Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons

Abstract

The correlation between codon and anticodon pools influences the efficiency of translation, but whether differences exist in these pools across individual cells is unknown. We determined that codon usage and amino acid demand are highly stable across different cell types using available mouse and human single-cell RNA sequencing atlases. After demonstrating the robustness of ATAC-seq measurements for the analysis of tRNA gene usage, we quantified anticodon usage and amino acid supply in both mouse and human single-cell ATAC-seq atlases. We found that tRNA gene usage is overall coordinated across cell types, except in neurons, which clustered separately from other cell types. Integration of these datasets revealed a strong and statistically significant correlation between amino acid supply and demand across almost all cell types. Neurons have an enhanced translation efficiency over other cell types, driven by an increased supply of tRNAAla (AGC) anticodons. This results in faster decoding of the Ala-GCC codon, as determined by cell type-specific ribosome profiling, suggesting that the reduction of tRNAAla (AGC) anticodon pools may be implicated in neurological pathologies. This study, the first such examination of codon usage, anticodon usage, and translation efficiency resolved at the cell type level with single-cell information, identifies a conserved landscape of translation elongation across mammalian cellular diversity and evolution.

Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation

“…1f and Supplementary Fig. 1d, e ), as it has been done previously 19 . Both hybridisation-based techniques and RNA sequencing can provide total quantitation for specific tRNAs with the same anticodon but none of these methods are able to discriminate between specific anticodon groups and isodecoders that differ by one or more bases.…”

Mechanisms and Delivery of tRNA Therapeutics

“…While synthetic tRNAs can be specifically dosed, when delivered as DNA, tRNA dosage becomes dependent on the promoter and enhancer sequences used to regulate transcription. These promoter elements can be designed to be expressed ubiquitously or can be modified to produce differing levels of tRNA depending on the cell-type and tissue environment. ,− …”

CRISPR/Cas9 deletions induce adverse on-target genomic effects leading to functional DNA in human cells

“…First, we quantified tRNA gene usage across the different genotypes based on Pol III occupancy by ChIP-seq. Pol III ChIP-seq read counting is widely used for measuring tRNA gene usage (17)(18)(19)(20)(21)(22)(23)(24). Unlike RNA-based methods, Pol III ChIP-seq provides tRNA genespecific information and prevents inaccurate measurements caused by the complex tRNA structure and numerous modifications that block reverse transcription (61).…”

“…Nuclear encoded tRNA genes are transcribed by RNA polymerase III (Pol III) through the recognition of internal promoter binding motifs (15,16). Pol III occupancy of tRNA genes is widely used to quantify tRNA gene usage (17)(18)(19)(20)(21)(22)(23)(24). In addition, Pol III-bound tRNA genes reside in euchromatic genomic regions, which are marked by active histones, such as histone 3 lysine 4 trimethylation (H3K4me3) (15,21,22,25,26).…”