Translation regulation gets its ‘omics’ moment

Abstract

The fate of cellular RNA is largely determined by complex networks of protein-RNA interactions through ribonucleoprotein (RNPs) complexes. Despite their relatively short half-life, transcripts associate with many different proteins that process, modify, translate, and degrade the RNA. Following biogenesis some mRNPs are immediately directed to translation and produce proteins, but many are diverted and regulated by processes including miRNA-mediated mechanisms, transport and localization as well as turnover. Because of this complex interplay estimates of steady state expression by methods such as RNAseq alone cannot capture critical aspects of cellular fate, environmental response, tumorigenesis or gene expression regulation. More selective and integrative tools are needed to measure protein-RNA complexes and the regulatory processes involved. One focus area are measurements of the transcriptome associated with ribosomes and translation. These so-called polysome or ribosome profiling techniques can evaluate translation efficiency as well as the interplay between translation initiation, elongation and termination - subject areas not well understood at a systems biology level. Ribosome profiling is a highly promising technique which provides mRNA positional information of ribosome occupancy, potentially bridging the gap between gene expression (i.e. RNAseq and microarray analysis) and protein quantification (i.e. mass spectrometry). In combination with methods such as RNA immunoprecipitation, miRNA profiling, or proteomics, we obtain a fresh view of global post-transcriptional and translational gene regulation. In addition, these techniques also provide new insight into new regulatory elements, such as alternative open reading frames, and translation regulation under different conditions.

High-throughput analyses of hnRNP H1 dissects its multi-functional aspect

“…[22][23][24] Unfortunately, due to the complex nature of RBP-mediated regulation, studies employing only a single method fall short on providing a clear assessment of RBP function, as discussed in. 25 Effective analyses must therefore combine binding assays with strategies to verify their functional outcomes. 26 To identify a high-confidence set of RNA species associated with hnRNP H1, we combined 2 distinct high-throughput approaches: iCLIP and a modified RIP-Seq method devised by our lab (see 26 for detailed protocol).…”

Mapping the non-standardized biases of ribosome profiling

“…Without doubt, ribosome profiling is a powerful technology to address various aspects of translation regulation on a genome-wide scale, and several excellent reviews summarize the power of this technology (Morris, 2009;Kuersten et al, 2013;Michel and Baranov, 2013;Ingolia, 2014). However, this approach is relatively young, with steadily evolving experimental protocol and a non-standardized platform for data analysis.…”

Anti-inflammatory effects of alpinone 3-acetate from Alpinia japonica seeds

“…These changes have been the subject of numerous experiments employing DNA microarray technology (transcriptome analysis), which focuses on differences in transcript levels, and more recently in high-throughput screening using wholetranscriptome sequencing [1,2]. However, cellular abundances of proteins are predominantly controlled at the translation level [3], and correlations between mRNA and protein levels are generally limited [4]. Therefore, the ''translatome'' is increasingly investigated using analytical approaches that provide substantial and somewhat surprising new information [5].…”