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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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(A) Log-odds values around the TSS of gene HEY2 for nucleosome mid-positions in HepG2 unstimulated (labeled TGFB−) cells (Nucl Interior log-odds TGFβ−) and TGFβ stimulated (labeled TGFB+) cells (Nucl Interior log-odds TGFβ+). For comparison, counts of reads extended to the average fragment length of sequenced DNA, combined signal, are shown (Nucleosome TGFβ− and Nucleosome TGFβ+). Locations of inferred nucleosome interior regions in TGFβ− cells (Nucleosome interiors TGFβ−) and TGFβ+ cells (Nucleosome interiors TGFβ+) as well as locations of inferred nucleosome depletions in TGFβ+ cells (Nucleosome depletion TGFβ+) are depicted in the bottom panels. Data were uploaded as custom tracks to the UCSC Genome Browser where the graphics were produced. (B) and (C) Average signal footprints of log-odds (black lines, left vertical axes), counts of strand-directed fragment-length extended reads (gray lines, right vertical axes) and DNaseI hypersensitivity (blue dashed lines, scaled to fit) around TSSs of the top 5000 high-expressed protein-coding genes (B) and 25 651 JUND binding sites (C) .
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Figure 1: (A) Log-odds values around the TSS of gene HEY2 for nucleosome mid-positions in HepG2 unstimulated (labeled TGFB−) cells (Nucl Interior log-odds TGFβ−) and TGFβ stimulated (labeled TGFB+) cells (Nucl Interior log-odds TGFβ+). For comparison, counts of reads extended to the average fragment length of sequenced DNA, combined signal, are shown (Nucleosome TGFβ− and Nucleosome TGFβ+). Locations of inferred nucleosome interior regions in TGFβ− cells (Nucleosome interiors TGFβ−) and TGFβ+ cells (Nucleosome interiors TGFβ+) as well as locations of inferred nucleosome depletions in TGFβ+ cells (Nucleosome depletion TGFβ+) are depicted in the bottom panels. Data were uploaded as custom tracks to the UCSC Genome Browser where the graphics were produced. (B) and (C) Average signal footprints of log-odds (black lines, left vertical axes), counts of strand-directed fragment-length extended reads (gray lines, right vertical axes) and DNaseI hypersensitivity (blue dashed lines, scaled to fit) around TSSs of the top 5000 high-expressed protein-coding genes (B) and 25 651 JUND binding sites (C) .

Mentions: We applied SuMMIt on nucleosome data from unstimulated cells and the resulting log-odds scores provided clear indications of which positions had good support from both strands. The positioning was made at a very high resolution since only nucleosome mid-positions were called. Plotting these values gave a crisp view of the nucleosome landscape revealing details that were hidden using mere counts of read alignments. This is apparent around the TSS of gene HEY2 (Figure 1A) where log-odds values indicate several nucleosomes positioned at loci where peak shapes of read counts indicate only one nucleosome. Exploiting the 5′ ends of read alignments rather than their genome coverage proved very useful in detecting differences in positioning among cell populations in the same sample. This is clearly visible downstream of the TSS of gene HEY2 (Figure 1A), where seemingly three different proximal preferential positions of a nucleosome were detected.


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)

(A) Log-odds values around the TSS of gene HEY2 for nucleosome mid-positions in HepG2 unstimulated (labeled TGFB−) cells (Nucl Interior log-odds TGFβ−) and TGFβ stimulated (labeled TGFB+) cells (Nucl Interior log-odds TGFβ+). For comparison, counts of reads extended to the average fragment length of sequenced DNA, combined signal, are shown (Nucleosome TGFβ− and Nucleosome TGFβ+). Locations of inferred nucleosome interior regions in TGFβ− cells (Nucleosome interiors TGFβ−) and TGFβ+ cells (Nucleosome interiors TGFβ+) as well as locations of inferred nucleosome depletions in TGFβ+ cells (Nucleosome depletion TGFβ+) are depicted in the bottom panels. Data were uploaded as custom tracks to the UCSC Genome Browser where the graphics were produced. (B) and (C) Average signal footprints of log-odds (black lines, left vertical axes), counts of strand-directed fragment-length extended reads (gray lines, right vertical axes) and DNaseI hypersensitivity (blue dashed lines, scaled to fit) around TSSs of the top 5000 high-expressed protein-coding genes (B) and 25 651 JUND binding sites (C) .
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Related In: Results  -  Collection

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Figure 1: (A) Log-odds values around the TSS of gene HEY2 for nucleosome mid-positions in HepG2 unstimulated (labeled TGFB−) cells (Nucl Interior log-odds TGFβ−) and TGFβ stimulated (labeled TGFB+) cells (Nucl Interior log-odds TGFβ+). For comparison, counts of reads extended to the average fragment length of sequenced DNA, combined signal, are shown (Nucleosome TGFβ− and Nucleosome TGFβ+). Locations of inferred nucleosome interior regions in TGFβ− cells (Nucleosome interiors TGFβ−) and TGFβ+ cells (Nucleosome interiors TGFβ+) as well as locations of inferred nucleosome depletions in TGFβ+ cells (Nucleosome depletion TGFβ+) are depicted in the bottom panels. Data were uploaded as custom tracks to the UCSC Genome Browser where the graphics were produced. (B) and (C) Average signal footprints of log-odds (black lines, left vertical axes), counts of strand-directed fragment-length extended reads (gray lines, right vertical axes) and DNaseI hypersensitivity (blue dashed lines, scaled to fit) around TSSs of the top 5000 high-expressed protein-coding genes (B) and 25 651 JUND binding sites (C) .
Mentions: We applied SuMMIt on nucleosome data from unstimulated cells and the resulting log-odds scores provided clear indications of which positions had good support from both strands. The positioning was made at a very high resolution since only nucleosome mid-positions were called. Plotting these values gave a crisp view of the nucleosome landscape revealing details that were hidden using mere counts of read alignments. This is apparent around the TSS of gene HEY2 (Figure 1A) where log-odds values indicate several nucleosomes positioned at loci where peak shapes of read counts indicate only one nucleosome. Exploiting the 5′ ends of read alignments rather than their genome coverage proved very useful in detecting differences in positioning among cell populations in the same sample. This is clearly visible downstream of the TSS of gene HEY2 (Figure 1A), where seemingly three different proximal preferential positions of a nucleosome were detected.

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
Related in: MedlinePlus