Dynamic transition of transcription and chromatin landscape during fission yeast adaptation to glucose starvation
Dynamic transition of transcription and chromatin landscape during fission yeast adaptation to glucose starvation
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DOI：
10.1111/gtc.12229
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发表时间：
2015-05-01
期刊：
影响因子：
2.1
通讯作者：
Ohta, Kunihiro
中科院分区：
文献类型：
--
作者：
Oda, Arisa;Takemata, Naomichi;Ohta, Kunihiro
葡萄糖是所有生物体的主要能量来源，葡萄糖的缺乏是影响细胞活力的最关键压力之一。葡萄糖饥饿迅速诱导mRNA和非编码RNA（ncRNA）转录的变化。我们以前报道过葡萄糖饥饿诱导裂殖酵母染色体异生基因fbp 1（+）的5个片段中的长ncRNA（lncRNA）转录，这导致fbp 1（+）启动子周围的逐步染色质改变和随后的稳健基因激活。在这里，我们通过链特异性RNA测序分析了全基因组转录，并通过免疫沉淀测序（ChIP-seq）分析了染色质景观。聚类分析表明，不同的mRNA和ncRNA诱导的早期，中期和后期阶段的细胞响应葡萄糖饥饿。饥饿诱导的转录在很大程度上依赖于应激反应转录因子Atf 1。使用一种新的计算机程序，检查表达模式的动态变化，我们确定了与fbp 1（+）lncRNA具有相似行为的ncRNA。我们证实了有连续的lncRNA与组蛋白密度的局部降低相关。与这些lncRNA的转录区域重叠，反义RNA在富含葡萄糖的条件下被拮抗性地转录。这些结果表明，Atf 1依赖的mRNA和lncRNA的整合网络管理响应于葡萄糖饥饿的细胞生理学的急剧变化。
Shortage of glucose, the primary energy source for all organisms, is one of the most critical stresses influencing cell viability. Glucose starvation promptly induces changes in mRNA and noncoding RNA (ncRNA) transcription. We previously reported that glucose starvation induces long ncRNA (lncRNA) transcription in the 5 segment of a fission yeast gluconeogenesis gene (fbp1(+)), which leads to stepwise chromatin alteration around the fbp1(+) promoter and to subsequent robust gene activation. Here, we analyzed genomewide transcription by strand-specific RNA sequencing, together with chromatin landscape by immunoprecipitation sequencing (ChIP-seq). Clustering analysis showed that distinct mRNAs and ncRNAs are induced at the early, middle and later stages of cellular response to glucose starvation. The starvation-induced transcription depends substantially on the stress-responsive transcription factor Atf1. Using a new computer program that examines dynamic changes in expression patterns, we identified ncRNAs with similar behavior to the fbp1(+) lncRNA. We confirmed that there are continuous lncRNAs associated with local reduction of histone density. Overlapping with the regions for transcription of these lncRNAs, antisense RNAs are antagonistically transcribed under glucose-rich conditions. These results suggest that Atf1-dependent integrated networks of mRNA and lncRNA govern drastic changes in cell physiology in response to glucose starvation.