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Massively parallel functional annotation of 3′ untranslated regions

Nature Biotechnology volume 32, pages 387–391 (2014)Cite this article

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Abstract

Functional characterization of noncoding sequences is crucial for understanding the human genome and learning how genetic variation contributes to disease. 3′ untranslated regions (UTRs) are an important class of noncoding sequences, but their functions remain largely uncharacterized1. We developed a method for massively parallel functional annotation of sequences from 3′ UTRs (fast-UTR) and used this approach to measure the effects of a total of >450 kilobases of 3′ UTR sequences from >2,000 human genes on steady-state mRNA abundance, mRNA stability and protein production. We found widespread regulatory effects on mRNA that were coupled to effects on mRNA stability and protein production. Furthermore, we discovered 87 novel cis-regulatory elements and measured the effects of genetic variation within known and novel 3′ UTR motifs. This work shows how massively parallel approaches can improve the functional annotation of noncoding sequences, advance our understanding of cis-regulatory mechanisms and quantify the effects of human genetic variation.

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Figure 1: The fast-UTR system.
Figure 2: Effects of conserved 3′ UTR sequences on steady-state mRNA, mRNA stability and protein production.
Figure 3: Functional elements identified using fast-UTR.

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Primary accessions

Sequence Read Archive

Referenced accessions

Gene Expression Omnibus

NCBI Reference Sequence

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Acknowledgements

We thank K.M. Ansel, R. Barbeau, A. Barczak, S.E. Brenner, K. Chin, C. Eisley, E. Ostrin, S.-W. Park, A. Sayce, T. Wang and G. Zhang for advice and technical assistance. We thank A. Shyu (University of Texas Health Science Center at Houston) for providing BEAS-2B tTA cells. This work was supported by research grants (D.J.E.) and a training grant (D.P.B.) from the US National Institutes of Health.

Author information

Authors and Affiliations

  1. Lung Biology Center, University of California San Francisco, San Francisco, California, USA

    Wenxue Zhao, Joshua L Pollack, Denitza P Blagev, Noah Zaitlen & David J Erle

  2. Diabetes Center, University of California San Francisco, San Francisco, California, USA

    Michael T McManus

  3. Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA

    Michael T McManus

Authors
  1. Wenxue Zhao
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  2. Joshua L Pollack
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  6. David J Erle
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Contributions

D.J.E. and W.Z. conceived of key aspects of the project and designed the experiments. W.Z. and D.P.B. carried out the experimental work. M.T.M. contributed to the design and interpretation of the experiments. D.J.E., J.L.P., N.Z. and W.Z. analyzed the data. D.J.E. and W.Z. wrote the manuscript. All authors reviewed and commented on the manuscript.

Corresponding author

Correspondence to David J Erle.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7, Supplementary Tables 1–4, and Supplementary Notes 1 and 2 (PDF 1429 kb)

Supplementary Data 1

CXCL2 fast-UTR genome browser tracks (TXT 26 kb)

Supplementary Data 2

Conserved 3′ UTR segment sequences (XLS 857 kb)

Supplementary Data 3

3′ UTR effects on mRNA levels and stability (XLS 350 kb)

Supplementary Data 4

3′ UTR sequences enriched in sorted cells with high or low reporter protein levels (XLS 90 kb)

Supplementary Data 5

miRNA profiling of BEAS-2B cells (XLS 181 kb)

Supplementary Data 6

Cis-regulatory elements identified using fast-UTR (XLS 87 kb)

Supplementary Data 7

Conserved 3′ UTR segment fast-UTR genome browser tracks (TXT 554 kb)

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Zhao, W., Pollack, J., Blagev, D. et al. Massively parallel functional annotation of 3′ untranslated regions. Nat Biotechnol 32, 387–391 (2014). https://doi.org/10.1038/nbt.2851

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