Evolutionarily conserved inhibitory uORFs sensitize Hox mRNA translation to start codon selection stringency.

Area of Science:

• Molecular Biology
• Genetics
• Gene Regulation

Background:

• Translation start site selection in eukaryotes is governed by sequence context and translation initiation factors (eIFs).
• Homeobox (Hox) genes play crucial roles in development, and their precise regulation is essential.

Purpose of the Study:

• To investigate the role of upstream open reading frames (uORFs) and translation initiation factors in regulating Hox gene expression.
• To analyze the 5' leaders of Hox mRNAs for conserved uORFs and their functional impact.

Main Methods:

• Bioinformatic analysis of mammalian genes and cap analysis of gene expression (CAGE-seq) data.
• Reporter assays to assess Hox gene expression modulated by uORFs and eIFs.
• Manipulation of ribosome homeostasis via protein depletion or puromycin treatment.

Main Results:

• Identified conserved uORFs in the 5' leaders of 13 Hox genes, often in suboptimal sequence contexts.
• Demonstrated that these conserved uORFs inhibit Hox reporter gene expression.
• Showed that altering levels of eIF1 or eIF5, or modifying ribosome homeostasis, modulates Hox reporter expression by affecting start codon selection stringency.

Conclusions:

• Conserved uORFs in Hox mRNA 5' leaders act as regulatory elements that inhibit translation initiation.
• Start codon selection stringency, influenced by eIFs and ribosome homeostasis, provides a mechanism for gene-specific regulation of Hox genes.
• Global translation changes can lead to specific effects on gene expression through altered translation initiation.