Effect of 5′UTR introns on gene expression in Arabidopsis thaliana

Chung, Betty Y.W., Simons, Cas, Firth, Andrew E., Brown, Chris M., & Hellens, Roger P. (2006) Effect of 5′UTR introns on gene expression in Arabidopsis thaliana. BMC Genomics, 7(120).

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The majority of introns in gene transcripts are found within the coding sequences (CDSs). A small but significant fraction of introns are also found to reside within the untranslated regions (5′UTRs and 3′UTRs) of expressed sequences. Alignment of the whole genome and expressed sequence tags (ESTs) of the model plant Arabidopsis thaliana has identified introns residing in both coding and non-coding regions of the genome.


A bioinformatic analysis revealed some interesting observations:

(1) the density of introns in 5′UTRs is similar to that in CDSs but much higher than that in 3′UTRs;

(2) the 5′UTR introns are preferentially located close to the initiating ATG codon;

(3) introns in the 5′UTRs are, on average, longer than introns in the CDSs and 3′UTRs; and

(4) 5′UTR introns have a different nucleotide composition to that of CDs and 3′UTR introns.

Furthermore, we show that the 5′UTR intron of the A. thaliana EFIα-A3 gene affects the gene expression and the size of the 5′UTR intron influences the level of gene expression.


Introns within the 5′UTR show specific features that distinguish them from introns that reside within the coding sequence and the 3′UTR. In the EFIα-A3 gene, the presence of a long intron in the 5′UTR is sufficient to enhance gene expression in plants in a size dependent manner.

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91 citations in Scopus
85 citations in Web of Science®
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ID Code: 71299
Item Type: Journal Article
Refereed: Yes
Additional Information: Cited By (since 1996):66
Export Date: 6 May 2014
Source: Scopus
Art. No.: 120
PubMed ID: 16712733
DOI: 10.1186/1471-2164-7-120
ISSN: 1471-2164
Divisions: Current > QUT Faculties and Divisions > Science & Engineering Faculty
Copyright Owner: Copyright 2006 Chung et al; licensee BioMed Central Ltd.
Copyright Statement: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Deposited On: 09 May 2014 03:03
Last Modified: 21 Jun 2017 06:02

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