Effects of cycloheximide on the interpretation of ribosome profiling experiments in Schizosaccharomyces pombe.
Effects of cycloheximide on the interpretation of ribosome profiling experiments in Schizosaccharomyces pombe.
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DOI：
10.1038/s41598-017-10650-1
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发表时间：
2017-09-04
影响因子：
4.6
通讯作者：
Mata J
中科院分区：
文献类型：
--
作者：
Duncan CDS;Mata J
应激条件导致RNA翻译的全局和基因特异性变化。核糖体分析实验已经确定了核糖体沿着mRNA分布的全基因组变化。然而，这些变化是否反映了真实的反应，或者它们是否是使用翻译抑制剂（特别是放线菌酮）引起的假象，这是有争议的。为了解决这个问题，我们进行了核糖体分析与裂变酵母裂殖酵母粟酒裂殖酵母的指数增长（无压力）和氮饥饿（营养压力）的条件下，在存在和不存在放线菌酮。我们研究了翻译反应的几个方面，包括编码序列上的核糖体足迹密度，5′前导核糖体密度，核糖体沿着编码序列的分布，以及核糖体密码子占据。放线菌酮对总体核糖体密度的影响较小，主要影响编码核糖体蛋白的mRNA。氮饥饿引起核糖体在环己酰亚胺处理和未处理的细胞中的5′前导序列上的积累。相反，胁迫诱导的核糖体在编码序列5′端的积累是环己酰亚胺依赖的。最后，密码子占有率在环己酰亚胺处理和未处理的细胞中显示出强的正相关性。我们的研究结果表明，放线菌酮确实影响核糖体分析实验的一些结果，虽然目前还不清楚这种影响是否总是人为的。
Stress conditions lead to global and gene-specific changes in RNA translation. Ribosome profiling experiments have identified genome-wide alterations in the distribution of ribosomes along mRNAs. However, it is contentious whether these changes reflect real responses, or whether they are artefacts caused by the use of inhibitors of translation (notably cycloheximide). To address this issue we performed ribosome profiling with the fission yeast Schizosaccharomyces pombe under conditions of exponential growth (unstressed) and nitrogen starvation (nutritional stress), and both in the presence and absence of cycloheximide. We examined several aspects of the translational response, including density of ribosomal footprints on coding sequences, 5′ leader ribosomal densities, distribution of ribosomes along coding sequences, and ribosome codon occupancies. Cycloheximide had minor effects on overall ribosome density, which affected mostly mRNAs encoding ribosomal proteins. Nitrogen starvation caused an accumulation of ribosomes on 5′ leaders in both cycloheximide-treated and untreated cells. By contrast, stress-induced ribosome accumulation on the 5′ side of coding sequences was cycloheximide-dependent. Finally, codon occupancy showed strong positive correlations in cycloheximide-treated and untreated cells. Our results demonstrate that cycloheximide does influence some of the results of ribosome profiling experiments, although it is not clear if this effect is always artefactual.
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影响因子：
9.8
作者：
Charneski CA;Hurst LD
通讯作者：
Hurst LD
影响因子：
14.9
作者：
Rustici G;Kolesnikov N;Brandizi M;Burdett T;Dylag M;Emam I;Farne A;Hastings E;Ison J;Keays M;Kurbatova N;Malone J;Mani R;Mupo A;Pedro Pereira R;Pilicheva E;Rung J;Sharma A;Tang YA;Ternent T;Tikhonov A;Welter D;Williams E;Brazma A;Parkinson H;Sarkans U
通讯作者：
Sarkans U
DOI：
10.1038/nrm4069
发表时间：
2015-11
期刊：
Nature reviews. Molecular cell biology
影响因子：
--
作者：
Brar GA;Weissman JS
通讯作者：
Weissman JS
影响因子：
16
作者：
Liu, Botao;Han, Yan;Qian, Shu-Bing
通讯作者：
Qian, Shu-Bing
影响因子：
4.5
作者：
Hussmann, Jeffrey A.;Patchett, Stephanie;Press, William H.
通讯作者：
Press, William H.