Two splicing isoforms of the Y-box protein ctYB-1 appear on the same mRNA molecule

The Balbiani Ring Story: Synthesis, Assembly, Processing, and Transport of Specific Messenger RNA-Protein Complexes

Eukaryotic gene expression is the result of the integrated action of multimolecular machineries. These machineries associate with gene transcripts, often already nascent precursor messenger RNAs (pre-mRNAs). They rebuild the transcript and convey properties allowing the processed transcript, the mRNA, to be exported to the cytoplasm, quality controlled, stored, translated, and degraded. To understand these integrated processes, one must understand the temporal and spatial aspects of the fate of the gene transcripts in relation to interacting molecular machineries. Improved methodology is necessary to study gene expression in vivo for endogenous genes. A complementary approach is to study biological systems that provide exceptional experimental possibilities. We describe such a system, the Balbiani ring (BR) genes in polytene cells in the dipteran Chironomus tentans. The BR genes, along with their pre-mRNA-protein complexes (pre-mRNPs) and mRNA-protein complexes (mRNPs), allow the visualization of intact cell nuclei and enable analyses of where and when different molecular machineries associate with and act on the BR pre-mRNAs and mRNAs.

Frac-seq reveals isoform-specific recruitment to polyribosomes

Pre-mRNA splicing is required for the accurate expression of virtually all human protein coding genes. However, splicing also plays important roles in coordinating subsequent steps of pre-mRNA processing such as polyadenylation and mRNA export. Here, we test the hypothesis that nuclear pre-mRNA processing influences the polyribosome association of alternative mRNA isoforms. By comparing isoform ratios in cytoplasmic and polyribosomal extracts, we determined that the alternative products of ∼30% (597/1954) of mRNA processing events are differentially partitioned between these subcellular fractions. Many of the events exhibiting isoform-specific polyribosome association are highly conserved across mammalian genomes, underscoring their possible biological importance. We find that differences in polyribosome association may be explained, at least in part by the observation that alternative splicing alters the cis-regulatory landscape of mRNAs isoforms. For example, inclusion or exclusion of upstream open reading frames (uORFs) in the 5′UTR as well as Alu-elements and microRNA target sites in the 3′UTR have a strong influence on polyribosome association of alternative mRNA isoforms. Taken together, our data demonstrate for the first time the potential link between alternative splicing and translational control of the resultant mRNA isoforms.

Close coupling between transcription and exit of mRNP from the cell nucleus

Transcription is intimately coupled to co-transcriptional formation of mRNP particles and their preparation for export. In the dipteran Chironomus tentans we have now investigated whether on-going transcription is closely linked also to the ensuing transfer of the mRNPs from genes to cytoplasm. The assembly and nucleocytoplasmic transport of a specific mRNP particle, the Balbiani ring (BR) RNP granule, were visualized in larval salivary glands by electron microscopy. When transcription was inhibited with DRB or actinomycin D (AMD), the growing BR mRNPs disappeared from the genes. The two inhibitors affected the distribution of BR mRNPs in the nucleoplasm and in the nuclear pores in essentially the same way. At the nuclear pore complexes (NPCs) the basket-associated and translocating mRNPs were substantially reduced in number, the translocating RNPs being essentially absent after 90 min treatment. Remarkably, the amount of BR mRNPs in the nucleoplasm did not change. We conclude that on-going transcription is required for the mRNPs to exit from the cell nucleus. Interruption of transcription seems to primarily affect the intranuclear movement of BR mRNPs and/or prevent the binding of mRNPs to the NPCs rather than to directly interfere with translocation per se.