Translation efficiency calculation based on single cell sequencing data

NAISS 2024/5-32


NAISS Medium Compute

Principal Investigator:

Claudia Kutter


Karolinska Institutet

Start Date:


End Date:


Primary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)



During translation elongation, the ribosome moves three nucleotides at a time along the mRNA transcript, as each codon complementarily binds to a corresponding anticodon triplet on a tRNA, which is charged with a specific amino acid (AA) that is then added. Previous studies calculate translation efficiency (TE) using bulk RNA-seq. However, a major limitation using bulk methods to quantify codon and anticodon pools is that by aggregating data from multiple different cell types within a tissue, they may blur out heterogeneity across cell types. Because cell types use not only different levels of the same proteins but also different types of proteins to perform their various functions, it is possible that their codon pools are different. In this study, we will use scRNA-seq and ATAC-seq data to calculate TE in different tissues. By examining these important contributors to translation elongation for the first time systematically at the cell-type level, this study paves the way for future high-resolution studies of mammalian translation.