A new parameter to study compositional properties of non-coding regions in eukaryotic genomes
A new parameter to study compositional properties of non-coding regions in eukaryotic genomes
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DOI：
10.1016/j.gene.2006.05.030
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发表时间：
2006-12-30
期刊：
影响因子：
3.5
通讯作者：
Pizzi, Elisabetta
中科院分区：
文献类型：
--
作者：
Bultrini, Emanuele;Pizzi, Elisabetta
基因组的特征是全局和局部的组成属性，这些属性从进化的角度来看是有趣的，但也为识别一些功能元件提供了有用的信息。在前人研究的基础上，本论文研究了四个真核生物基因组(线虫、黑腹线虫、博物馆线虫、智人线虫)非编码序列的组成特征。我们开发了一种基于主成分分析(PCA)和线性判别分析(LDA)的方法来识别内含子(内含子词汇)中过度表达的五聚体，并定义了一个反映给定序列的寡核苷酸组成的新参数(LD)。我们分析了基因组序列，发现基因组的所有非编码部分都具有相似的LD值。此外，我们使用新的参数来分析潜在的监管区域。我们提取了黑腹蛇和智人的非冗余启动子序列，并研究了它们的组成(G+C含量和LD参数)和构象(弯曲倾向)特性。我们发现，紧挨着转录起始点周围的区域是可区分的，因为它们的%G+C、LD和可弯曲性值。(C)2006爱思唯尔B.V.保留所有权利。
Genomes are characterized by global and local compositional properties that are interesting in an evolutionary perspective but also provide useful information for the identification of some functional elements. Following previous studies, in this work we investigated compositional properties of non-coding sequences in four eukaryotic genomes (C. elegans, D. melanogaster, M. museulus, H. sapiens). We developed a procedure based on Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) to identify pentamers that are over-represented in introns (intron vocabulary) and to define a new parameter (LD) that reflects oligonucleotide composition of a given sequence. We analyzed genomic sequences and we found that all non-coding parts of a genome are characterized by similar LD values. Furthermore, we used the new parameter to analyze potentially regulatory regions. We extracted non-redundant sets of promoter sequences for D. melanogaster and H. sapiens and we studied their compositional (G+C content and LD parameter) and conformational (bendability propensity) properties. We found that regions immediately surrounding transcription start sites are distinguishable because of their %G+C, LD and bendability values. (c) 2006 Elsevier B.V. All rights reserved.