Post-transcriptional regulation of gene expression in developing neurons

Where do we look for answers?

We are convinced that gene expression changes in differentiating cells must be extensively coordinated at the post-transcriptional level. First, transcription of mammalian genes often takes hours to complete. This includes time required to assemble initiation complexes at the promoter and to synthesize full-length messenger RNA precursors (pre-mRNAs) at an average elongation rate of just a few kilobases per minute. Since differentiation decisions are often made on a comparable time scale, many gene regulation functions have to be delegated to faster post-transcriptional processes. Second, half-lives of many mammalian transcripts are measured in hours and, sometimes, days. This provides ample opportunity for implementing post-transcriptional controls of mRNA composition and abundance. Third, mammalian gene expression is an inherently wasteful process. Only ~5% of a typical human gene encodes exons, elements that contribute to mature mRNA. The remaining bulk of intronic sequences are typically degraded following transcription and pre-mRNA splicing. This suggests that the energy wastage associated with regulating gene expression through controlled RNA processing, translation and degradation is probably negligible in comparison with the overall balance of cellular RNA metabolism. Fourth, a number of post-transcriptional regulators orchestrating gene expression in differentiating cells have been identified in recent studies. These include RNA-binding proteins and non-coding RNAs that control processing, localization, translational efficiency and stability of multiple (pre-)mRNAs. We believe that our current understanding of these molecular components is incomplete and additional work in this area is bound to generate interesting new insights. Finally, the extent of post-transcriptional control is underscored by a growing list of human diseases that are linked to defects in RNA processing.

What models do we use?

We focus predominantly on post-transcriptional regulation of gene expression during development of neurons, the main functional units of the brain. We use a range of experimental techniques, from transcriptome-wide gene expression analyses to in-depth molecular characterization of specific genes and regulation mechanisms. We work with mammalian cell lines, primary neural cells and laboratory rodents. Our studies increasingly rely on bioinformatics and we believe that advancing this direction will be essential to accelerate discovery of novel mechanisms and to better understand systems-level effects of already known ones. We are currently investigating three groups of post-transcriptional processes: the microRNA pathway, alternative pre-mRNA splicing and RNA quality control (QC). Our studies suggest that these distinct mechanisms can assemble into interlinked gene regulation circuitries. An important example of this trend is provided by neuron-enriched microRNA miR-124 that down-regulates expression of an RNA-binding protein called polypyrimidine tract-binding protein (Ptbp1/PTB/hnRNP I) (see figure). Ptbp1 is a splicing regulator and its miR-124-mediated decline results in large-scale reprogramming of alternative pre-mRNA splicing patterns in developing neurons. Many of these splicing changes lead to corresponding alterations in the protein products encoded by the regulated mRNAs. However, a considerable fraction of Ptbp1 targets is also controlled at the level of mRNA abundance through coupling between alternative splicing and RNA QC mechanisms such as nuclear retention and elimination of incompletely spliced mRNAs or cytoplasmic nonsense-mediated decay (NMD) of mRNAs containing premature termination codons (PTCs). These regulation possibilities are briefly summarized in the diagram below.

What is next?

We plan to continue characterising the impact of the miR-124/Ptbp1 pathway on neuronal differentiation using both transcriptome-wide and gene-specific approaches. We will additionally search for novel post-transcriptional mechanisms essential for proper development and function of the nervous system using a combination of bioinformatics, biochemistry and neuroscience.