Transcriptional regulation is a determinant of stability of recombinant protein production in CHO cells. Fundamental studies of recombinant gene transcription in relation to chromatin environment and promoter regulation are important for CHO cell line development and selection. This study has developed a methodology based on a cell/vector system to study recombinant transcription and expression stability of different promoters and/or proteins in the similar genomic environment.The CHO-FRT mini-pools developed in this project were mini-pools of CHO-S cell lines containing Flp Recombination Target (FRT) sites with ß-galactosidase gene, under the influence of a SV40 promoter. Continuous culture of these mini-pools for 8 weeks using a robotic system demonstrated that 20% of the mini-pools studied revealed an unstable profile (with 30% loss of protein expression). Two of these mini-pools with different characteristics, CHO-FRT 1 (low producer/unstable) and CHO-FRT 108 (high producer/stable), were selected to be used on the study of influence of SV40 and CMV promoters in long-term recombinant expression. Genes encoding fluorescent proteins were integrated in a site-directed manner under the influence of SV40 or CMV promoters. A sub-clonal population of the top 10% yellow fluorescent protein (YFP) expressing cells of each mini-pool/promoter combination was selected by cell sorting and cultured for 4 weeks. During this period protein expression was monitored by flow cytometry and compared between both promoters. The results revealed that both SV40 and CMV promoters had an unstable expression with different degrees of instability and long-term expressing behaviours. For CMV, instability was considerably high displaying a long-term logarithmic loss of 50-80% of productivity while for SV40 the loss of productivity observed was only 40-45% with a linear behaviour during long-term culture.The vector system generated contained an MS2-RNA tag sequence cloned 3'- of the recombinant gene to track the recombinant mRNA by using the MS2/MCP-GFP system. This study showed the development of a protocol to measure the transcriptional output of recombinant promoters in CHO cells. The results showed background signal in CHO cells that requires further optimisation studies to allow the direct live cell image quantification of the transcriptional activity of recombinant promoters. Although not yet optimised, the successful combination of site-directed integration with recombinant mRNA tagging method has the potential to become a valuable tool to study the mechanisms of transcriptional activity and stability of transcription driven by different promoters in CHO cells.