Disome-seq
Disome-seq involves the sequencing of mRNA fragments protected by two ribosomes packed together, a product of translational pausing where an upstream elongating ribosome runs into a downstream paused one (1). Mapping of these ‘disome footprints’ provides a new benchmark for the investigation of ribosomal collisions transcriptome-wide, allowing the full extent of ribosome pausing and queuing to be elucidated.
Ribosome collisions are noted to occur across most of the transcriptome and are known to facilitate co-translational folding of the nascent peptide chain as well as the recruitment of signalling molecules to peptides which require subcellular or extracellular localization (2). However, collisions can also arise due to transcript mutations or defective nascent peptides which can lead to both the transcript and the nascent polypeptide being targeted for degradation (3).
While RIBO-seq can also be used to predict the locations of stalled ribosomes, disome footprints densities have been found to reveal insights related to signalling and structural features which are absent from monosome footprint data (2).
Overview: Ribosomes are pharmacologically frozen in place on transcripts. Nucleases digest any unprotected RNA before disomes are enriched for based on their size. Disome footprints are purified and size selected on Urea PAGE gels. Footprints are converted into a cDNA library which undergoes deep sequencing.
Applications
Explore links between ribosome collisions and structural features of the nascent polypeptide chain to better understand translational control of protein folding and assembly.
Investigate the ability of small RNA targeting molecules to selectively affect translation of individual transcripts, modulating their protein synthesis.
Identify codon usage signatures contributing to ribosome collisions to inform strategies for modulating translation kinetics and optimize protein titer for specific transcripts.
References
1. Zhao, T., Chen, Y-M., Li, Y., Wang, J., Chen, S., Gao, N. and Qian, W. (2021). Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding. Genome Biol. 22(1):16.
2. Arpat, A.B., Liechti, A., De Matos, M., Dreos, R., Janich, P. and Gatfield, D. (2020). Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing. Genome Res. 30(7):985-999.
3. Han, P., Shichino, Y., Schneider-Poetsch, T., Mito, M., Hashimoto, S., Udagawa, T., Kohno, K., Yoshida, M., Mishima, Y., Inada, T. and Iwasaki, S. (2020). Genome‐wide survey of ribosome collision. Cell Rep. 31(5):107610.