Mathematical model to predict regions of chromatin attachment to the nuclear matrix
Mathematical model to predict regions of chromatin attachment to the nuclear matrix
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DOI：
10.1093/nar/25.7.1419
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发表时间：
1997-04-01
影响因子：
14.9
通讯作者：
Krawetz, SA
中科院分区：
文献类型：
--
作者：
Singh, GB;Kramer, JA;Krawetz, SA
转录的增强和随后的启动是复杂的生物学现象，染色质纤维与核基质的附着区域，称为基质附着区或支架附着区（MAR或SAR）被认为是真核基因组的转录调节所必需的。由于表达的序列应包含在这些区域中，因此回答以下问题变得重要：这些区域是否可以单独从一级序列数据中鉴定出来并随后用作表达序列的标记？本文描述了一种用于检测MAR的数学模型，该模型将矩阵相关区域的位置与各种序列模式联系起来，因此，使用ANP-OR公式编制这些模式的列表并将其表示为一组决策规则，然后搜索DNA序列中这些模式的存在，并将统计学显著性与各种模式的出现频率相关联。随后，计算数学势值，MAR-势，被分配给序列区域，其与观察到的模式群体随机发生的概率成反比。这种MAR检测过程被应用于多种已知的含有MAR的序列的分析。由软件预测的矩阵关联的区域基本上对应于实验确定的那些，还分析了人类T细胞受体和果蝇双胸区的DNA序列，这表明了所述方法作为指导实验资源的手段的有用性。
The potentiation and subsequent initiation of transcription are complex biological phenomena, The region of attachment of the chromatin fiber to the nuclear matrix, known as the matrix attachment region or scaffold attachment region (MAR or SAR), are thought to be requisite for the transcriptional regulation of the eukaryotic genome, As expressed sequences should be contained in these regions, it becomes significant to answer the following question: can these regions be identified from the primary sequence data alone and subsequently used as markers for expressed sequences? This paper represents an effort toward achieving this goal and describes a mathematical model for the detection of MARs, The location of matrix associated regions has been linked to a variety of sequence patterns, Consequently, a list of these patterns is compiled and represented as a set of decision rules using an ANP-OR formulation, The DNA sequence was then searched for the presence of these patterns and a statistical significance was associated with the frequency of occurrence of the various patterns, Subsequently, a mathematical potential value, MAR-Potential, was assigned to a sequence region as the inverse proportion to the probability that the observed pattern population occurred at random, Such a MAR detection process was applied to the analysis of a variety of known MAR containing sequences, Regions of matrix association predicted by the software essentially correspond to those determined experimentally, The human T-cell receptor and the DNA sequence from the Drosophila bithorax region were also analyzed, This demonstrates the usefulness of the approach described as a means to direct experimental resources.