DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome.
DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome.
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DOI：
10.1101/gr.188516.114
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发表时间：
2015-11
期刊：
影响因子：
7
通讯作者：
Landweber LF
中科院分区：
文献类型：
--
作者：
Beh LY;Müller MM;Muir TW;Kaplan N;Landweber LF
真核生物染色质结构的一个保守标志是转录起始位点（TSS）下游位置良好的核小体的独特阵列。最近的研究表明，反式作用因子建立了这种刻板印象。在这里，我们提出了第一个全基因组的体外和体内核小体图的纤毛四膜虫嗜热。与以前的研究相比，在酵母中，我们发现，刻板的核小体阵列被保存在体外重建的地图，这是由核小体的DNA序列偏好。值得注意的是，这种平均的体外模式来自于核小体的子集的存在，而不是整个阵列，在个别四膜虫基因。GC含量的变化有助于这些序列导向的核小体的定位，并影响基因中的密码子使用和氨基酸组成。鉴于AT-丰富的四膜虫基因组本质上是不利的核小体形成，我们建议，这些“种子”核小体与反式作用因子，可能有助于建立核小体阵列内的基因在体内，同时最大限度地减少潜在的编码序列的变化。
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.