Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics

Renana Sabi,Tamir Tuller

doi:10.1038/s41540-019-0089-0

Abstract

The ability to dynamically control mRNA translation has a great impact on many intracellular processes. Whereas it is believed that translational control in eukaryotes occurs mainly at initiation, the condition-specific changes at the elongation level and their potential regulatory role remain unclear. Using computational approaches applied to ribosome profiling data, we show that elongation rate is dynamic and can change considerably during the yeast meiosis to facilitate the selective translation of stage-specific transcripts. We observed unique elongation changes during meiosis II, including a global inhibition of translation elongation at the onset of anaphase II accompanied by a sharp shift toward increased elongation for genes required at this meiotic stage. We also show that ribosomal proteins counteract the global decreased elongation by maintaining high initiation rates. Our findings provide new insights into gene expression regulation during meiosis and demonstrate that codon usage evolved, among others, to optimize timely translation.

Highlights

For over decades, most of the gene expression studies were based on transcript levels measured by techniques such as microarrays and RNA-seq.[1]
We utilize the Mean of the Typical codon Decoding Rate (MTDR), a novel estimation of translation elongation efficiency based on the analysis of ribosome profiling data.[23]
MTDR calculation consists of the following major steps: (1) generating codon-specific histograms of ribo-seq read count (RC); (2) fitting each histogram into an exponentially modified gaussian, a superposition of a normal distribution and a negative exponential distribution; (3) using the maximum-likelihood estimation (MLE) to infer the mean of each normal distribution, which represents the mean of the typical decoding rate of each codon

Summary

Introduction

Most of the gene expression studies were based on transcript levels measured by techniques such as microarrays and RNA-seq.[1]. In contrast decoding rate over its synonymous codons such that each codon to C1, C2 was mainly composed of highly expressed genes, contributes to the average TDR according to its genomic translated with high elongation efficiency during most time points frequency (Methods).

Results

Conclusion