Regulatory cis- and trans-elements of mitochondrial D-loop-driven reporter genes in budding tunicates

Highlight
- Mitochondrial NCR-containing reporter gene is expressed in a pattern similar to 16S rRNA.
- The reporter gene can be expressed in vivo in the cell nucleus in addition to mitochondria.
- Tunicate TFAM is an ageing-dependent trans-element to facilitate reporter gene expression.
- PmTFAM requires the TATA-like box and the adequate upstream region on NCR.
- PmTFAM expression depends on nuclear histone methylation.

To unveil the underlying mechanism of mitochondrial gene regulation associated with ageing and budding in the tunicate Polyandrocarpa misakiensis, mitochondrial non-coding-region (NCR)-containing reporter genes were constructed. PmNCR2.3K/GFP was expressed spatiotemporally in a pattern quite similar to mitochondrial 16S rRNA. The reporter gene expression was sensitive to high dose of rifampicin similar to mitochondrial genes, suggesting that the transcription indeed occurs in mitochondria. However, the gene expression also occurred in vivo in the cell nucleus and in vitro in the nuclear extracts. Mitochondrial transcription factor A (PmTFAM) enhanced reporter gene expression, depending on the NCR length. A budding-specific polypeptide TC14-3 is an epigenetic histone methylation inducer. It heavily enhanced reporter gene expression that was interfered by histone methylation inhibitors and PmTFAM RNAi. Our results indicate for the first time that the nuclear histone methylation is involved in mitochondrial gene activity via TFAM gene regulation.