mRNA sequence features that contribute to translational regulation in Arabidopsis

Ribosome profiling technology (Ribo-Seq) allowed to highlight more details of mRNA translation in cell and get additional information on importance of mRNA sequence features for this process. Application of translation inhibitors like harringtonine and cycloheximide along with mRNA-Seq technique helped to assess such important characteristic as translation efficiency. We assessed the translational importance of features of mRNA sequences with the help of statistical analysis of Ribo-Seq and mRNA-Seq data. Translationally important features known from literature as well as proposed by the authors were used in analysis. Such comparisons as protein coding versus non-coding RNAs and high- versus low-translated mRNAs were performed. We revealed a set of features that allowed to discriminate the compared categories of RNA. Significant relationships between mRNA features and efficiency of translation were also established.

Download Full-text

Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast

10.1101/085522 ◽

2016 ◽

Cited By ~ 1

Author(s):

Jun Cheng ◽

Kerstin C. Maier ◽

Žiga Avsec ◽

Petra Rus ◽

Julien Gagneur

Keyword(s):

Codon Usage ◽

Mrna Stability ◽

Half Life ◽

Regulatory Elements ◽

Quantitative Model ◽

Mrna Sequence ◽

Functional Dependencies ◽

Sequence Features ◽

Sequence Elements ◽

The Stability

ABSTRACTThe stability of mRNA is one of the major determinants of gene expression. Although a wealth of sequence elements regulating mRNA stability has been described, their quantitative contributions to half-life are unknown. Here, we built a quantitative model for Saccharomyces cerevisiae based on functional mRNA sequence features that explains 60% of the half-life variation between genes and predicts half-life at a median relative error of 30%. The model revealed a new destabilizing 3’UTR motif, ATATTC, which we functionally validated. Codon usage proves to be the major determinant of mRNA stability. Nonetheless, single-nucleotide variations have the largest effect when occurring on 3’UTR motifs or upstream AUGs. Analyzing mRNA half-life data of 34 knockout strains showed that the effect of codon usage not only requires functional decapping and deadenylation, but also the 5’-to-3’ exonuclease Xrn1, the non-sense mediated decay genes, but not no-go decay. Altogether, this study quantitatively delineates the contributions of mRNA sequence features on stability in yeast, reveals their functional dependencies on degradation pathways, and allows accurate prediction of half-life from mRNA sequence.

Download Full-text

Overexpression of sgm 5’ UTR mRNA reduces gentamicin resistance in both Escherichia coli and Micromonospora melanosporea cells

Archives of Biological Sciences ◽

10.2298/abs0704273k ◽

2007 ◽

Vol 59 (4) ◽

pp. 273-280

Author(s):

M. Kojic ◽

Sandra Vojnovic ◽

Natasa Vukov ◽

Branka Vasiljevic

Keyword(s):

Escherichia Coli ◽

16S Rrna ◽

Untranslated Region ◽

Translational Regulation ◽

Regulatory Region ◽

Mrna Sequence ◽

E Coli ◽

Ribosome Binding ◽

Gentamicin Resistance ◽

A Site

The 16S rRNA methylases are expressed by most of the antibiotic producing bacteria in order to protect themselves against antibiotics by methylation of 16S rRNA at positions which are crucial for their action. The sgm sisomicin-gentamicin resistance gene from Micromonospora zionensis methylates G1405 positioned in the A site of 16S rRNA, which includes a CCGCCC hexanucleotide. The same hexanucleotide is also present 14 nucleotides in front of the ribosome binding site of sgm mRNA. The model proposed for translational regulation of sgm assumes that Sgm binds to this motif, both on 16S rRNA and on the 5? untranslated region (UTR) of its own mRNA. The 5? UTR mRNA sequence was overexpressed on 3?-truncated sgm mRNA, and the effect on gentamicin resistance conferred by Sgm was tested in Escherichia coli and in Micromonospora melanosporea. Overexpression of the sgm mRNA regulatory region decreases the resistance to gentamicin in both E. coli and M. melanosporea. This effect is likely to be due to titration of Sgm molecules by the overexpressed 5? UTR.

Download Full-text