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Nucleosome regulatory dynamics in response to TGFβ.

Enroth S, Andersson R, Bysani M, Wallerman O, Termén S, Tuch BB, De La Vega FM, Heldin CH, Moustakas A, Komorowski J, Wadelius C - Nucleic Acids Res. (2014)

Bottom Line: We found that the average pattern is present at very few sites and, in case of TF binding, the double peak surrounding the sites is just an artifact of averaging over many loci.We systematically searched for depleted nucleosomes in stimulated cells compared to unstimulated cells and identified 24 318 loci.Strikingly many of these loci were associated with expression changes, as measured by RNA sequencing.

View Article: PubMed Central - PubMed

Affiliation: The Linnaeus Centre for Bioinformatics, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden.

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Annotations of nucleosomes in HepG2 unstimulated cells. Left pie chart shows the distribution of nucleosomes in exonic, intronic and intergenic regions. For comparison (right pie chart), the genomic sequence coverage of these regions is shown.
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Figure 4: Annotations of nucleosomes in HepG2 unstimulated cells. Left pie chart shows the distribution of nucleosomes in exonic, intronic and intergenic regions. For comparison (right pie chart), the genomic sequence coverage of these regions is shown.

Mentions: In accordance with our previous findings in CD4+ T-cells (6), a clear preference for exonic positioning was observed (Figure 4) when comparing the inferred nucleosomal locations to the genomic sequence coverage. We also found a preference for intragenic over intergenic positioning (51% of regions in 37% of sequence). In fact, the center-to-center distance between adjacent non-conflicting nucleosome interiors in exons, introns and intergenic regions (median values of 194 bp, 253 bp and 292 bp, respectively) indicated higher density of well-supported nucleosomes in exons than in introns and in intragenic than in intergenic regions (Supplementary Figure S2).


Nucleosome regulatory dynamics in response to TGFβ.

Enroth S, Andersson R, Bysani M, Wallerman O, Termén S, Tuch BB, De La Vega FM, Heldin CH, Moustakas A, Komorowski J, Wadelius C - Nucleic Acids Res. (2014)

Annotations of nucleosomes in HepG2 unstimulated cells. Left pie chart shows the distribution of nucleosomes in exonic, intronic and intergenic regions. For comparison (right pie chart), the genomic sequence coverage of these regions is shown.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4066760&req=5

Figure 4: Annotations of nucleosomes in HepG2 unstimulated cells. Left pie chart shows the distribution of nucleosomes in exonic, intronic and intergenic regions. For comparison (right pie chart), the genomic sequence coverage of these regions is shown.
Mentions: In accordance with our previous findings in CD4+ T-cells (6), a clear preference for exonic positioning was observed (Figure 4) when comparing the inferred nucleosomal locations to the genomic sequence coverage. We also found a preference for intragenic over intergenic positioning (51% of regions in 37% of sequence). In fact, the center-to-center distance between adjacent non-conflicting nucleosome interiors in exons, introns and intergenic regions (median values of 194 bp, 253 bp and 292 bp, respectively) indicated higher density of well-supported nucleosomes in exons than in introns and in intragenic than in intergenic regions (Supplementary Figure S2).

Bottom Line: We found that the average pattern is present at very few sites and, in case of TF binding, the double peak surrounding the sites is just an artifact of averaging over many loci.We systematically searched for depleted nucleosomes in stimulated cells compared to unstimulated cells and identified 24 318 loci.Strikingly many of these loci were associated with expression changes, as measured by RNA sequencing.

View Article: PubMed Central - PubMed

Affiliation: The Linnaeus Centre for Bioinformatics, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden.

Show MeSH