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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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Nucleosome positions of the native URA3 promoter and selected lys2::URA3 promoter mutants. Using tiling qPCR, we determined the nucleosome positions of (A) the wild-type URA3 promoter at its native locus (same as Figure 2A). In addition, we determined the nucleosome profile of selected lys2::URA3 promoter mutants, i.e. mutants (B) 366, (C) 221, (D) 174, (E) 168, (F) 167, (G) 165, (H) 164, (I) 163, (J) 162, (K) 161 and (L) Δpoly(dA:dT). Peak positions corresponding to nucleosome positions were measured (Table 1). Red dotted lines mark the positions of the −1 and +1 nucleosomes in the wild-type URA3 promoter at its native locus.
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gkr1311-F4: Nucleosome positions of the native URA3 promoter and selected lys2::URA3 promoter mutants. Using tiling qPCR, we determined the nucleosome positions of (A) the wild-type URA3 promoter at its native locus (same as Figure 2A). In addition, we determined the nucleosome profile of selected lys2::URA3 promoter mutants, i.e. mutants (B) 366, (C) 221, (D) 174, (E) 168, (F) 167, (G) 165, (H) 164, (I) 163, (J) 162, (K) 161 and (L) Δpoly(dA:dT). Peak positions corresponding to nucleosome positions were measured (Table 1). Red dotted lines mark the positions of the −1 and +1 nucleosomes in the wild-type URA3 promoter at its native locus.

Mentions: To investigate if the chromatin structure of the various mutants depends on the genomic location of the URA3 marker, we determined the nucleosome positions of various truncated URA3 promoters when inserted at nucleotide 721 of the LYS2 locus (Figure 4, Table 1). For the full-length URA3 promoter (mutant 366), we find a NFR surrounded by two well-positioned nucleosomes. Due to the altered genomic context upstream of the URA3 promoter, the position of the −1 nucleosome changes, but the position of the +1 nucleosome remains the same. As a consequence, the NFR doubles in size (Figure 4B, Table 1). However, this does not affect URA3 expression (Figure 3), presumably because the accessibility of the functional cis elements in the URA3 promoter is not affected.Figure 4.


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)

Nucleosome positions of the native URA3 promoter and selected lys2::URA3 promoter mutants. Using tiling qPCR, we determined the nucleosome positions of (A) the wild-type URA3 promoter at its native locus (same as Figure 2A). In addition, we determined the nucleosome profile of selected lys2::URA3 promoter mutants, i.e. mutants (B) 366, (C) 221, (D) 174, (E) 168, (F) 167, (G) 165, (H) 164, (I) 163, (J) 162, (K) 161 and (L) Δpoly(dA:dT). Peak positions corresponding to nucleosome positions were measured (Table 1). Red dotted lines mark the positions of the −1 and +1 nucleosomes in the wild-type URA3 promoter at its native locus.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3351160&req=5

gkr1311-F4: Nucleosome positions of the native URA3 promoter and selected lys2::URA3 promoter mutants. Using tiling qPCR, we determined the nucleosome positions of (A) the wild-type URA3 promoter at its native locus (same as Figure 2A). In addition, we determined the nucleosome profile of selected lys2::URA3 promoter mutants, i.e. mutants (B) 366, (C) 221, (D) 174, (E) 168, (F) 167, (G) 165, (H) 164, (I) 163, (J) 162, (K) 161 and (L) Δpoly(dA:dT). Peak positions corresponding to nucleosome positions were measured (Table 1). Red dotted lines mark the positions of the −1 and +1 nucleosomes in the wild-type URA3 promoter at its native locus.
Mentions: To investigate if the chromatin structure of the various mutants depends on the genomic location of the URA3 marker, we determined the nucleosome positions of various truncated URA3 promoters when inserted at nucleotide 721 of the LYS2 locus (Figure 4, Table 1). For the full-length URA3 promoter (mutant 366), we find a NFR surrounded by two well-positioned nucleosomes. Due to the altered genomic context upstream of the URA3 promoter, the position of the −1 nucleosome changes, but the position of the +1 nucleosome remains the same. As a consequence, the NFR doubles in size (Figure 4B, Table 1). However, this does not affect URA3 expression (Figure 3), presumably because the accessibility of the functional cis elements in the URA3 promoter is not affected.Figure 4.

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