Ribo-Seq: Understanding the effect of translational regulation on protein abundance in the cell

Examining changes in gene expression has become one of the most powerful tools in molecular biology today. However, the correlation between mRNA expression and protein levels is often poor. Thus, being able to identify precisely which transcripts are being actively translated, and the rate at which they are being translated, could be a huge boon to the field and give us more insight into which genes are carried through all the way from the mRNA to the protein level–and Ribo-seq (also known as ribosome profiling) technology gives us just that!

Historic nature of ribosome profiling

Ribo-seq is based upon the much older technique of in vitro ribosome footprinting, which stretches back nearly 50 years ago and was used by Joan Steitz and Marilyn Kozak in important studies to map the locations of translation initiation [1, 2]. Due to the technological limitations of the time, these experiments were performed with cell-free in vitro translational systems. These days, we can actually extract actively translating ribosomes from cells and directly observe their locations on the mRNAs they are translating!

Method

So how does this innovative new technique work? The workflow is actually remarkably simple.

  1. We start by lysing the cells by first flash-freezing them, and then harvesting them in the presence of cyclohexamide (see explanation for this under ‘Drawbacks and complications’).
  2. Next, we treat the lysates with RNase 1, which digests the part of the mRNA not protected by the ribosome.
  3. The ribosomes are then separated using a sucrose cushion and centrifugation at very high speeds.
  4. RNA from the ribosome fraction obtained above are then purified with a miRNeasy kit and then gel purified to obtain the 26 – 34 nt region. These are the ribosome footprints.
  5. From there, the RNA is dephosphorylated and the linker DNA is added.
  6. The hybrid molecule is then subjected to reverse transcription into cDNA.
  7. The cDNA is then circularized, PCR amplified, and then used for deep sequencing.

Ribo-seq vs. RNA-seq

Ribosome profiling as a next-generation sequencing technique was developed quite recently by Nicholas Ingolia and Jonathan Weissman [3, 4]. One of their most interesting findings was that there is a roughly 100-fold range of translation efficiency across the yeast transcriptome, meaning that just because an mRNA is very abundant, that does not mean that it is highly translated. They concluded that translation efficiency, which cannot be measured by RNA-seq experiments, is a significant factor in whether or not a gene makes it all the way from an mRNA to a protein product.

Additionally, they looked at the correlation between the abundance of proteins (measured by mass spectrometry) and either the data obtained from Ribo-seq or RNA-seq. They found that Ribo-seq measurements had a much higher correlation with protein abundance than RNA-seq ( = 0.60 vs. = 0.17), meaning that Ribo-seq is actually a better measurement of gene expression analysis (depending on the type of experiment you’re interested in performing).

Of course, there are still significant advantages to RNA-seq over Ribo-seq–Ribo-seq will not be able to capture the expression of non-coding RNAs, for instance. Additionally, RNA-seq is considerably cheaper and easier to perform as of this moment. However, I believe that we are likely to see a trend towards ribosome profiling as this technique becomes more mature.

What else can we learn from ribosome profiling?

Ribosome profiling has already taught us many new things, including:

  • discovering that RNAs that had previously been thought to be non-coding RNAs due to their short length are actually translated, and indeed code for short peptide sequences, the exact functions of which remain unknown. [5]
  • detection of previously unknown translated short upstream ORFs (uORFs), which often possess a non-AUG start codon. These uORFs are likely responsible for regulating the protein-coding ORFs (which is true of the GCN4 gene)[6], though it remains to be seen if that is true for all uORFs or if they have other currently unknown functionalities.
  • determination of the approximate translation elongation rate (330 codons per minute)
  • examples of ribosome pausing or stalling at consecutive proline codons in eukaryotes and yeast [7, 6]

But who knows what else we will learn in the future? This technique can teach us a lot about how gene expression can be regulatated at the translational level. Additionally, we can learn a lot about how translation affects various diseases states, most notably cancer, since cellular stress will very likely affect both translation rate and regulation.

Drawbacks and complications 

While this technique is extremely powerful, there are a few drawbacks. The most prominent amongst them is that any attempt to lyse and harvest the cells for this procedure causes a change in the ribosome profile, making this technique particularly vulnerable to artefacts. Researchers often attempt to halt translation before harvesting with a 5 minute incubation with cyclohexamide, a drug that blocks translation elongation, to prevent ribosome run-off; however, this can result in an enormous increase in ribosome signal at the initiation sites, as ribosomes will still initiate translation and begin to pile up.

The best method of combatting these artefacts is to flash-freeze the cells prior to harvesting, lyse over them dry ice, and then continue the protocol in the presence of cyclohexamide. This technique should result in the best balance between prevention of run-off, and prevention of excessive ribosome accumulation at the initiation site [8].

Conclusions

Our understanding of the mechanisms involved in regulation of translation has been sorely limited by our lack of ability to study it directly. Ribosome profiling now provides a method for us to do just that. We’ve already made huge strides in our understanding of many events in the translation process, including the discovery of hundreds of non-canonical translation initiation sites as well the realization that not all ‘non-coding’ RNAs are non-coding after all! I expect that we’ll continue to see this technique put to new and innovate questions about translation and its role in the cell as the technology matures.

If you’re interested in Ribo-Seq services enter your basic project parameters on Genohub and send us a request. We’ll be happy to help.

 

 

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