Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
BMC Genomics. 2012;13 Suppl 1(Suppl 1):S11. doi: 10.1186/1471-2164-13-S1-S11. Epub 2012 Jan 17.
Head-to-head (h2h) genes are prone to have association in expression and in functionality and have been shown conserved in evolution. Currently there are many studies on such h2h gene pairs. We found that the previous studies extremely focused on human genome. Furthermore, they only focused on analyses that require only gene or protein sequences but not conducted a systematic investigation on other promoter features such as the binding evidence of specific transcription factors (TFs). This is mainly because of the incomplete resources of higher organisms, though they are relatively of interest, than model organisms such as Saccharomyces cerevisiae. The authors of this study recently integrated nine promoter features of 6603 genes of S. cerevisiae from six databases and five papers. These resources are suitable to conduct a comprehensive analysis of h2h genes in S. cerevisiae.
This study analyzed various promoter features, including transcription boundaries (TSS, 5'UTR and 3'UTR), TATA box, TF binding evidence, TF regulation evidence, DNA bendability and nucleosome occupancy. The expression profiles and gene ontology (GO) annotations were used to measure if two genes are associated. Based on these promoter features, we found that i) the frequency of h2h genes was close to the expectation, namely they were not relatively frequent in genome; ii) the distance between the TSSs of most h2h genes fell into the range of 0-600 bps and was more centralized in 0-200 bps of the highly associated ones; iii) the number of TFs that regulate both h2h genes influenced the co-expression and co-function of the genes, while the number of TFs that bind both h2h genes influenced only the co-expression of the genes; iv) the association of two h2h genes was influenced by the existence of specific TFs such as STP2; v) the association of h2h genes whose bidirectional promoters have no TATA box was slightly higher than those who have TATA boxes; vi) the association of two h2h genes was not influenced by the DNA bendability and nucleosome occupancy.
This study analyzed h2h genes with various promoter features that have not been used in analyzing h2h genes. The results can be applied to other genomes to confirm if the observations of this study are limited to S. cerevisiae or universal in most organisms.
头对头（h2h）基因在表达和功能上往往具有相关性，并在进化中得到了保守。目前有许多关于此类 h2h 基因对的研究。我们发现，之前的研究非常专注于人类基因组。此外，它们只专注于只需要基因或蛋白质序列的分析，而没有对其他启动子特征（如特定转录因子（TF）的结合证据）进行系统调查。这主要是因为高等生物的资源不完整，尽管它们比模式生物如酿酒酵母更受关注。本研究的作者最近整合了来自六个数据库和五篇论文的 6603 个酿酒酵母基因的九个启动子特征。这些资源适合对酿酒酵母中的 h2h 基因进行全面分析。
本研究分析了各种启动子特征，包括转录边界（TSS、5'UTR 和 3'UTR）、TATA 盒、TF 结合证据、TF 调节证据、DNA 弯曲性和核小体占有率。表达谱和基因本体论（GO）注释用于衡量两个基因是否相关。基于这些启动子特征，我们发现：i）h2h 基因的频率接近预期，即它们在基因组中并不相对频繁；ii）大多数 h2h 基因的 TSS 之间的距离落入 0-600 bps 的范围内，在高度相关的基因中更为集中在 0-200 bps 范围内；iii）调节两个 h2h 基因的 TF 的数量影响基因的共表达和共功能，而结合两个 h2h 基因的 TF 的数量仅影响基因的共表达；iv）特定 TF（如 STP2）的存在影响两个 h2h 基因的关联；v）无 TATA 盒的双向启动子的 h2h 基因的关联略高于具有 TATA 盒的基因；vi）两个 h2h 基因的关联不受 DNA 弯曲性和核小体占有率的影响。
本研究分析了具有各种启动子特征的 h2h 基因，这些特征以前未用于分析 h2h 基因。这些结果可应用于其他基因组，以确认本研究的观察结果是否仅限于酿酒酵母或在大多数生物中普遍存在。
