Development of single-cell ribosome profiling for aging and longevity studies

Shintaro Iwasaki

Cluster for Pioneering Research(CPR)
RNA Systems Biochemistry Laboratory
Chief Scientist


Protein synthesis in aging cells

Since recent studies have revealed that the reduced translation leads longevity of yeast, nematodes, flies, and mice (1), understanding of translation regulation and its loss during aging has been attractive topic. Since aging appears to differentially affect the fundamental processes in a stochastic manner, it is quite likely that diverse translation alteration is induced in individual cells along aging. Thus, the measurement of comprehensive protein synthesis in every single cell will promise to provide a new layer of knowledge of aging-mediated translation dysregulation. However, systematic approach to translation at single-cell level has been an experimental challenge.
To overcome such a hurdle, here I proposed the development of a novel technique: single-cell ribosome profiling. The essence of ribosome profiling technique is a deep sequencing of ribosome-protected RNA fragment (ribosome footprint) generated by RNase-treatment (2) (Fig). Since the identified location of the ribosome footprint along mRNA directly represents the place of ribosome, we can measure the relative number of ribosome on RNA, or translation efficiency. In addition, the region the ribosome footprint originated from can also delineate the coding region on an mRNA and estimate elongation speed at every codon.
Application of this technology to single-cell level will allow us to address the broad sweep of translation-directed phenomena, which were totally inaccessible by earlier methodologies: the measurement of fluctuations of mRNA translation among aged cells, identification of sub-populations of the cells defined by translation status, and monitoring transitions from regular to aged cells led by protein synthesis.

  1. S. C. Johnson, P. S. Rabinovitch, M. Kaeberlein, Nature 493, 338 (2013).
  2. N. T. Ingolia, S. Ghaemmaghami, J. R. Newman, J. S. Weissman, Science 324, 218 (2009).