Studying Isoform-Specific mRNA Recruitment to Polyribosomes with Frac-seq

Gene expression profiling is widely used as a measure of the protein output of cells. However, it is becoming more evident that there are multiple layers of post-transcriptional gene regulation that greatly impact protein output (Battle et al., Science 347:664–667, 2014; Khan et al., Science 342:1100–1104, 2013; Vogel et al., Mol Syst Biol 6:400, 2010). Alternative splicing (AS) impacts the expression of protein coding genes in several ways. Firstly, AS increases exponentially the coding-capacity of genes generating multiple transcripts from the same genomic sequence. Secondly, alternatively spliced mRNAs are subjected differentially to RNA-degradation via pathways such as nonsense mediated decay (AS-NMD) or microRNAs (Shyu et al., EMBO J 27:471–481, 2008). And thirdly, cytoplasmic export from the nucleus and translation are regulated in an isoform-specific manner, adding an extra layer of regulation that impacts the protein output of the cell (Martin and Ephrussi, Cell 136:719–730, 2009; Sterne-Weiler et al., Genome Res 23:1615–1623, 2013). These data highlight the need of a method that allows analyzing both the nuclear events (AS) and the cytoplasmic fate (polyribosome-binding) of individual mRNA isoforms.

Source: Springer protocols feed by Genetics/Genomics - October 16, 2015 Category: Genetics & Stem Cells Source Type: news