Fortin Connor H, Schulze Katharina V, Babbitt Gregory A
Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623 USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA.
Source Code Biol Med. 2015 Sep 25;10:10. doi: 10.1186/s13029-015-0040-8. eCollection 2015.
It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence logos plots are severely limited in that they convey no explicit information regarding the structural dynamics of DNA backbone, a feature often critical to binding specificity.
We present TRX-LOGOS, an R software package and Perl wrapper code that interfaces the JASPAR database for computational regulatory genomics. TRX-LOGOS extends the traditional sequence logo plot to include Shannon information content calculated with regard to the dinucleotide-based BI-BII conformation shifts in phosphate linkages on the DNA backbone, thereby adding a visual measure of intrinsic DNA flexibility that can be critical for many DNA-protein interactions. TRX-LOGOS is available as an R graphics module offered at both SourceForge and as a download supplement at this journal.
To demonstrate the general utility of TRX logo plots, we first calculated the information content for 416 Saccharomyces cerevisiae transcription factor binding sites functionally confirmed in the Yeastract database and matched to previously published yeast genomic alignments. We discovered that flanking regions contain significantly elevated information content at phosphate linkages than can be observed at nucleobases. We also examined broader transcription factor classifications defined by the JASPAR database, and discovered that many general signatures of transcription factor binding are locally more information rich at the level of DNA backbone dynamics than nucleobase sequence. We used TRX-logos in combination with MEGA 6.0 software for molecular evolutionary genetics analysis to visually compare the human Forkhead box/FOX protein evolution to its binding site evolution. We also compared the DNA binding signatures of human TP53 tumor suppressor determined by two different laboratory methods (SELEX and ChIP-seq). Further analysis of the entire yeast genome, center aligned at the start codon, also revealed a distinct sequence-independent 3 bp periodic pattern in information content, present only in coding region, and perhaps indicative of the non-random organization of the genetic code.
TRX-LOGOS is useful in any situation in which important information content in DNA can be better visualized at the positions of phosphate linkages (i.e. dinucleotides) where the dynamic properties of the DNA backbone functions to facilitate DNA-protein interaction.
现在人们普遍认为，定义DNA-蛋白质相互作用的DNA序列在功能上取决于DNA主链的局部生物物理特征，这些特征对于确定基因组中的结合相互作用位点很重要（例如DNA形状、电荷和内在动力学）。然而，在传统序列标志图中分析和查看单个核苷酸碱基处计算的香农信息含量时，DNA聚合物的这些物理特征并不直接明显。因此，序列标志图存在严重局限性，因为它们没有传达关于DNA主链结构动力学的明确信息，而这一特征通常对结合特异性至关重要。
我们展示了TRX-LOGOS，这是一个R软件包和Perl包装代码，它连接用于计算调控基因组学的JASPAR数据库。TRX-LOGOS扩展了传统序列标志图，将基于二核苷酸的DNA主链磷酸键BI-BII构象变化计算的香农信息含量纳入其中，从而增加了一种对内在DNA灵活性的直观度量，这对许多DNA-蛋白质相互作用可能至关重要。TRX-LOGOS可作为R图形模块在SourceForge上获取，也可作为本期刊的下载补充内容。
为了证明TRX标志图的一般实用性，我们首先计算了在Yeastract数据库中功能得到确认并与先前发表的酵母基因组比对相匹配的416个酿酒酵母转录因子结合位点的信息含量。我们发现侧翼区域在磷酸键处的信息含量明显高于核苷酸碱基处。我们还研究了JASPAR数据库定义的更广泛的转录因子分类，发现许多转录因子结合的一般特征在DNA主链动力学水平上比核苷酸碱基序列在局部更具信息丰富性。我们将TRX标志图与用于分子进化遗传学分析的MEGA 6.0软件结合使用，以直观比较人类叉头框/FOX蛋白进化与其结合位点进化。我们还比较了通过两种不同实验室方法（SELEX和ChIP-seq）确定的人类TP53肿瘤抑制因子的DNA结合特征。对以起始密码子为中心对齐的整个酵母基因组的进一步分析还揭示了信息含量中一种独特的、与序列无关的3bp周期性模式，仅存在于编码区，可能表明遗传密码的非随机组织。
在任何情况下，只要在DNA主链动态特性有助于DNA-蛋白质相互作用的磷酸键（即二核苷酸）位置能更好地可视化DNA中的重要信息含量，TRX-LOGOS就很有用。
