Single-nucleosome mapping of histone modifications in S. cerevisiae. Saccharomyces cerevisiae

We have used a high-resolution tiled microarray, with single-nucleosome resolution, to investigate the in vivo occurrence of combinations of 12 histone modifications on thousands of nucleosomes in actively growing S. cerevisiae. We found that histone modifications do not occur independently; there are roughly two groups of co-occurring modifications. We find no evidence for a deterministic code of many discrete states, but instead see blended, continuous patterns that distinguish nucleosomes at one location (promoter nucleosomes, for example) from those at another location (over the 3’ ends of coding regions, for example). These results are consistent with the idea of a simple, redundant histone code, in which multiple modifications share the same role. Keywords: ChIP-chip Overall design: In mid-log phase S. cerevisiae, we performed ChIP-chip on 12 different histone modifications and compared their enrichment levels within the genome based on nucleosome position data in series GSE2563. Each TLAD-amplified ChIP sample was labeled with Cy5 and hybridized against Cy3-labeled, TLAD-amplified input on oligonucleotide tiling arrays. At least 3 biological/technical replicates were performed per epitope, with more than one technical replicate for some of the biological replicates, for a total of 64 arrays.

本研究采用具备单核小体分辨率的高分辨率平铺微阵列（tiled microarray），对活跃生长的酿酒酵母（Saccharomyces cerevisiae，缩写为S. cerevisiae）中数千个核小体上12种组蛋白修饰组合的体内发生情况展开了探究。研究发现组蛋白修饰并非独立存在，大致可分为两类共现修饰组合。未发现存在由多种离散状态构成的确定性组蛋白密码的证据，反而观察到混合连续的模式，此类模式可区分不同位置的核小体——例如启动子区域核小体与编码区3'端区域的核小体。上述结果与简单且冗余的组蛋白密码假说相符，该假说认为多种组蛋白修饰可发挥相同功能。
关键词：染色质免疫沉淀芯片（ChIP-chip）
实验设计概述：在对数中期的酿酒酵母中，本研究针对12种不同的组蛋白修饰开展了染色质免疫沉淀芯片（ChIP-chip）实验，并基于GEO数据库系列GSE2563中的核小体位置数据，比较了它们在全基因组范围内的富集水平。每份经TLAD扩增的ChIP样本均用Cy5荧光基团标记，并与经Cy3荧光基团标记、同样经TLAD扩增的输入对照样本在寡核苷酸平铺阵列上进行杂交。每种靶标修饰至少开展3次生物学重复实验，部分生物学重复还设置了多次技术重复，总计完成64张阵列实验。