Implication of bidirectional promoters containing duplicated GGAA motifs of mitochondrial function-associated genes

Fumiaki Uchiumi; Makoto Fujikawa; Satoru Miyazaki; Sei-ichi Tanuma; Fumiaki Uchiumi; Makoto Fujikawa; Satoru Miyazaki; Sei-ichi Tanuma

doi:10.3934/molsci.2013.1.1

AIMS Molecular Science

2014, Volume 1, Issue 1: 1-26. doi: 10.3934/molsci.2013.1.1

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Implication of bidirectional promoters containing duplicated GGAA motifs of mitochondrial function-associated genes

1.
Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamazaki 2641, Noda-shi, Chiba-ken 278-8510, Japan;
2.
Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamazaki 2641, Noda-shi, Chiba-ken 278-8510, Japan;
3.
Department of Bioinformatics, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamazaki 2641, Noda-shi, Chiba-ken 278-8510, Japan;
4.
Research Center for RNA Science, RIST, Tokyo University of Science, Yamazaki 2641, Noda-shi, Chiba-ken 278-8510, Japan

Received: 13 October 2013 Accepted: 27 November 2013 Published: 12 December 2013

Mitochondria are well known as the primary required organelle in all eukaryotic cells. They have their own mtDNA containing genes that encode tRNAs, rRNAs and a set of functional proteins required for energy (ATP) production. However, almost all (99%) of mitochondrial proteins are encoded by host nuclear genes. Therefore, expression of mitochondrial protein-encoding genes should be regulated similarly to genes that are present in the host nuclear chromosomes. Interestingly, from genomic database assisted surveillance, it was revealed that a lot of mitochondrial function associated protein-encoding genes are oppositely linked in a head-head manner. If the two head-head conjugated genes are regulated by the same transcription factor(s), their expression would be dependent on the direction of transcription machinery that contains RNA polymerase II to execute mRNA synthesis. In this article, we will focus on several examples of the mitochondrial and the partner gene sets and discuss putative functions of transcription factor binding elements in the bidirectional promoters of mitochondrial function-associated genes in chromosomes.
- bidirectional promoter,
- gene loop,
- GGAA-motif,
- interferon stimulated genes,
- mitochondria,
- TATA less promoter
Citation: Fumiaki Uchiumi, Makoto Fujikawa, Satoru Miyazaki, Sei-ichi Tanuma. Implication of bidirectional promoters containing duplicated GGAA motifs of mitochondrial function-associated genes[J]. AIMS Molecular Science, 2014, 1(1): 1-26. doi: 10.3934/molsci.2013.1.1

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Abstract

Mitochondria are well known as the primary required organelle in all eukaryotic cells. They have their own mtDNA containing genes that encode tRNAs, rRNAs and a set of functional proteins required for energy (ATP) production. However, almost all (99%) of mitochondrial proteins are encoded by host nuclear genes. Therefore, expression of mitochondrial protein-encoding genes should be regulated similarly to genes that are present in the host nuclear chromosomes. Interestingly, from genomic database assisted surveillance, it was revealed that a lot of mitochondrial function associated protein-encoding genes are oppositely linked in a head-head manner. If the two head-head conjugated genes are regulated by the same transcription factor(s), their expression would be dependent on the direction of transcription machinery that contains RNA polymerase II to execute mRNA synthesis. In this article, we will focus on several examples of the mitochondrial and the partner gene sets and discuss putative functions of transcription factor binding elements in the bidirectional promoters of mitochondrial function-associated genes in chromosomes.

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