Chromosome Conformation Capture of All 13 Genomic Loci in the Transcriptional Regulation of the Multisubunit Bigenomic Cytochrome c Oxidase in Neurons

Abstract

Cytochrome c oxidase (COX) is the terminal enzyme of the electron transport chain composed of 13 subunits; three are mitochondria-encoded, and 10 are nucleus-inscribed on nine different chromosomes within the mammalian genome. The transcriptional regulation of such a multisubunit, multichromosomal, and bigenomic enzyme is mechanistically challenging. Transcription factories have been proposed as one mechanism by which genes from different genomic loci congregate to transcribe functionally related genes, and chromosome conformation capture (3C) is a means by which such interactions can be revealed. Thus far, however, only loci from the same chromosome or at most two chromosomes have been co-localized by 3C. The present study used 3C to test our hypothesis that not only the 10 genomic loci from nine chromosomes encoding the 10 nuclear subunits of COX, but also genes from three chromosomes encoding mitochondrial transcription factors A and B (Tfam, Tfb1m, and Tfb2m) critical for the transcription of the three mitochondria-encoded COX subunit genes all occupy common intranuclear sites in the murine neuronal nuclei. The pairing of various COX subunit genes and Tf genes indicates that interactions are present among all of them. On the other hand, genes for a non-mitochondrial protein (calreticulin) as well as a mitochondrial enzyme (citrate synthase) did not interact with COX genes. Furthermore, interactions between COX subunit and Tf genes were up-regulated by depolarizing stimulation and down-regulated by impulse blockade in primary neurons. Thus, a viable mechanism is in place for a synchronized, coordinated transcriptional regulation of this multisubunit, bigenomic COX enzyme in neurons.Cytochrome c oxidase (COX) 2 or complex IV of the mitochondrial electron transport chain is made up of three subunits encoded in the mitochondrial genome and 10 nucleus-encoded subunits located on nine different chromosomes (1-3). The 10 nucleus-encoded COX subunits are 4, 5a, 5b, 6a, 6b, 6c, 7a, 7b, 7c, and 8a. Subunits 4, 6a, 6b, 7a, and 8a each has a ubiquitous isoform and a tissue-specific isoform. Transcription of all ubiquitously expressed subunits in neurons are coordinately regulated according to the cell's ATP requirement (4). Transcriptional regulators of COX in rats, mice, and humans include NRF-1 and NRF-2 (nuclear respiratory factors 1 and 2) (5-8).In particular, both NRF-1 and NRF-2 activate the transcription of all 10 nucleus-encoded COX subunits and modulate the level of transcription in response to changing cellular energy demands in neurons (9 -14). Additionally, NRF-1 and NRF-2 indirectly activate the three mitochondria-encoded COX subunit genes by regulating Tfam, Tfb1m, and Tfb2m (mitochondrial transcription factors A, B1, and B2) critical for mitochondrial DNA transcription and replication (15-18). Transcriptional coactivators, such as PGC-1␣ (peroxisome proliferator-activated receptor ␥-coactivator 1␣) (19,20), also play an important role in stimulating COX transcription in the presence of upstream signals i...

Epigenetics in the Human Brain

“…Despite of the growing realization of the importance of these and other higher order chromatin structures for transcriptional regulation, very little is known about their role in the nervous system. Until recently, there were only three studies in the literature that explored loop formations in brain tissue (Dhar et al, 2009;Horike et al, 2005;Jiang et al, 2010), with a few additional papers using the brain as negative control for their studies on the sensory epithelium of the nose (Lomvardas et al, 2006) or the hematopoetic system (Simonis et al, 2006). However, to date, nothing is known about chromatin loopings in human brain.…”

Coordination of cytochrome c oxidase gene expression in the remodelling of skeletal muscle

“…The 13 subunits are encoded by two genomes (three mitochondrial, 10 nuclear). The expression of the genes involves the coordination of expression of individual genes and genome-wide structural regulation (Dhar et al, 2009). Once subunits are translated and imported, they are assembled into a holoenzyme that includes haem units (a, a 3 ), and metals (Cu A , Cu B ).…”

Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites

“…However, the introduction of techniques like chromosome conformation capture (Dekker et al, 2002) and single-molecule RNA fluorescence in situ hybridization (FISH; Femino et al, 1998) now show that co-expressed genes are often found together in 3D nuclear space (e.g. Cai et al, 2006;Simonis et al, 2006;Dhar et al, 2009;Schoenfelder et al, 2010;Noordemeer et al, 2011;Li et al, 2012;Papantonis et al, 2012), closely associated with sub-nuclear structures known as 'transcription factories' (Cook, 2010;Edelman and Fraser, 2012). Such factories have been defined as sites where at least two different genes are transcribed at one time, and they contain many of the molecular components necessary for the production of the mature message (Cook, 2010;Melnik et al, 2011).…”