you can measure mt DNA copy number by simple PCR, you can also measure the induction of biogenesis genes (pgc1 alpha, nfr1, nrf2, and mito-specific factors), and mtDNA-encoded transcripts and proteins levels. 

Thanks Celine, but which is more sensitive (mtDNA or Biogenesis genes) and what about mitochondrial immunostaining on fixative tissues

Hi there, in order to quantify mt into muscle fibers I used TOM20 antibody and it worked perfectly, also staining by NADH portocol could help you to score mt ammount in muscle tissue.

Citrate synthase activity is often used as an indicator of mitochondrial content. Fairly easy assay to do too!

Thans a lot