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Analysis of human upstream open reading frames and impact on gene expression

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Abstract

The upstream open reading frame (uORF) is a post-transcriptional regulatory element in the 5′ untranslated region (5′UTR), which modulates the translation levels of main open reading frame (mORF). Earlier studies showed that disturbed uORF-mediated translation control can result in drastic changes in translation levels of mORF, leading to genetic disorders. To date, there has been no systematic investigation into the relationship between variations in patients and uORF status. Here, taking the advantage of several datasets, including gene ontology (GO) annotations and sequence feature analysis, we have examined uORF impacts in human transcripts. GO annotations indicate that uORF-containing genes are enriched in certain features such as oncogenes and transcription factors. Sequence feature analysis reveals that uORF is a factor for determination of the translation initiation site (TIS) in human transcripts. We show that genes with uORFs have lower protein expression levels than genes without uORFs in multiple human tissues. Moreover, by examining three disease variation databases, we identified uORF-altering mutations from a total of 3,740,225 variations, which are highly suspected to be associated with changed levels of gene expression. For an experimental validation, we found four mutations with significant effects on protein expression but with only modest changes in transcription levels. These findings will provide researchers on related diseases with new insights into the importance of known mutations.

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Notes

  1. UCSC human genome annotation database (hg19, GRCh37), http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/.

  2. Human mRNA collection, ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/.

  3. UCSC human genome annotation database (hg19, GRCh37), http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/.

  4. Gene Ontology Consortium, http://geneontology.org/.

  5. Human Proteome Map, http://www.humanproteomemap.org/.

  6. ClinVar, ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/.

  7. COSMIC, http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/.

  8. TCGA, http://cancergenome.nih.gov/.

  9. AnimalTFDB, http://www.bioguo.org/AnimalTFDB/index.php.

  10. Comprehensive Perl Archive Network, http://www.cpan.org/.

  11. Python, https://www.python.org/.

  12. The Comprehensive R Archive Network, http://cran.r-project.org/.

  13. NCBI Genome Remapping Service, http://www.ncbi.nlm.nih.gov/genome/tools/remap.

  14. Promega, Madison, Wisconsin, USA.

  15. Life Technologies, NY, USA.

  16. TaKaRa Biotechnology, Dalian, China.

  17. Toyobo, Osaka, Japan.

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Acknowledgments

The authors would like to thank Hao Zhu, Dun Liu, Jiang Li and Weiyan Shen for helpful discussions. This study was supported by National Natural Science Foundation of China (NSFC)-Guangdong Joint Fund (No. U1201222), National Public Health Grand Research Foundation (Nos. 201202017 and 201302001), Science and Technology Program of Guangzhou (201300000095) and the National Key Technology Research and Development Program (2012BAI09B01).

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Authors and Affiliations

  1. Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China

    Yuhua Ye, Yidan Liang, Qiuxia Yu, Lingling Hu, Haoli Li & Xiangmin Xu

  2. State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, Guangdong, 510515, China

    Zhenhai Zhang

  3. National Clinical Research Center for Kidney Disease, Southern Medical University, Guangzhou, Guangdong, 510515, China

    Zhenhai Zhang

  4. Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China

    Zhenhai Zhang

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  1. Yuhua Ye
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  2. Yidan Liang
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  3. Qiuxia Yu
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  4. Lingling Hu
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  5. Haoli Li
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  7. Xiangmin Xu
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Correspondence to Xiangmin Xu.

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Ye, Y., Liang, Y., Yu, Q. et al. Analysis of human upstream open reading frames and impact on gene expression. Hum Genet 134, 605–612 (2015). https://doi.org/10.1007/s00439-015-1544-7

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  • DOI: https://doi.org/10.1007/s00439-015-1544-7

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