I've heard from several independent people that their Cas9 cell lines that constitutively express Cas9 is being silenced. I've heard it for neuronal stem cells as well as for HEK293 cells. I also noticed that prolonged expression of a Cas9-Puro fusion (from pLentiCrisprV2) w/o sgRNA and constant Puro selection makes neuronal stem cells look bad in culture after several passages. They are still able to grow but I do not know how for how long that will last.

I also think it is odd that I could not find any mouse lines that express Cas9 with a tissue-specific promoter but maybe because people rather use the R26:LSL-Cas9GFP mouse line.

In line with that, a recent paper showed silencing of the Cas9-GFP fusions within a tumor when being expressed from a virus as opposed to Feng Zhangs R26:LSL-Cas9GFP mouse with viral Cre delivery. The link is here; http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4297.html

Maybe it introduces some novel splicing as shown in that paper from my former lab for another bacterial gene but I am not sure of course. Did anybody check splicing in transgenic intron-less Cas9 yet? The link is here: http://dev.biologists.org/content/143/22/4272  

Does anybody have an alternative idea why that silencing takes place? Could an intron resolve that silencing? I always thought that is a plant thing but you never know. The Cas9 is codon optimized so how does the cell specifically target that? Other intron-less genes are usually not silenced. 

I would be happy for any comments, especially if you ran into the problem yourself or if you know a way around that or what you think can be the general problem here.