Genome-Wide Prediction of Nucleosome Occupancy in Maize Reveals Plant Chromatin Structural Features at Genes and Other Elements at Multiple Scales
Genome-Wide Prediction of Nucleosome Occupancy in Maize Reveals Plant Chromatin Structural Features at Genes and Other Elements at Multiple Scales
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DOI：
10.1104/pp.113.216432
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发表时间：
2013-06-01
期刊：
影响因子：
7.4
通讯作者：
Bass, Hank W.
中科院分区：
文献类型：
--
作者：
Fincher, Justin A.;Vera, Daniel L.;Bass, Hank W.
核小体是一个基本的结构和功能的染色质单位，影响几乎所有的DNA模板在真核生物基因组中的事件。它也是高阶顺式作用基因表达编码的生化底物和多尺度染色质包装的单体结构单元。为了预测模型植物基因组的核小体景观，我们使用了在人类染色质上训练的支持向量机计算算法来预测玉米（Zea mays）基因组中的核小体占用可能性（NOL）。实验验证的NOL图提供了一种新的基因组注释，突出了基因结构，重复元件和染色体尺度域可能反映区域基因密度。我们建立了一个新的基因组浏览器（http：www.genomaize.org），用于查看基于支持向量机的NOL评分。该注释提供了整个基因组的基于序列的全面覆盖，包括通常从实验基因组学数据中排除的重复基因组区域。我们发现，转座因子往往显示家庭特定的NOL配置文件，其中包括不同的地区，特别是在其末端附近，预测有很强的亲和力核小体。我们检查了玉米基因组的转录起始位点共有NOL图，发现大多数玉米基因在起始位点的下游而不是上游显示出典型的+1核小体定位信号。这种-1核小体定位信号的总体缺乏也通过我们的方法对拟南芥（Arabidopsis thaliana）基因进行了预测，并通过对先前发表的拟南芥MNase-Seq数据的额外分析进行了验证，揭示了植物启动子的一般特征。我们的研究通过定义DNA序列对观察到的核小体定位的潜在贡献来推进植物染色质研究，并提供了一个不变的基线注释，可以与其他基因组数据进行比较。
The nucleosome is a fundamental structural and functional chromatin unit that affects nearly all DNA-templated events in eukaryotic genomes. It is also a biochemical substrate for higher order, cis-acting gene expression codes and the monomeric structural unit for chromatin packaging at multiple scales. To predict the nucleosome landscape of a model plant genome, we used a support vector machine computational algorithm trained on human chromatin to predict the nucleosome occupancy likelihood (NOL) across the maize (Zea mays) genome. Experimentally validated NOL plots provide a novel genomic annotation that highlights gene structures, repetitive elements, and chromosome-scale domains likely to reflect regional gene density. We established a new genome browser (http://www.genomaize.org) for viewing support vector machine-based NOL scores. This annotation provides sequence-based comprehensive coverage across the entire genome, including repetitive genomic regions typically excluded from experimental genomics data. We find that transposable elements often displayed family-specific NOL profiles that included distinct regions, especially near their termini, predicted to have strong affinities for nucleosomes. We examined transcription start site consensus NOL plots for maize gene sets and discovered that most maize genes display a typical +1 nucleosome positioning signal just downstream of the start site but not upstream. This overall lack of a -1 nucleosome positioning signal was also predicted by our method for Arabidopsis (Arabidopsis thaliana) genes and verified by additional analysis of previously published Arabidopsis MNase-Seq data, revealing a general feature of plant promoters. Our study advances plant chromatin research by defining the potential contribution of the DNA sequence to observed nucleosome positioning and provides an invariant baseline annotation against which other genomic data can be compared.