Nucleosome regulatory dynamics in response to TGFβ
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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.
Original language | English |
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Journal | Nucleic Acids Research |
Volume | 42 |
Issue number | 11 |
Pages (from-to) | 6921-6934 |
Number of pages | 14 |
ISSN | 0305-1048 |
DOIs | |
Publication status | Published - 2014 |
Externally published | Yes |
Bibliographical note
Funding Information:
Swedish Research Council [521-2010-3505 and 621-2011-6052]; Diabetes Foundation, Sweden; Ernfors Family Foundation; Diabetes Wellness Network, Sverige; Network of Excellence ‘ENFIN’ [LSHG-CT-2005-518254], European Union FP6 Program; Polish Ministry of Science and Higher Education [N301 239536 to J.K., in part]; eSSENCE Program [to J.K., in part]. Conflict of interest statement. None declared.
Funding Information:
Sequencing was performed at the Applied Biosystems R&D laboratories in Beverly, MA, USA. The authors would also like to acknowledge Catalin Barbacioru, Heather Peckham, Kevin McKernan and Clarence Lee for their assistance in the sequencing of the samples. Additional sequencing was performed at Uppsala Genome, Science for Life Laboratory at Uppsala University, a national infrastructure supported by the Swedish Research Council (VR-RFI) and the Knut and Alice Wallenberg Foundation. Taqman gene expression assays were performed with assistance from Yoshi-taka Nishikawa.
ID: 275935707