Effect of 5UTR introns on gene expression in Arabidopsis thaliana.docVIP

BMC Genomics BioMedCentral Research article Open Access Effect of 5UTR introns on gene expression in Arabidopsis thaliana Betty YW Chung1,4, Cas Simons2,3, Andrew E Firth1, Chris M Brown1 and Roger P Hellens*2 Address: 1Biochemistry Department, University of Otago, Dunedin, New Zealand, 2HortResearch, Auckland, New Zealand, 3Institute of Molecular Biosciences, Brisbane, Australia and 4Bioscience Institute, University College Cork, Cork, Ireland Email: Betty YW Chung - b.ying-wenchung@ucc.ie; Cas Simons - c.simons@.au; Andrew E Firth - aef@sanger.otago.ac.nz; Chris M Brown - chris.brown@stonebow.otago.ac.nz; Roger P Hellens* - rhellens@hortresearch.co.nz * Corresponding author Published: 19 May 2006 Received: 18 April 2006 Accepted: 19 May 2006 BMC Genomics 2006, 7:120 doi:10.1186/1471-2164-7-120 This article is available from: /1471-2164/7/120 ? 2006 Chung et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: 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 (5UTRs and 3UTRs) 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. Results: A bioinformatic analysis revealed some interesting observations: (1) the density of introns in 5UTRs is similar to that in CDSs but much higher than that in 3UTRs; (2) the 5UTR introns are preferentially located close to the initiating ATG codon; (3) introns in the 5UTRs are, on average, longer than introns in the CDSs and 3UTRs; and (4) 5