Beh Leslie Y, Müller Manuel M, Muir Tom W, Kaplan Noam, Landweber Laura F
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA;
Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA;
Genome Res. 2015 Nov;25(11):1727-38. doi: 10.1101/gr.188516.114. Epub 2015 Sep 1.
A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream from transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from the presence of subsets of nucleosomes, rather than the whole array, in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes and affects codon usage and amino acid composition in genes. Given that the AT-rich Tetrahymena genome is intrinsically unfavorable for nucleosome formation, we propose that these "seed" nucleosomes--together with trans-acting factors--may facilitate the establishment of nucleosome arrays within genes in vivo, while minimizing changes to the underlying coding sequences.
真核染色质结构的一个保守特征是转录起始位点（TSS）下游排列整齐的核小体阵列。最近的研究表明，反式作用因子建立了这种刻板的阵列。在这里，我们展示了嗜热四膜虫的首张全基因组体外和体内核小体图谱。与之前在酵母中的研究不同，我们发现这种刻板的核小体阵列在体外重构图谱中得以保留，该图谱仅由核小体的DNA序列偏好决定。值得注意的是，这种平均体外模式源于单个嗜热四膜虫基因中核小体子集的存在，而非整个阵列。GC含量的变化有助于这些序列导向核小体的定位，并影响基因中的密码子使用和氨基酸组成。鉴于富含AT的嗜热四膜虫基因组本质上不利于核小体形成，我们提出这些“种子”核小体——连同反式作用因子——可能有助于在体内基因内建立核小体阵列，同时将对基础编码序列的改变降至最低。
