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Conserved upstream open reading frames in higher plants.

Tran MK, Schultz CJ, Baumann U - BMC Genomics (2008)

Bottom Line: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency.In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci.We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

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Affiliation: Australian Centre for Plant Functional Genomics PMB 1 Glen Osmond SA 5064, Australia. michael.tran@acpfg.com.au

ABSTRACT

Background: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants.

Results: We used a homology-based approach to identify conserved uORFs in five cereals (monocots) that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs.

Conclusion: This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

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Tran_Figure1.eps. 'Overview of the uORFSCAN pipeline'. The pipeline consists of four steps: 1) Identifying putative orthologues using a modified reciprocal best hit (rbh) method, 2) Clustering of orthologues according to how many cereal species they are found in, 3) Using uORFSCAN program to find conserved uORFs using a comparative approach, and 4) manual curation of predicted conserved cereal and Arabidopsis uORFs.
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Figure 1: Tran_Figure1.eps. 'Overview of the uORFSCAN pipeline'. The pipeline consists of four steps: 1) Identifying putative orthologues using a modified reciprocal best hit (rbh) method, 2) Clustering of orthologues according to how many cereal species they are found in, 3) Using uORFSCAN program to find conserved uORFs using a comparative approach, and 4) manual curation of predicted conserved cereal and Arabidopsis uORFs.

Mentions: The uORFSCAN pipeline used rice full-length cDNAs [39] and wheat, barley, maize, and sorghum assembled EST data for comparative analysis (Figure 1). In the first step of the pipeline, we identified rice genes that had orthologues in wheat, barley, maize, and sorghum. The use of orthologous sequences allowed us to more accurately predict the main coding region and define the 5'-UTR that is necessary to identify conserved uORFs.


Conserved upstream open reading frames in higher plants.

Tran MK, Schultz CJ, Baumann U - BMC Genomics (2008)

Tran_Figure1.eps. 'Overview of the uORFSCAN pipeline'. The pipeline consists of four steps: 1) Identifying putative orthologues using a modified reciprocal best hit (rbh) method, 2) Clustering of orthologues according to how many cereal species they are found in, 3) Using uORFSCAN program to find conserved uORFs using a comparative approach, and 4) manual curation of predicted conserved cereal and Arabidopsis uORFs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2527020&req=5

Figure 1: Tran_Figure1.eps. 'Overview of the uORFSCAN pipeline'. The pipeline consists of four steps: 1) Identifying putative orthologues using a modified reciprocal best hit (rbh) method, 2) Clustering of orthologues according to how many cereal species they are found in, 3) Using uORFSCAN program to find conserved uORFs using a comparative approach, and 4) manual curation of predicted conserved cereal and Arabidopsis uORFs.
Mentions: The uORFSCAN pipeline used rice full-length cDNAs [39] and wheat, barley, maize, and sorghum assembled EST data for comparative analysis (Figure 1). In the first step of the pipeline, we identified rice genes that had orthologues in wheat, barley, maize, and sorghum. The use of orthologous sequences allowed us to more accurately predict the main coding region and define the 5'-UTR that is necessary to identify conserved uORFs.

Bottom Line: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency.In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci.We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

View Article: PubMed Central - HTML - PubMed

Affiliation: Australian Centre for Plant Functional Genomics PMB 1 Glen Osmond SA 5064, Australia. michael.tran@acpfg.com.au

ABSTRACT

Background: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants.

Results: We used a homology-based approach to identify conserved uORFs in five cereals (monocots) that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs.

Conclusion: This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

Show MeSH