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Title: Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation
Authors: Vandenbon, Alexis
Kumagai, Yutaro
Lin, Mengjie
Suzuki, Yutaka
Nakai, Kenta
Author's alias: 熊谷, 雄太郎
鈴木, 穣
中井, 謙太
Keywords: Histone modifications
Dendritic cells
Epigenetics
Transcription factors
ChIP-seq
Time series
Issue Date: 2018
Publisher: Springer Nature America, Inc
Journal title: Genome Biology
Volume: 19
Issue: 1
Thesis number: 138
Abstract: Background: The importance of transcription factors (TFs) and epigenetic modifications in the control of gene expression is widely accepted. However, causal relationships between changes in TF binding, histone modifications, and gene expression during the response to extracellular stimuli are not well understood. Here, we analyze the ordering of these events on a genome-wide scale in dendritic cells in response to lipopolysaccharide (LPS) stimulation. Results: Using a ChIP-seq time series dataset, we find that the LPS-induced accumulation of different histone modifications follows clearly distinct patterns. Increases in H3K4me3 appear to coincide with transcriptional activation. In contrast, H3K9K14ac accumulates early after stimulation, and H3K36me3 at later time points. Integrative analysis with TF binding data reveals potential links between TF activation and dynamics in histone modifications. Especially, LPS-induced increases in H3K9K14ac and H3K4me3 are associated with binding by STAT1/2 and were severely impaired in Stat1-/- cells. Conclusions: While the timing of short-term changes of some histone modifications coincides with changes in transcriptional activity, this is not the case for others. In the latter case, dynamics in modifications more likely reflect strict regulation by stimulus-induced TFs and their interactions with chromatin modifiers.
Description: Waves of changes in genome structure in immune response. 京都大学プレスリリース. 2019-02-21.
Rights: © The Author(s). 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
URI: http://hdl.handle.net/2433/236569
DOI(Published Version): 10.1186/s13059-018-1524-z
PubMed ID: 30231913
Related Link: https://www.kyoto-u.ac.jp/en/research/research_results/2018/180919_2.html
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