Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors.

Previous compositional studies of pre-mRNA processing complexes have been performed in vitro on synthetic pre-mRNAs containing a single intron. To provide a more comprehensive list of polypeptides associated with the pre-mRNA splicing apparatus, we have determined the composition of the bulk pre-mRNA processing machinery in living cells. We purified endogenous nuclear pre-mRNA processing complexes from human and chicken cells comprising the massive (>200S) supraspliceosomes (a.k.a. polyspliceosomes). As expected, RNA components include a heterogeneous mixture of pre-mRNAs and the five spliceosomal snRNAs. In addition to known pre-mRNA splicing factors, 5' end binding factors, 3' end processing factors, mRNA export factors, hnRNPs and other RNA binding proteins, the protein components identified by mass spectrometry include RNA adenosine deaminases and several novel factors. Intriguingly, our purified supraspliceosomes also contain a number of structural proteins, nucleoporins, chromatin remodeling factors and several novel proteins that were absent from splicing complexes assembled in vitro. These in vivo analyses bring the total number of factors associated with pre-mRNA to well over 300, and represent the most comprehensive analysis of the pre-mRNA processing machinery to date.

Epitope tagging of proteins at the native chromosomal loci of genes in mice and in cultured vertebrate cells.

Adding epitope tags to proteins is an important method for biochemical analyses and is generally accomplished in metazoan cells using ectopically expressed, tagged trans-genes. In Saccharomyces cerevisiae, the addition of epitope tags to proteins is easily achieved at the genomic locus of a gene of interest due to the high efficiency of homologous recombination in that organism. Most metazoan cells do not exhibit this high homologous recombination efficiency, and therefore trans-genes with in-frame epitope tags are used. Although epitope tagged trans-genes have proven useful, replacing the native promoter with a heterologous promoter introduces numerous artifactual possibilities. These include overexpression, which can lead to promiscuous interactions, and the loss of native transcriptional control, which in live animals often leads to developmental defects and embryonic lethality. We describe an efficient method that overcomes the problems encountered using epitope tagged trans-genes by introducing the epitope tag into the native chromosomal gene locus in vertebrate cells, embryonic stem cells and live mice. These tagged proteins are physically associated with the expected relevant particles, and highly sensitive as shown by co-purification of homologues of the yeast pre-mRNA splicing factors Prp38p and Prp39p, not previously shown to be associated with metazoan snRNPs. These techniques will enhance the validity of conclusions made regarding epitope-tagged proteins and improve our understanding of proteomic dynamics in cultured vertebrate cells and live animals.