Department of Medical Biochemistry and Microbiology (IMBIM), University of Uppsala, SE-751 23 Uppsala, Sweden.
Genome Res. 2010 Mar;20(3):361-71. doi: 10.1101/gr.098558.109. Epub 2010 Jan 19.
Gene transcription is associated with local changes in chromatin, both in nucleosome positions and in chemical modifications of the histones. Chromatin dynamics has mostly been studied on a single-gene basis. Those genome-wide studies that have been made primarily investigated steady-state transcription. However, three studies of genome-wide changes in chromatin during the transcriptional response to heat shock in the budding yeast Saccharomyces cerevisiae revealed nucleosome eviction in promoter regions but only minor effects in coding regions. Here, we describe the short-term response to nitrogen starvation in the fission yeast Schizosaccharomyces pombe. Nitrogen depletion leads to a fast induction of a large number of genes in S. pombe and is thus suitable for genome-wide studies of chromatin dynamics during gene regulation. After 20 min of nitrogen removal, 118 transcripts were up-regulated. The distribution of regulated genes throughout the genome was not random; many up-regulated genes were found in clusters, while large parts of the genome were devoid of up-regulated genes. Surprisingly, this up-regulation was associated with nucleosome eviction of equal magnitudes in the promoters and in the coding regions. The nucleosome loss was not limited to induction by nitrogen depletion but also occurred during cadmium treatment. Furthermore, the lower nucleosome density persisted for at least 60 min after induction. Two highly induced genes, urg1(+) and urg2(+), displayed a substantial nucleosome loss, with only 20% of the nucleosomes being left in the coding region. We conclude that nucleosome loss during transcriptional activation is not necessarily limited to promoter regions.
基因转录与染色质的局部变化有关，包括核小体位置和组蛋白的化学修饰。染色质动力学主要在单个基因的基础上进行研究。那些已经进行的全基因组研究主要调查了稳态转录。然而，对酿酒酵母（Saccharomyces cerevisiae）在热休克转录反应过程中染色质全基因组变化的三项研究表明，启动子区域的核小体被逐出，但编码区域的影响较小。在这里，我们描述了裂殖酵母（Schizosaccharomyces pombe）在氮饥饿时的短期反应。氮的消耗导致大量基因在 S. pombe 中快速诱导，因此适合研究基因调控过程中染色质动力学的全基因组研究。在去除氮 20 分钟后，有 118 个转录物上调。受调控基因在基因组中的分布并非随机；许多上调基因位于簇中，而基因组的大部分区域没有上调基因。令人惊讶的是，这种上调与启动子和编码区域中核小体逐出的幅度相等有关。核小体的丢失不仅限于氮饥饿的诱导，在镉处理时也会发生。此外，诱导后至少 60 分钟，核小体密度仍保持较低水平。两个高度诱导的基因 urg1(+)和 urg2(+)显示出大量核小体丢失，编码区中仅剩下 20%的核小体。我们得出结论，转录激活过程中的核小体丢失不一定仅限于启动子区域。
