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RNA polymerase III transcribes human microRNAs

Abstract

Prior work demonstrates that mammalian microRNA (miRNA or miR) expression requires RNA polymerase II (Pol II). However, the transcriptional requirements of many miRNAs remain untested. Our genomic analysis of miRNAs in the human chromosome 19 miRNA cluster (C19MC) revealed that they are interspersed among Alu repeats. Because Alu transcription occurs through RNA Pol III recruitment, and we found that Alu elements upstream of C19MC miRNAs retain sequences important for Pol III activity, we tested the promoter requirements of C19MC miRNAs. Chromatin immunoprecipitation and cell-free transcription assays showed that Pol III, but not Pol II, is associated with miRNA genomic sequence and sufficient for transcription. Moreover, the mature miRNA sequences of approximately 50 additional human miRNAs lie within Alu and other known repetitive elements. These findings extend the current view of miRNA origins and the transcriptional machinery driving their expression.

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Figure 1: The C19MC cluster and assessment of 5′ Alu transcriptional activity.
Figure 2: Analysis of miR-517a and miR-517c 5′ promoter elements.
Figure 3: C19MC 5′ Alus are transcribed by Pol III.
Figure 4: Cartoon depicting the arrangement of C19MC miRNAs with Alus.

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Acknowledgements

The authors are grateful to Robert Roeder at Rockefeller University for antibodies to Pol III, TFIIIB and TFIIIC subunits, for the BN51 cell line and for suggestions for the ChIP studies. We also thank S. Harper, R. Boudreau, C. Stein and S. Eliason for assistance and discussions, M. Welsh, R. Cornell and P. McCray for manuscript review and C. McLennan for manuscript assistance. This work was supported by the US National Institutes of Health (HD 44093; NS 50210) and the Roy J. Carver Trust.

Author information

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Authors

Contributions

G.M.B. conceived the study, collected the experimental data and contributed to the identification of repetitive element–microRNA associations, design and planning of the wet-lab experimentation, analysis of the experimental and computational findings and writing of the manuscript. W.L. contributed to the identification of repetitive element–microRNA associations and computational analysis. B.L.D. contributed to design and planning of the wet-lab experimentation, analysis of the experimental and computational findings and writing of the manuscript. All authors edited and approved the final version of the manuscript.

Corresponding author

Correspondence to Beverly L Davidson.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Pol-III subunits and antibody specificity. (PDF 680 kb)

Supplementary Table 1

Human miRNA repetitive element alignments. (PDF 7577 kb)

Supplementary Table 2

C19MC ESTs. (PDF 522 kb)

Supplementary Table 3

Additional human Pol III–driven miRNAs. (PDF 1023 kb)

Supplementary Table 4

C19MC negative strand Pol III terminators. (PDF 4425 kb)

Supplementary Table 5

Oligonucleotide masterlist. (PDF 2181 kb)

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Borchert, G., Lanier, W. & Davidson, B. RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol 13, 1097–1101 (2006). https://doi.org/10.1038/nsmb1167

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