AstraZeneca R&D Boston, Waltham, Massachusetts, United States of America.
PLoS One. 2011;6(8):e23490. doi: 10.1371/journal.pone.0023490. Epub 2011 Aug 11.
Nucleosomes can block access to transcription factors. Thus the precise localization of nucleosomes relative to transcription start sites and other factor binding sites is expected to be a critical component of transcriptional regulation. Recently developed microarray approaches have allowed the rapid mapping of nucleosome positions over hundreds of kilobases (kb) of human genomic DNA, although these approaches have not yet been widely used to measure chromatin changes associated with changes in transcription. Here, we use custom tiling microarrays to reveal changes in nucleosome positions and abundance that occur when hormone-bound glucocorticoid receptor (GR) binds to sites near target gene promoters in human osteosarcoma cells. The most striking change is an increase in measured nucleosome occupancy at sites spanning ∼1 kb upstream and downstream of transcription start sites, which occurs one hour after addition of hormone, but is lost at 4 hours. Unexpectedly, this increase was seen both on GR-regulated and GR-non-regulated genes. In addition, the human SWI/SNF chromatin remodeling factor (a GR co-activator) was found to be important for increased occupancy upon hormone treatment and also for low nucleosome occupancy without hormone. Most surprisingly, similar increases in nucleosome occupancy were also seen on both regulated and non-regulated promoters during differentiation of human myeloid leukemia cells and upon activation of human CD4+ T-cells. These results indicate that dramatic changes in chromatin structure over ∼2 kb of human promoters may occur genomewide and in response to a variety of stimuli, and suggest novel models for transcriptional regulation.
核小体可以阻止转录因子的进入。因此，核小体相对于转录起始位点和其他因子结合位点的精确定位有望成为转录调控的关键组成部分。最近开发的微阵列方法允许快速绘制数百千碱基（kb）的人类基因组 DNA 上的核小体位置，尽管这些方法尚未广泛用于测量与转录变化相关的染色质变化。在这里，我们使用定制的平铺微阵列来揭示激素结合的糖皮质激素受体（GR）与人类骨肉瘤细胞中靶基因启动子附近的位点结合时发生的核小体位置和丰度的变化。最引人注目的变化是在转录起始位点上下游跨越约 1kb 的位点上测量到的核小体占有率增加，这发生在添加激素后 1 小时，但在 4 小时时丢失。出乎意料的是，这种增加在 GR 调节和 GR 非调节基因上都可以看到。此外，发现人类 SWI/SNF 染色质重塑因子（GR 共激活因子）对于激素处理后增加的占有率以及没有激素时的低核小体占有率很重要。最令人惊讶的是，在人类髓样白血病细胞分化和人 CD4+T 细胞激活期间，在调节和非调节启动子上也观察到核小体占有率的类似增加。这些结果表明，人类启动子约 2kb 范围内的染色质结构可能发生剧烈变化，这是全基因组范围内发生的，并响应各种刺激，这为转录调控提出了新的模型。
