experimental artifacts.chromatin structure | histone-DNA interactions | nucleosome positioning | biophysical models I n eukaryotes, 75%-90% of genomic DNA is packaged into histone-DNA complexes called nucleosomes, with adjacent nucleosomes separated by stretches of linker DNA (1). Each nucleosome consists of 147 base pairs (bp) of DNA wrapped around a histone octamer in a left-handed superhelix (2). Arrays of nucleosomes fold into filamentous chromatin fibers which constitute building blocks for higher-order structures (3). DNA wrapped in a nucleosome is occluded from interacting with other DNA-binding proteins such as transcription factors, RNA polymerase, and DNA repair complexes (2). On the other hand, histone tail domains act as substrates for posttranslational modifications, providing binding sites for chromatin-associated proteins which facilitate transitions between active and silent chromatin states (4).Several distinct factors affect nucleosome positions in living cells. First of all, intrinsic histone-DNA interactions are sequence-specific: for example, polyðdA∶dTÞ tracts are well known to disfavor nucleosome formation (5, 6). In addition, nucleosome-depleted regions can be generated through the action of ATP-dependent chromatin remodeling enzymes (7) and histone acetylases (8). Finally, non-histone DNA-binding factors can alter nucleosome positions through binding their cognate sites and either displacing nucleosomes or hindering their subsequent formation (9, 10).The nucleosome code hypothesis states that DNA sequence is the primary determinant of nucleosome positions in living cells (11). This hypothesis is often contrasted with the idea of statistical positioning which asserts that most nucleosomes are ordered into regular arrays simply by steric exclusion (12, 13). In this view the nucleosoma...

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The conformation dependent hydrolysis of DNA by micrococcal nuclease

Cited by 72 publications

References 15 publications

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

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

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

High-throughput sequencing reveals a simple model of nucleosome energetics

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