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Distal chromatin structure influences local nucleosome positions and gene expression.

Jansen A, van der Zande E, Meert W, Fink GR, Verstrepen KJ - Nucleic Acids Res. (2012)

Bottom Line: In addition, we show that changes in the nucleosome positions in the URA3 promoter strongly affect the promoter activity.Most interestingly, in addition to demonstrating the effect of the local DNA sequence, our study provides novel in vivo evidence that nucleosome positions are also affected by the position of neighboring nucleosomes.Nucleosome structure may therefore be an important selective force for conservation of gene order on a chromosome, because relocating a gene to another genomic position (where the positions of neighboring nucleosomes are different from the original locus) can have dramatic consequences for the gene's nucleosome structure and thus its expression.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, B-3001, Leuven, Belgium.

ABSTRACT
The positions of nucleosomes across the genome influence several cellular processes, including gene transcription. However, our understanding of the factors dictating where nucleosomes are located and how this affects gene regulation is still limited. Here, we perform an extensive in vivo study to investigate the influence of the neighboring chromatin structure on local nucleosome positioning and gene expression. Using truncated versions of the Saccharomyces cerevisiae URA3 gene, we show that nucleosome positions in the URA3 promoter are at least partly determined by the local DNA sequence, with so-called 'anti-nucleosomal elements' like poly(dA:dT) tracts being key determinants of nucleosome positions. In addition, we show that changes in the nucleosome positions in the URA3 promoter strongly affect the promoter activity. Most interestingly, in addition to demonstrating the effect of the local DNA sequence, our study provides novel in vivo evidence that nucleosome positions are also affected by the position of neighboring nucleosomes. Nucleosome structure may therefore be an important selective force for conservation of gene order on a chromosome, because relocating a gene to another genomic position (where the positions of neighboring nucleosomes are different from the original locus) can have dramatic consequences for the gene's nucleosome structure and thus its expression.

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Expression of a truncated URA3 gene depends on the genomic context. A truncated URA3 construct in which 163 bp of the URA3 promoter remain (URA3-163), was inserted at various locations in the LYS2 gene. (A) Different insertion sites of the truncated URA3-163 construct within the LYS2 ORF. The nucleosome profile for regions of the LYS2 gene as it was experimentally determined by tiling qPCR is shown. Dotted lines indicate insertion sites which are labeled by their location inside the LYS2 ORF (coordinates refer to the position relative to the LYS2 translation start). (B) Different insertion sites lead to different growth patterns on SC-ura and 5-FOA medium. Mutants are labeled by their location inside the LYS2 ORF. These mutants also show differences in doubling times (C), and normalized mean Ura3-YFP protein abundance (D) for growth in liquid YPD (black bars) and liquid SC-ura (gray bars) media. Error bars denote standard deviation.
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gkr1311-F5: Expression of a truncated URA3 gene depends on the genomic context. A truncated URA3 construct in which 163 bp of the URA3 promoter remain (URA3-163), was inserted at various locations in the LYS2 gene. (A) Different insertion sites of the truncated URA3-163 construct within the LYS2 ORF. The nucleosome profile for regions of the LYS2 gene as it was experimentally determined by tiling qPCR is shown. Dotted lines indicate insertion sites which are labeled by their location inside the LYS2 ORF (coordinates refer to the position relative to the LYS2 translation start). (B) Different insertion sites lead to different growth patterns on SC-ura and 5-FOA medium. Mutants are labeled by their location inside the LYS2 ORF. These mutants also show differences in doubling times (C), and normalized mean Ura3-YFP protein abundance (D) for growth in liquid YPD (black bars) and liquid SC-ura (gray bars) media. Error bars denote standard deviation.

Mentions: To further investigate the influence of the genomic environment on local URA3 activity and chromatin structure, we inserted a truncated URA3 promoter into twelve different locations within the LYS2 gene (Figure 5A). Construct URA3-163 (i.e. the 163 bp most proximal to the START codon remain, see Figure 1A) was used because our previous results indicate that this construct is sensitive to the surrounding chromatin in which it is embedded. In parallel, the same experiments were performed with construct URA3-162 (see Supplementary Figures S7, S9, S10 and S13 and Table SVI).Figure 5.


Distal chromatin structure influences local nucleosome positions and gene expression.

Jansen A, van der Zande E, Meert W, Fink GR, Verstrepen KJ - Nucleic Acids Res. (2012)

Expression of a truncated URA3 gene depends on the genomic context. A truncated URA3 construct in which 163 bp of the URA3 promoter remain (URA3-163), was inserted at various locations in the LYS2 gene. (A) Different insertion sites of the truncated URA3-163 construct within the LYS2 ORF. The nucleosome profile for regions of the LYS2 gene as it was experimentally determined by tiling qPCR is shown. Dotted lines indicate insertion sites which are labeled by their location inside the LYS2 ORF (coordinates refer to the position relative to the LYS2 translation start). (B) Different insertion sites lead to different growth patterns on SC-ura and 5-FOA medium. Mutants are labeled by their location inside the LYS2 ORF. These mutants also show differences in doubling times (C), and normalized mean Ura3-YFP protein abundance (D) for growth in liquid YPD (black bars) and liquid SC-ura (gray bars) media. Error bars denote standard deviation.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC3351160&req=5

gkr1311-F5: Expression of a truncated URA3 gene depends on the genomic context. A truncated URA3 construct in which 163 bp of the URA3 promoter remain (URA3-163), was inserted at various locations in the LYS2 gene. (A) Different insertion sites of the truncated URA3-163 construct within the LYS2 ORF. The nucleosome profile for regions of the LYS2 gene as it was experimentally determined by tiling qPCR is shown. Dotted lines indicate insertion sites which are labeled by their location inside the LYS2 ORF (coordinates refer to the position relative to the LYS2 translation start). (B) Different insertion sites lead to different growth patterns on SC-ura and 5-FOA medium. Mutants are labeled by their location inside the LYS2 ORF. These mutants also show differences in doubling times (C), and normalized mean Ura3-YFP protein abundance (D) for growth in liquid YPD (black bars) and liquid SC-ura (gray bars) media. Error bars denote standard deviation.
Mentions: To further investigate the influence of the genomic environment on local URA3 activity and chromatin structure, we inserted a truncated URA3 promoter into twelve different locations within the LYS2 gene (Figure 5A). Construct URA3-163 (i.e. the 163 bp most proximal to the START codon remain, see Figure 1A) was used because our previous results indicate that this construct is sensitive to the surrounding chromatin in which it is embedded. In parallel, the same experiments were performed with construct URA3-162 (see Supplementary Figures S7, S9, S10 and S13 and Table SVI).Figure 5.

Bottom Line: In addition, we show that changes in the nucleosome positions in the URA3 promoter strongly affect the promoter activity.Most interestingly, in addition to demonstrating the effect of the local DNA sequence, our study provides novel in vivo evidence that nucleosome positions are also affected by the position of neighboring nucleosomes.Nucleosome structure may therefore be an important selective force for conservation of gene order on a chromosome, because relocating a gene to another genomic position (where the positions of neighboring nucleosomes are different from the original locus) can have dramatic consequences for the gene's nucleosome structure and thus its expression.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, B-3001, Leuven, Belgium.

ABSTRACT
The positions of nucleosomes across the genome influence several cellular processes, including gene transcription. However, our understanding of the factors dictating where nucleosomes are located and how this affects gene regulation is still limited. Here, we perform an extensive in vivo study to investigate the influence of the neighboring chromatin structure on local nucleosome positioning and gene expression. Using truncated versions of the Saccharomyces cerevisiae URA3 gene, we show that nucleosome positions in the URA3 promoter are at least partly determined by the local DNA sequence, with so-called 'anti-nucleosomal elements' like poly(dA:dT) tracts being key determinants of nucleosome positions. In addition, we show that changes in the nucleosome positions in the URA3 promoter strongly affect the promoter activity. Most interestingly, in addition to demonstrating the effect of the local DNA sequence, our study provides novel in vivo evidence that nucleosome positions are also affected by the position of neighboring nucleosomes. Nucleosome structure may therefore be an important selective force for conservation of gene order on a chromosome, because relocating a gene to another genomic position (where the positions of neighboring nucleosomes are different from the original locus) can have dramatic consequences for the gene's nucleosome structure and thus its expression.

Show MeSH