A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
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DOI：
10.1101/gr.078261.108
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发表时间：
2008-07-01
期刊：
影响因子：
7
通讯作者：
Pugh, B. Franklin
中科院分区：
文献类型：
--
作者：
Mavrich, Travis N.;Ioshikhes, Ilya P.;Pugh, B. Franklin
大多数核小体在酿酒酵母基因的 5' 端组织良好，其中“-1”和“+1”核小体包围着无核小体启动子区域 (NFR)。核小体组织是如何由基因组指定的尚不清楚。在这里，我们通过对来自超过一百万个免疫纯化的酿酒酵母核小体的 DNA 进行测序，建立并相互关联了控制基因组核小体组织的规则（显示在 http://atlas.bx.psu.edu/）。有证据表明，整个基因中核小体的组织很大程度上是统计包装原理的结果。基因组序列指定了 -1 和 +1 核小体的位置。 +1 核小体形成了核小体堆积的屏障，导致均匀定位，在距屏障较远的距离处衰减。我们提供了新的 3' NFR 的证据，该 3' NFR 存在于 > 95% 的所有基因中。 3' NFR 对于转录终止和反义起始可能很重要。我们提出了 TFIIB 位置的高分辨率全基因组图谱，该图谱暗示了基因循环中的 3' NFR。
Most nucleosomes are well-organized at the 5' ends of S. cerevisiae genes where "-1" and "+1" nucleosomes bracket a nucleosome-free promoter region (NFR). How nucleosomal organization is specified by the genome is less clear. Here we establish and inter-relate rules governing genomic nucleosome organization by sequencing DNA from more than one million immunopurified S. cerevisiae nucleosomes ( displayed at http://atlas.bx.psu.edu/). Evidence is presented that the organization of nucleosomes throughout genes is largely a consequence of statistical packing principles. The genomic sequence specifies the location of the -1 and +1 nucleosomes. The +1 nucleosome forms a barrier against which nucleosomes are packed, resulting in uniform positioning, which decays at farther distances from the barrier. We present evidence for a novel 3' NFR that is present at > 95% of all genes. 3' NFRs may be important for transcription termination and anti-sense initiation. We present a high-resolution genome-wide map of TFIIB locations that implicates 3' NFRs in gene looping.