cis versus trans-acting factors

Most often, signal elements act only on the intramolecular nucleotide sequence to which they are attached, and they are said to act "in cis". Intron removal in eukaryotes involves cis-splicing. Interaction with signal factors -- usually protein molecules -- turns signal elements on or off.

When protein factors are free to diffuse within the cell they can act on target elements that may not be derived from the same genome segment. Protein factors capable of acting upon other intermolecular genome segments are called "trans-acting factors".

One form of trans-splicing is the 'spliced leader' type, which is primarily found in protozoans (e.g. trypanosomes) and in lower invertebrates such as nematodes. This results in the addition of a capped, noncoding, spliced leader sequence to the 5' end of mRNAs.

Another form of trans-splicing is the 'discontinuous group II intron' type that occurs in plant/algal chloroplasts and plant mitochondria. This results in the joining of two independently transcribed coding sequences. Both spliced-leader and discontinuous group II intron trans-splicing are mechanistically similar to conventional nuclear pre-mRNA cis-splicing. Trans-splicing also occurs in mammalian cells, just as cis-splicing occurs in trypanosomes. It has been suggested that both trans- and cis-splicing are ancient acquisitions of the eukaryotic cell. (Abstract)