2012年森基金　研究成果報告

Entropy based assessment of cell type-specific and frequent histone modification

 

政策・メディア研究科 修士課程2年

野崎慎

研究内容

Modified histones which are specific to certain cellular types or those which are modified in most cell types are linked to cell type-specific or shared cellular functions respectively. To evaluate variations of histone modification patterns in cell types, we introduced two measurements (Hs and Hu). They are based on Shannon entropy which has been applied to the analysis of cell type specificities of gene expression or DNA methylation patterns. Unlike previous definition of entropy, Hs entropy efficiently deals with 0, which correspond to no modified histones, the observation very common in histone modification data. In addition, Hu can evaluate both variances and frequencies; they have been specialized to assess the cell type specificity and the frequency of histone modifications. Applying them to ChIP-Seq data obtained in seven human cell types, we extracted cell type-specific and shared modifications, which were subsequently inspected visually. Comparing entropies of gene expression patterns with Hs of histone modification around genes, we found correlation between the specificity of histone modifications and gene expression patterns. Interestingly, we found differences in the histone modification specificities around enhancers and TSS for some modification types, and genes with frequently modified histones were associated with CpG islands around TSSs compared to cell type-specific histone modifications. Therefore these two measurements enabled us to extract novel characteristics of histone modifications. We believe that in the future, these measures will be useful for epigenetic researches to uncover association between epigenetic regulation and cellular functions.

 

※本報告書はweb公開であるため，論文発表前の具体的な解析データを除いて作成した

 

2012年度　研究業績

国際学会発表 (ポスター)

Entropy-based assessment of cell type-specific and frequent histone modification.

Tadasu Nozaki, Yuki Shindo, Rintaro Saito, Masaru Tomita.

ISMB 2012, Long Beach USA, July 2012

国際査読付き論文発表(査読付き)

Computational analysis of associations between alternative splicing and histone modifications.

Shindo Y, Nozaki T, Saito R, Tomita M.

FEBS Lett. 2013 Mar 1;587(5):516-21. doi: 10.1016/j.febslet.2013.01.032. Epub 2013 Jan 24.

Local nucleosome dynamics facilitate chromatin accessibility in living mammalian cells.

Hihara S, Pack CG, Kaizu K, Tani T, Hanafusa T, Nozaki T, Takemoto S, Yoshimi T, Yokota H, Imamoto N, Sako Y, Kinjo M, Takahashi K, Nagai T, Maeshima K.

Cell Rep. 2012 Dec 27;2(6):1645-56. doi: 10.1016/j.celrep.2012.11.008. Epub 2012 Dec 13.