Ribosome Profiling

Ribosome analysis has gradually become a widely used strategy for exhaustive and quantitative assessment of translation through deep sequencing of specific messenger RNA (mRNA) fragments. As a world-leading ribosome analysis service provider, Creative Biolabs focuses on providing high-quality ribosome profiling services to customers around the world.

Overview of Ribosome Profiling

As is known, translation plays a significant role in life activities. The translation process is closely related to the ribosome. For that reason, determining the number and location of ribosomes on mRNA in vivo is critical for understanding the process and regulation of translation. Excitingly, ribosome profiling methods provide new perspectives to learn more about the numbers and locations of ribosomes on mRNAs.

Ribosome profiling, also commonly referred to as Ribo-Seq (ribosome sequencing), is a strategy that relies primarily on mRNA sequencing to confirm which mRNAs are actively translated. The principle of the technology is relatively simple. Each ribosome covers a short segment of the mRNA. These short fragments of overlaid mRNA are protected from digestion by exogenous RNases due to ribosome protection. Therefore, for organisms for which we know the transcriptome sequence, the location of the ribosome is determined by generating these fragments and analyzing their sequence. It is worth noting that Ribo-Seq primarily targets mRNA sequences protected by ribosomes during translation while RNA-Seq sequences all mRNAs of a given sequence present in a sample.

Fig.1 Ribosome profiling workflow. (Chugunova, 2018)

Ribo-Seq Process

The basic process of Ribo-Seq in different cell types is roughly the same, and the main process of this technology includes the following steps:

Fig.2 Procedures of ribosome profiling workflow.

Limitation

• The sequences of ribosome-protected RNA fragments depend on the mapping of the fragments to the genome.
• The ribosome binding fragments are short and cannot be read using paired-end sequencing.
• Ribo-Seq discards some information found in polysome profiling.
• Nuclease digestion degrades the 5' and 3' UTRs of transcripts, which may contain regulatory information.

Applications

• Sequences of ribosome-protected mRNA.
• Identify proteins that are actively translated in cells.
• Forecast the abundance of protein.
• Evaluation of the active mRNA translation.
• Affirm the translation efficiency of specific mRNA.
• Estimate the extent of mRNA translation.
• Investigation of transcriptional control and post-transcriptional regulation.

In recent years, Creative Biolabs has been committed to the development and application of ribosome analysis technology. With experienced scientists and advanced platforms, we can provide the best service to satisfy every customers' requirements. If you are interested in Ribo-Seq, please feel free to contact us for more information.

Reference

1. Chugunova, A.; et al. Mining for small translated ORFs. Journal of proteome research. 2018, 17(1): 1-11.