The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data

Chung, Ho‐Ryun; Dunkel, Ilona; Heise, Franziska; Linke, Christian; Krobitsch, Sylvia; Ehrenhofer‐Murray, Ann E.; Sperling, Silke; Vingron, Martin

doi:10.1371/journal.pone.0015754

Cited by 110 publications

(111 citation statements)

References 50 publications

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“…In A. thaliana and rice, the DHSs contain the cis-regulatory elements bound by known TFs (Zhang et al 2012;Sullivan et al 2014;Wu et al 2014). Despite the differences in digestion mechanism and cleavage bias between MNase for determining nucleosome occupancy (Chung et al 2010;Vierstra et al 2014) and DNase I for revealing open chromatic regions (Sung et al 2014;Vierstra et al 2014), the positive correlation between motif-specific nucleosome depletion and heightened chromatin accessibility supports the notion that nucleosome-depleted motifs may be bound by TFs.…”

Section: G/c Content and Nucleosome Occupancymentioning

confidence: 76%

Determinants of nucleosome positioning and their influence on plant gene expression

et al. 2015

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Nucleosome positioning influences the access of transcription factors (TFs) to their binding sites and gene expression. Studies in plant, animal, and fungal models demonstrate similar nucleosome positioning patterns along genes and correlations between occupancy and expression. However, the relationships among nucleosome positioning, cis-regulatory element accessibility, and gene expression in plants remain undefined. Here we showed that plant nucleosome depletion occurs on specific 6-mer motifs and this sequence-specific nucleosome depletion is predictive of expression levels. Nucleosome-depleted regions in Arabidopsis thaliana tend to have higher G/C content, unlike yeast, and are centered on specific G/C-rich 6-mers, suggesting that intrinsic sequence properties, such as G/C content, cannot fully explain plant nucleosome positioning. These 6-mer motif sites showed higher DNase I hypersensitivity and are flanked by strongly phased nucleosomes, consistent with known TF binding sites. Intriguingly, this 6-mer-specific nucleosome depletion pattern occurs not only in promoter but also in genic regions and is significantly correlated with higher gene expression level, a phenomenon also found in rice but not in yeast. Among the 6-mer motifs enriched in genes responsive to treatment with the defense hormone jasmonate, there are no significant changes in nucleosome occupancy, suggesting that these sites are potentially preconditioned to enable rapid response without changing chromatin state significantly. Our study provides a global assessment of the joint contribution of nucleosome occupancy and motif sequences that are likely cis-elements to the control of gene expression in plants. Our findings pave the way for further understanding the impact of chromatin state on plant transcriptional regulatory circuits.

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Section: G/c Content and Nucleosome Occupancymentioning

confidence: 76%

Determinants of nucleosome positioning and their influence on plant gene expression

et al. 2015

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“…In comparison with other nucleosome-mapping methods, this method is less destructive than MNase for mapping the DNA at the ends of the nucleosome or chemical mapping, which cleaves the DNA at the center of the nucleosome (19). MNase cleavage also has sequence specificity, which can bias the results of nucleosome mapping (38)(39)(40)(41). Although chemical mapping nucleosomes by incorporation of a modified histone circumvents the sequence specificity, it is not a very efficient reaction and thus can only map a fraction of the nucleosomes within a cell (19,41).…”

Section: Resultsmentioning

confidence: 99%

Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity

Small

Wang

et al. 2014

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

100

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Significance Nucleosomes limit access to DNA, which antagonizes gene expression and prevents recruitment of transcription factors that cannot bind DNA wrapped around the histone octamer. Numerous studies using large cell populations determined that active genes promoters tend to be nucleosome-depleted. We developed a method to examine nucleosome positioning in single cells and revealed significant heterogeneity of nucleosome configurations within a population. In an inactive gene loaded with nucleosomes, a small subpopulation of nucleosome-depleted cells exists that were engaged in transcription. Single-cell mapping revealed that even in apparently nucleosome-free regions, some cells were occupied by nucleosomes. These data reveal an underlying complexity of nucleosome positioning and its role in regulating gene expression.

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“…Both suggested fast depletion of nucleosome over poly (dA-dT) tracts but no significant depletion over poly (dG-dC) tracts. Because MNase preferentially degrades A/T-rich nucleosomes (32), which are more common in S. pombe than in S. cerevisiae ( Fig. 2 B and C), we speculate that the observed high depletion rate over poly (dA-dT) tracts from the S. pombe MNase maps may be inflated.…”

Section: Significancementioning

confidence: 92%

“…Recent micrococcal nuclease (MNase) mapping studies (16,28,29) revealed substantial differences between the two species in nucleosomal DNA sequence features and chromatin organization, including how histone-DNA sequence preferences affect nucleosome positioning and nucleosome occupancy patterns around transcription start sites (TSSs) and DNA replication origins. To address these questions at higher resolution and to control for potential sequence-specificity bias due to different MNase digestion extent (30)(31)(32), the in vivo chemical mapping approach of Brogaard et al (33) was used to map nucleosome centers directly in S. pombe in this study. This map achieved unprecedented accuracy, leading to a number of discoveries regarding nucleosome positioning and chromatin structure, which provide additional insights from an evolutionary perspective into our understanding of the intrinsic and extrinsic mechanisms in nucleosome positioning.…”

mentioning

confidence: 99%

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning

Moyle-Heyrman¹,

Zaichuk²,

et al. 2013

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

115

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Using a recently developed chemical approach, we have generated a genome-wide map of nucleosomes in vivo in Schizosaccharomyces pombe (S. pombe) at base pair resolution. The shorter linker length previously identified in S. pombe is due to a preponderance of nucleosomes separated by ∼4/5 bp, placing nucleosomes on opposite faces of the DNA. The periodic dinucleotide feature thought to position nucleosomes is equally strong in exons as in introns, demonstrating that nucleosome positioning information can be superimposed on coding information. Unlike the case in Saccharomyces cerevisiae, A/T-rich sequences are enriched in S. pombe nucleosomes, particularly at ±20 bp around the dyad. This difference in nucleosome binding preference gives rise to a major distinction downstream of the transcription start site, where nucleosome phasing is highly predictable by A/T frequency in S. pombe but not in S. cerevisiae, suggesting that the genomes and DNA binding preferences of nucleosomes have coevolved in different species. The poly (dA-dT) tracts affect but do not deplete nucleosomes in S. pombe, and they prefer special rotational positions within the nucleosome, with longer tracts enriched in the 10-to 30-bp region from the dyad. S. pombe does not have a welldefined nucleosome-depleted region immediately upstream of most transcription start sites; instead, the −1 nucleosome is positioned with the expected spacing relative to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. Although there is generally very good agreement between nucleosome maps generated by chemical cleavage and micrococcal nuclease digestion, the chemical map shows consistently higher nucleosome occupancy on DNA with high A/T content.chromatin structure | heterochromatin | gene regulation E ukaryotic DNA is organized into nucleosome arrays that facilitate proper genome compaction and regulation of the genetic information. Genome-wide nucleosome maps from different organisms have provided important insights into how nucleosome positioning regulates chromosome functions (1-6). It is commonly accepted that the DNA sequence itself plays a major role in the exact positions where histone octamers bind DNA to form nucleosomes (7-9). Most remarkably, nucleosomes prefer special dinucleotide motifs at specific rotational angles within the nucleosome core (10, 11) and disfavor poly (dA-dT) tracts (12-15). Although the ability of DNA to interact with the histone core is important, nucleosome occupancy is influenced by additional extrinsic factors, including species-specific DNA binding proteins (16), ATP-dependent remodeling complexes (17,18), and the transcription machinery (19)(20)(21)(22).The underlying mechanisms for the species-or cell typespecific nucleosome positioning features have not been well understood. The fission yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae are two highly diverged model organisms widely used to study basic biological processes in eukaryotes (23). Although similar in siz...

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The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data

Cited by 110 publications

References 50 publications

Determinants of nucleosome positioning and their influence on plant gene expression

Determinants of nucleosome positioning and their influence on plant gene expression

Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning

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