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Nucleic Acids Res. 2014 Jun;42(11):6921-34. doi: 10.1093/nar/gku326. Epub 2014 Apr 25.

Nucleosome regulatory dynamics in response to TGFβ.

Author information

1
The Linnaeus Centre for Bioinformatics, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden.
2
Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Box 815, Uppsala University, SE-75108 Uppsala, Sweden.
3
Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Box 595, SE-75124 Uppsala, Sweden.
4
Applied Biosystems, part of Life Technologies, Foster City, CA 94404, USA.
5
Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Box 595, SE-75124 Uppsala, Sweden Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Box 582, SE-75123 Uppsala, Sweden.
6
The Linnaeus Centre for Bioinformatics, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, 01-248 Warszawa, Poland.
7
Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Box 815, Uppsala University, SE-75108 Uppsala, Sweden claes.wadelius@igp.uu.se.

Abstract

Nucleosomes play important roles in a cell beyond their basal functionality in chromatin compaction. Their placement affects all steps in transcriptional regulation, from transcription factor (TF) binding to messenger ribonucleic acid (mRNA) synthesis. Careful profiling of their locations and dynamics in response to stimuli is important to further our understanding of transcriptional regulation by the state of chromatin. We measured nucleosome occupancy in human hepatic cells before and after treatment with transforming growth factor beta 1 (TGFβ1), using massively parallel sequencing. With a newly developed method, SuMMIt, for precise positioning of nucleosomes we inferred dynamics of the nucleosomal landscape. Distinct nucleosome positioning has previously been described at transcription start site and flanking TF binding sites. 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. Depending on genomic annotation, 44-78% of them were over-represented in binding motifs for TFs. Changes in binding affinity were verified for HNF4α by qPCR. Strikingly many of these loci were associated with expression changes, as measured by RNA sequencing.

PMID:
24771338
PMCID:
PMC4066760
DOI:
10.1093/nar/gku326
[Indexed for MEDLINE]
Free PMC Article

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