Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

Abstract
Data availability
Article and author information
Metrics

Abstract

Codon usage biases are found in all genomes and influence protein expression levels. The codon usage effect on protein expression was thought to be mainly due to its impact on translation. Here we show that transcription termination is an important driving force for codon usage bias in eukaryotes. Using Neurospora crassa as a model organism, we demonstrated that introduction of rare codons results in premature transcription termination (PTT) within open reading frames and the abolishment of full-length mRNA. PTT is a wide-spread phenomenon in Neurospora and there is a strong negative correlation between codon usage bias and PTT events. Rare codons lead to the formation of putative poly(A) signals and PTT. A similar role for codon usage bias was also observed in mouse. Together, these results suggest that codon usage biases co-evolve with the transcription termination machinery to suppress premature termination of transcription and thus allow for optimal gene expression.

Data availability

The following data sets were generated

1. Zhipeng Zhou
(2017) PolyA-seq
Accession# PRJNA419320.

https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA419320

Article and author information

Author details

Zhipeng Zhou

Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, United States

Competing interests
The authors declare that no competing interests exist.
Yunkun Dang

State Key Laboratory of Natural Resource Conservation and Utilization in Yunnan, Yunnan University, Kunming, China

For correspondence
yunkun_dang@126.com

Competing interests
The authors declare that no competing interests exist.
Mian Zhou

State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China

Competing interests
The authors declare that no competing interests exist.
Haiyan Yuan

Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, United States

Competing interests
The authors declare that no competing interests exist.
Yi Liu

Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, United States

For correspondence
yi.liu@utsouthwestern.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-8801-9317

Funding

National Institute of General Medical Sciences (R35GM118118)

Yi Liu

Cancer Prevention and Research Institute of Texas (RP160268)

Yi Liu

Welch Foundation (I-1560)

Yi Liu

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.