The codon composition of coding sequences plays an important role in the regulation of gene expression. Herein, we report systematic differences in the usage of synonymous codons among Arabidopsis thaliana genes that are expressed specifically in distinct tissues. Although we observed that both regionally and transcriptionally associated mutational biases were associated significantly with codon bias, they could not explain the observed differences fully. Similarly, given that transcript abundances did not account for the differences in codon usage, it is unlikely that selection for translational efficiency can account exclusively for the observed codon bias. Thus, we considered the possible evolution of codon bias as an adaptive response to the different abundances of tRNAs in different tissues. Our analysis demonstrated that in some cases, codon usage in genes that were expressed in a broad range of tissues was influenced primarily by the tissue in which the gene was expressed maximally. On the basis of this finding we propose that genes that are expressed in certain tissues might show a tissue-specific compositional signature in relation to codon usage. These findings might have implications for the design of transgenes in relation to optimizing their expression.

The Relation of Codon Bias to Tissue-Specific Gene Expression in Arabidopsis thaliana / S., Camiolo; Farina, Lorenzo; A., Porceddu. - In: GENETICS. - ISSN 0016-6731. - STAMPA. - 192:2(2012), pp. 641-+. [10.1534/genetics.112.143677]

The Relation of Codon Bias to Tissue-Specific Gene Expression in Arabidopsis thaliana

FARINA, Lorenzo;
2012

Abstract

The codon composition of coding sequences plays an important role in the regulation of gene expression. Herein, we report systematic differences in the usage of synonymous codons among Arabidopsis thaliana genes that are expressed specifically in distinct tissues. Although we observed that both regionally and transcriptionally associated mutational biases were associated significantly with codon bias, they could not explain the observed differences fully. Similarly, given that transcript abundances did not account for the differences in codon usage, it is unlikely that selection for translational efficiency can account exclusively for the observed codon bias. Thus, we considered the possible evolution of codon bias as an adaptive response to the different abundances of tRNAs in different tissues. Our analysis demonstrated that in some cases, codon usage in genes that were expressed in a broad range of tissues was influenced primarily by the tissue in which the gene was expressed maximally. On the basis of this finding we propose that genes that are expressed in certain tissues might show a tissue-specific compositional signature in relation to codon usage. These findings might have implications for the design of transgenes in relation to optimizing their expression.
2012
01 Pubblicazione su rivista::01a Articolo in rivista
The Relation of Codon Bias to Tissue-Specific Gene Expression in Arabidopsis thaliana / S., Camiolo; Farina, Lorenzo; A., Porceddu. - In: GENETICS. - ISSN 0016-6731. - STAMPA. - 192:2(2012), pp. 641-+. [10.1534/genetics.112.143677]
File allegati a questo prodotto
File Dimensione Formato  
VE_2012_11573-503340.pdf

solo gestori archivio

Tipologia: Versione editoriale (versione pubblicata con il layout dell'editore)
Licenza: Tutti i diritti riservati (All rights reserved)
Dimensione 860.71 kB
Formato Adobe PDF
860.71 kB Adobe PDF   Contatta l'autore

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/503340
 Attenzione

Attenzione! I dati visualizzati non sono stati sottoposti a validazione da parte dell'ateneo

Citazioni
  • ???jsp.display-item.citation.pmc??? 19
  • Scopus 35
  • ???jsp.display-item.citation.isi??? 36
social impact