Abstract
Post-transcriptional gene regulation frequently occurs through elements in mRNA 3′ untranslated regions (UTRs)1,2. Although crucial roles for 3′UTR-mediated gene regulation have been found in Caenorhabditis elegans3,4,5, most C. elegans genes have lacked annotated 3′UTRs6,7. Here we describe a high-throughput method for reliable identification of polyadenylated RNA termini, and we apply this method, called poly(A)-position profiling by sequencing (3P-Seq), to determine C. elegans 3′UTRs. Compared to standard methods also recently applied to C. elegans UTRs8, 3P-Seq identified 8,580 additional UTRs while excluding thousands of shorter UTR isoforms that do not seem to be authentic. Analysis of this expanded and corrected data set suggested that the high A/U content of C. elegans 3′UTRs facilitated genome compaction, because the elements specifying cleavage and polyadenylation, which are A/U rich, can more readily emerge in A/U-rich regions. Indeed, 30% of the protein-coding genes have mRNAs with alternative, partially overlapping end regions that generate another 10,480 cleavage and polyadenylation sites that had gone largely unnoticed and represent potential evolutionary intermediates of progressive UTR shortening. Moreover, a third of the convergently transcribed genes use palindromic arrangements of bidirectional elements to specify UTRs with convergent overlap, which also contributes to genome compaction by eliminating regions between genes. Although nematode 3′UTRs have median length only one-sixth that of mammalian 3′UTRs, they have twice the density of conserved microRNA sites, in part because additional types of seed-complementary sites are preferentially conserved. These findings reveal the influence of cleavage and polyadenylation on the evolution of genome architecture and provide resources for studying post-transcriptional gene regulation.
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Acknowledgements
We thank C. Burge and members of the Bartel lab for discussions and the WIBR Genome Technology Core for sequencing. This work was supported by NIH grant GM067031 (D.P.B.), a National Science Foundation predoctoral fellowship (C.H.J.) and a Krell Institute/Department of Energy Computational Sciences Graduate Fellowship (R.C.F.).
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C.H.J. performed the experiments and computational analyses of 3P-Seq data. R.C.F. performed the computational analyses of miRNA targeting and motif conservation. J.G.R. performed the computational analyses of miRNAs. All authors contributed to study design and manuscript preparation.
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Additional information
3P-Seq reads and 3P tags were deposited at the GEO as fastq and BED files, respectively (GSE24924). MicroRNA genes were deposited at miRBase (miR4805–miR4816).
Supplementary information
Supplementary Information
The file contains a Supplementary Discussion, additional references, Supplementary Tables 1-5 and 7-10 (see separate file for Supplementary Table 6) and Supplementary Figures 1-15 with legends. (PDF 16422 kb)
Supplementary Dataset 1
This file contains the coordinates of processed data used in the analyses. (TXT 3714 kb)
Supplementary Dataset 2
This file contains coordinates of UTRs defined in the study. It was noticed that a small fraction (<0.5%) of the UTRs listed in the original file were likely artefacts so a revised dataset 2 file was added on 06 January 2011 and this file was replaced on 18 February 2011, after it was noticed that one of its columns was missing. (ZIP 1797 kb)
Supplementary Table 6
This file contains a table summarizing miRNA sequencing data, The original file was not displaying correctly and was replaced on 06 January 2011. (ZIP 214 kb)
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Jan, C., Friedman, R., Ruby, J. et al. Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs. Nature 469, 97–101 (2011). https://doi.org/10.1038/nature09616
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DOI: https://doi.org/10.1038/nature09616
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