Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data.
Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data.
复制标题
DOI：
10.1371/journal.pone.0025260
复制
发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Peng Z
中科院分区：
文献类型：
--
作者：
Malone BM;Tan F;Bridges SM;Peng Z
染色质免疫沉淀与高通量 DNA 测序 (ChIP-Seq) 相结合已成为对组蛋白和转录因子等 DNA 相关蛋白质的结合位点进行全基因组分析的强大工具。然而，尚无任何峰识别程序获得科学界的一致认可，成为 ChIP-Seq 数据分析的首选工具。对于大多数分子生物学实验室来说，分析 ChIP-Seq 研究生成的大型数据集仍然具有挑战性。在这里，我们使用 ChIP-Seq 方法分析水稻幼胚乳中的 H3K27me3 富集位点，并使用四种峰调用算法（FindPeaks、PeakSeq、USeq 和 MACS）分析数据。四种算法的比较表明，这些程序在峰大小、数量和相对于基因的位置方面产生非常不同的峰。我们使用 ChIP-PCR 验证峰值预测，以评估四种算法峰值预测的准确性。我们讨论每种算法的方法并比较结果的异同。尽管确定的峰存在差异，但所有程序都就 H3K27me3 对基因表达的影响得出相似的结论。它在基因上游或下游的存在主要与基因的抑制有关。此外，GO 分析发现，与水稻基因组的其余部分相比，与 H3K27me3 相关的基因参与多细胞生物发育、信号转导、对外部和内源刺激的响应以及次级代谢途径的比例要高得多。
Chromatin immunoprecipitation coupled with high throughput DNA Sequencing (ChIP-Seq) has emerged as a powerful tool for genome wide profiling of the binding sites of proteins associated with DNA such as histones and transcription factors. However, no peak calling program has gained consensus acceptance by the scientific community as the preferred tool for ChIP-Seq data analysis. Analyzing the large data sets generated by ChIP-Seq studies remains highly challenging for most molecular biology laboratories. Here we profile H3K27me3 enrichment sites in rice young endosperm using the ChIP-Seq approach and analyze the data using four peak calling algorithms (FindPeaks, PeakSeq, USeq, and MACS). Comparison of the four algorithms reveals that these programs produce very different peaks in terms of peak size, number, and position relative to genes. We verify the peak predictions using ChIP-PCR to evaluate the accuracy of peak prediction of the four algorithms. We discuss the approach of each algorithm and compare similarities and differences in the results. Despite their differences in the peaks identified, all of the programs reach similar conclusions about the effect of H3K27me3 on gene expression. Its presence either upstream or downstream of a gene is predominately associated with repression of the gene. Additionally, GO analysis finds that a substantially higher ratio of genes associated with H3K27me3 were involved in multicellular organism development, signal transduction, response to external and endogenous stimuli, and secondary metabolic pathways than the rest of the rice genome.
登录
查看更多内容
影响因子：
3
作者：
Nix DA;Courdy SJ;Boucher KM
通讯作者：
Boucher KM
影响因子：
64.8
作者：
Matsumoto, T;Wu, JZ;Sugiura, M
通讯作者：
Sugiura, M
影响因子：
11.6
作者：
He, Guangming;Zhu, Xiaopeng;Deng, Xing-Wang
通讯作者：
Deng, Xing-Wang
影响因子：
10.5
作者：
Baroux, U;Gagliardini, V;Grossniklaus, U
通讯作者：
Grossniklaus, U
影响因子：
30.8
作者：
Köhler, C;Page, DR;Grossniklaus, U
通讯作者：
Grossniklaus, U