Ribosome profiling
Ribosome profiling, or Ribo-Seq (also named ribosome footprinting), is an adaptation of a technique developed by
Description
It produces a “global snapshot” of all the
History
Ribosome profiling is based on the discovery that the mRNA within a ribosome can be isolated through the use of
Uses
There are three main uses of ribosome profiling: identifying translated mRNA regions, observing how nascent peptides are folded, and measuring the amount of specific proteins that are synthesized.
Identifying Translated mRNA Regions
By using specific drugs, ribosome profiling can identify initiating regions of mRNA, elongating regions, and areas of translation stalling.
Peptide Folding
Coupling ribosome profiling with ChIP can elucidate how and when newly synthesized proteins are folded.[1] Using the footprints provided by Ribo-Seq, specific ribosomes associated with factors, like chaperones, can be purified. Pausing the ribosome at specific time points, allowing it to translate a polypeptide over time, and exposing the different points to a chaperone and precipitating out using ChIP purifies these samples and can show at which point in time the peptide is being folded.[1]
Measuring Protein Synthesis
Ribo-Seq can also be used to estimate translation efficiency, a proxy for protein synthesis. For this application, ribosome profiling and matched RNA sequencing data are generated. The initial data analyses can be achieved by dedicated computational frameworks (ex.[8]). Translation efficiency can then be computed as the ribosome occupancy of each gene while controlling for its RNA expression.[9][10] This approach can be coupled with directed disruption of proteins that bind to RNA and using ribosome profiling to measure the difference in translation.[7] These disrupted mRNAs can be associated with proteins, whose binding sites have already been mapped on RNA, to indicate regulation.[1][7]
Procedure
- Lyse the cells or tissue and isolate the mRNA molecules bound to ribosomes.
- Immobilize complexes. This is commonly performed with cycloheximide but other chemicals can be employed. It is also possible to forgo translation inhibitors with translation-incompetent lysis conditions.
- Using ribonucleases, digest the RNA not protected by ribosomes.
- Isolate the mRNA-ribosome complexes using sucrose gradient density centrifugation or specialized chromatography columns.
- Phenol/chloroform purification of mixture to remove proteins.
- Size-select for previously-protected mRNA fragments.
- Ligate 3' adapter to fragments.
- Subtract known rRNA contaminants (optional).
- Reverse transcribe RNA to cDNA using reverse transcriptase.
- Amplify in strand-specific manner.
- Sequence reads.
- Align sequence results to genomic sequence to determine translational profile.[11]
- Analyze resulting data using computational approaches specifically designed for ribosome profiling.[12]
Materials
- RNA-ribosome complexes
- Cycloheximide
- Nucleases
- Phenol/Chloroform
- Reverse transcriptase
- dNTPs
- Sequencing method-cDNA library.[11]
References
External links
- GWIPS-viz browser
- RiboGalaxy
- RPF-DB Archived 2016-02-03 at the Wayback Machine
- Trips-VIZ browser
- RiboFlow, RiboR, RiboPy