Nucleosome regulatory dynamics in response to TGFβ.
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.
Affiliation: The Linnaeus Centre for Bioinformatics, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden.Show MeSH
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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.
Affiliation: The Linnaeus Centre for Bioinformatics, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden.