Perhaps enucleolation...!! Your agent might intercalate with DNA to cause DNA damage, or target RNA in the nucleoli. We observed nucleoli coming out of nucleus in response to LiCl and Cisplatin. See my paper which has TEM in main figure and supplemental materials.

https://www.researchgate.net/publication/233742776_Blebbishields_the_Emergency_Program_for_Cancer_Stem_Cells_Sphere_Formation_and_Tumorigenesis_after_Apoptosis

Article Blebbishields, the Emergency Program for Cancer Stem Cells: ...

Many chemicals (chemotherapeutics) inhibit RNA polymerase I or interfere with DNA replication. When this happens, the nucleolus often shrinks and under the phase contrast microscope it will look like the cells "lost the nucleolus" (often it is still there but just as a tiny dark dot). Sometimes when drugs interfere with DNA replication, the nucleolus may not be reformed after mitosis.  Other explanations such as the one proposed by Goodwin can´t be ruled out either. In any case, it seems as your treatment has some interesting effects on cells!

Thank you Goodwin and Mikael! I called it treatment, but I am actually silencing a gene. In immunofluorescence, the protein encoded by this gene stains mostly in nucleolus, so since I am targeting a gene that appears to be in nucleolus, does this could lead to enucleolation? 

It is possible that your target protein is involved in rRNA transcription or processing of pre-rRNA. Nucleoli often reorganize when either of these processes are perturbed. While rRNA transcription inhibition can lead to nucleolar segregation, where nucleolar body can still be observed, nucleolar fragmentation disintegrates the whole nucleoli. See Boulon et al. 2010 in Mol Cell for a good review.

http://www.sciencedirect.com/science/article/pii/S1097276510007525

Well if the protein is in the nucleolus and the nucleolus is "lost" my spontaneous though its that your protein has an important function in the nucleolus. Either it is requried for ribosome biogenesis (for example RNA pol I transcription) or it plays an important structural function as a supporting matrix/chromatin protein.Remember that the nucleolus is formed as a consequence of RNA pol I transcription.

Some other nucleolar proteins have more interesting effects for example FRGY that is involved in nucleolar dissassembly, and here is potential links to "enucleolation".

One could also think of more indirect effects, your nucleolar protein could be essential for cell proliferation in general and silencing of it induces a cell cycle arrest and a nucleolar "shut down".

Seems like you have silenced an important (nucleolar) protein. :)

Hope your observation is reproducible; my major question is: how does the viability or other characteristics of your cells change - perhaps, do they stop growing?

Hi Robert! I did this experiment more than once and the result is always the same! :)

And yes, there is a big impact in cell viability. They proliferate less than control.

So, are they just close to death. Are the surviving cells really also "without" nucleolus? - Anyway, sounds interesting and interesting to elucidate. Good luck!

PS: I would be curious, if this phenomenon occurs in all other cell types as well, including neurones, or slow growing, different cells.

Thank you all for the very interesting insights and papers! :)