**2.2. The duplicated GGAA-motifs that are contained in the 5′-upstream regions of immune response factor-encoding human genes**

importantly, recent metabolome analyses have led to the rediscovery that metabolites could be biomarkers for cancer and its development [4]. The "Warburg effect", which was shown by Dr Otto Warburg over 60 years ago, is the most essential discovery in the field of cancer science [5]. The "Warburg effect" refers to abnormal metabolism in cancer, which mainly utilizes glucose to produce ATP by glycolysis. In this regard, "cancer is a metabolic disease". This is not only important as an indicator of tumors, but also as one of the essential characteristics of cancer [6, 7]. A number of lines of evidence, including dysregulated TCA (Krebs/Citrate)-cycle progression and the insufficient oxidative phosphorylation in cancer cells, suggest that mitochondrial dysfunction might precede the metabolic change [8]. Thus, "cancer must be a mitochondrial disease". In this chapter, which focuses on the causative factors that lead to mitochondrial dysfunction, we discuss whether "cancer is a transcriptional disease". Most of the genes (99%) that encode mitochondria or their function-associated proteins are contained in nuclear genomes [9]. The mitochondrial functions might be recovered or improved at a transcriptional level. In this chapter, we propose the establishment of novel chemo-/gene-therapies with no side effects, to force

**2. The relevance of duplicated GGAA-motifs in the 5′-upstream regions** 

**2.1. The transcription factors that recognize and bind to the GGAA-containing motifs**

The most widely known transcription factors (TFs) that selectively recognize the GGAA-corecontaining sequences are the ETS (E26 transformation specific) family proteins, which consist of at least 27 members [10, 11]. Moreover, a genome-wide ChIP-seq analysis estimated that the promoter regions of human genes are very frequently occupied by ETS family or GGAA-binding proteins [12]. The duplication of the GGAA-motif could be advantageous to organisms, as it would allow the transcription of various genes to be controlled in a manner that is mainly dependent on the expression profile of the GGAA-binding proteins in the cells [13, 14]. Besides ETS family proteins, several TFs could bind to the motif. For example, some of the duplicated GGAA-motifs would be identical to IFN-stimulated response element (ISRE), the consensus sequence of which is 5′-GGAAANNGAAACT-3′ [15], if one of the Ns was G. The double-stranded sequence, 5′-AACTTT-3′, which is a core binding motif of the IRF1 [16], could be generated if CT was inserted between GGAA and TTCC. Moreover, NF-κB p65 (RELA) homodimer binds to two symmetric sequences, 5′-GGAATTTCC-3′ and 5′-GGAATTCCC-3′ [17]. IRF8 (ICSBP) either positively or negatively regulates transcription

Importantly, the ETS family proteins and other TFs cooperatively regulate the expression of various genes. For instance, STAT1 plays a role in the regulation of the expression of interferon (IFN) stimulated genes (ISGs) with ETS family proteins [20, 21]. Sp1 and Ets1 interact with each other to regulate mouse *Npr1* gene expression [22]. The ETS-binding consensus sequence is frequently found with a second ETS-binding sequence and with the Sp1-binding sequence, but not with a TATA element [23], implying the exclusive role of the GGAA- and TATA elements. The human

cancerous cells to regenerate into their normal differentiated state.

**of human genes to the regulation of biological events**

through binding to ISRE [18, 19].

108 Mitochondrial Diseases

Duplicated GGAA-motifs are found in the 5′-upstream of the ISGs [20, 26, 27]. The GGAAmotifs are also harbored in the IFN-stimulated response element (ISRE)-like sequences [28, 29]. Thus, the duplicated GGAA-motifs near TSSs may play roles in controlling the expression of ISGs. The ISG-encoded proteins include TFs, immune modulators, apoptosis mediators, and anti-viral factors [30]. Previously, the duplicated GGAA-motifs in the regulatory regions of ISGs have been analyzed [31]. We surveyed the 5′-upstream regions in a number of ISGs to find GGAA-motifs within 500-bp upstream from the TSSs [32], and reported that IFNβ-inducible human *OAS1* promoter activity is regulated by binding of ELF-1 (which belongs to the ETS family proteins) to a duplicated GGAA-motif, and by its interaction with Sp1 and Rb proteins [33].

Collectively, the majority of the promoter regions from ISGs contain duplicated GGAA-motifs but rarely with TATA element. This suggests that the mechanism by which transcription is initiated differs from that of the house-keeping genes or genes that are essentially required, such as those that encode cell structure components. IFNs, the expression of which should be suppressed under normal conditions, only play important roles when it is necessary to fight against viral infection and oncogenesis. The duplicated GGAA-motifs might have contributed, through evolution, to the development of an immune response at the transcriptional level. In addition, GGAA-binding factors, which are associated with other TFs around TSSs, facilitate the expression of each ISG as appropriate, depending on the different signals that are induced by IFN.
