Gaussian derivative wavelets identify dynamic changes in histone modification
Gaussian derivative wavelets identify dynamic changes in histone modification
复制标题
高斯导数小波识别组蛋白修饰的动态变化
DOI：
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Kyoung
中科院分区：
文献类型：
--
作者：
Nha Nguyen;Kyoung
表观遗传景观揭示了细胞如何以细胞类型或条件特异性方式调节基因。使用组蛋白修饰的全基因组调查显示了细胞类型特异性调控区域。设计了许多计算方法来使用表观基因组数据鉴定细胞类型特异性调控区域。其中大多数是为了鉴定组蛋白修饰或其变化的富集。然而，他们没有考虑表观遗传信号的形状，这代表了基因调控区蛋白质结合的条件。我们提出了一种计算方法来检测表观遗传的变化，使用组蛋白修饰的信号的形状。采用高斯导数小波（CGDWavelet）的方法，所提出的方法与高斯模型的核小体和检测的峰值和边缘的高斯。使用两个样本中检测到的参数，CGDWavelet对表观遗传变化进行分类。我们将CGDWavelet应用于小鼠胚胎干细胞（mESC）和神经祖细胞（mNPC）的组蛋白修饰数据，并确定了四组表观遗传变化。将各组与基因表达相关联，我们发现基因表达受到染色质结构以及组蛋白修饰强度的影响。我们发现，Smad1，Sox2和Nanog，而不是Oct4结合到H3K4me3的表观遗传可变区。软件可在http://wonk.med.upenn.edu/CGDWavelet上获得。
Epigenetic landscapes reveal how cells regulate genes in a cell-type or condition specific manner. Genome-wide surveys using histone modification showed cell-type specific regulatory regions. A number of computational methods were designed to identify cell-type specific regulatory regions using epigenome data. Most of them were designed to identify the enrichment of histone modification or their changes. However, they did not consider the shape of epigenetic signals, which represents the condition for protein binding at gene regulatory regions. We present a computational method to detect epigenetic changes using the shape of the signals for histone modification. Employing a Gaussian Derivative Wavelet (CGDWavelet) approach, the proposed method models a nucleosome with a Gaussian and detects the peak and the edges of the Gaussian. Using the detected parameters across two samples, CGDWavelet classifies epigenetic changes. We applied CGDWavelet to the histone modification data from mouse embryonic stem cells (mESCs) and neural progenitor cells (mNPCs) and identified four groups of epigenetic changes. Associating each group with gene expression, we found that gene expression is affected by chromatin structure as well as the intensity of histone modification. We found that Smad1, Sox2 and Nanog but not Oct4 bind to the epigenetically variable regions for H3K4me3. Software is available at http://wonk.med.upenn.edu/CGDWavelet.
影响因子：
16
作者：
Heinz S;Benner C;Spann N;Bertolino E;Lin YC;Laslo P;Cheng JX;Murre C;Singh H;Glass CK
通讯作者：
Glass CK
影响因子：
23.9
作者：
Hawkins RD;Hon GC;Lee LK;Ngo Q;Lister R;Pelizzola M;Edsall LE;Kuan S;Luu Y;Klugman S;Antosiewicz-Bourget J;Ye Z;Espinoza C;Agarwahl S;Shen L;Ruotti V;Wang W;Stewart R;Thomson JA;Ecker JR;Ren B
通讯作者：
Ren B
影响因子：
7
作者：
Ernst, Jason;Plasterer, Heather L.;Bar-Joseph, Ziv
通讯作者：
Bar-Joseph, Ziv