Fuzziness and noise in nucleosomal architecture.
Fuzziness and noise in nucleosomal architecture.
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DOI：
10.1093/nar/gku165
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发表时间：
2014-04
影响因子：
14.9
通讯作者：
Orozco M
中科院分区：
文献类型：
--
作者：
Flores O;Deniz Ö;Soler-López M;Orozco M
核小体组织在基因表达调控中起着关键作用。然而，尽管核小体图谱的准确性取得了惊人的进步，但在单个核小体的定位及其如何影响基因调控方面仍然存在严重的差异。核小体图谱之间的可变性，妨碍了对核小体定位的精细分析，可能来自不同的来源。我们通过比较不同条件下产生的微球菌核酸酶(MNase)-Seq衍生核小体图，仔细检查了可能诱导多样性的外部因素。此外，我们还通过生成来自细胞周期同步和异步酵母培养的附加图谱，探索了源自内在核小体动力学的变异。综上所述，我们的研究使我们能够测量噪声对核小体占用和定位的影响，并提供对潜在决定因素的见解。此外，我们提出了一种系统的方法，可以指导MNase-Seq实验的标准化，以产生可重复的全基因组核小体模式。
Nucleosome organization plays a key role in the regulation of gene expression. However, despite the striking advances in the accuracy of nucleosome maps, there are still severe discrepancies on individual nucleosome positioning and how this influences gene regulation. The variability among nucleosome maps, which precludes the fine analysis of nucleosome positioning, might emerge from diverse sources. We have carefully inspected the extrinsic factors that may induce diversity by the comparison of microccocal nuclease (MNase)-Seq derived nucleosome maps generated under distinct conditions. Furthermore, we have also explored the variation originated from intrinsic nucleosome dynamics by generating additional maps derived from cell cycle synchronized and asynchronous yeast cultures. Taken together, our study has enabled us to measure the effect of noise in nucleosome occupancy and positioning and provides insights into the underlying determinants. Furthermore, we present a systematic approach that may guide the standardization of MNase-Seq experiments in order to generate reproducible genome-wide nucleosome patterns.
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影响因子：
14.9
作者：
Gauthier NP;Jensen LJ;Wernersson R;Brunak S;Jensen TS
通讯作者：
Jensen TS
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
DOI：
10.1080/07391102.2010.10508585
发表时间：
2010-06-01
影响因子：
4.4
作者：
Arya, Gaurav;Maitra, Arijit;Grigoryev, Sergei A.
通讯作者：
Grigoryev, Sergei A.
影响因子：
5.8
作者：
Flores, Oscar;Orozco, Modesto
通讯作者：
Orozco, Modesto
DOI：
10.2202/1544-6115.1454
发表时间：
2009-01-01
影响因子：
0.9
作者：
Kuan, Pei Fen;Huebert, Dana;Keles, Sunduz
通讯作者：
Keles, Sunduz