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New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism

Abstract

Small (<200 nucleotide) RNA (sRNA) profiling of human cells using various technologies demonstrates unexpected complexity of sRNAs with hundreds of thousands of sRNA species present1,2,3,4. Genetic and in vitro studies show that these RNAs are not merely degradation products of longer transcripts but could indeed have a function1,2,5. Furthermore, profiling of RNAs, including the sRNAs, can reveal not only novel transcripts, but also make clear predictions about the existence and properties of novel biochemical pathways operating in a cell. For example, sRNA profiling in human cells indicated the existence of an unknown capping mechanism operating on cleaved RNA2, a biochemical component of which was later identified6. Here we show that human cells contain a novel type of sRNA that has non-genomically encoded 5′ poly(U) tails. The presence of these RNAs at the termini of genes, specifically at the very 3′ ends of known mRNAs, strongly argues for the presence of a yet uncharacterized endogenous biochemical pathway in cells that can copy RNA. We show that this pathway can operate on multiple genes, with specific enrichment towards transcript-encoding components of the translational machinery. Finally, we show that genes are also flanked by sense, 3′ polyadenylated sRNAs that are likely to be capped.

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Figure 1: Novel class of sRNAs antisense to 3′ ends annotations.
Figure 2
Figure 3: Verification of EEF2 TASRs using independent biochemical methods and possible mechanism for their production using endogenous RdRP-like activity.

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Data deposits

Sequencing datasets described in this study have been deposited at the National Center for Biotechnology Information (NCBI) Short Read Archive (SRA), accession no SRA012676.

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Acknowledgements

We wish to thank A. Willingham, J. Thompson and Z. Li for discussions and help in the preparation of the manuscript. S.E.A. is supported by the Swiss National Science Foundation, B.J. by the NIH (GM079756) and American Cancer Society (RSG0905401), and A.P.M. by the NIH (MH60774). S.F. acknowledges support by a grant from the Comunidad de Madrid and European Union (Exp. 11/2009).

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Authors

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P.K., F.O. and P.M.M. designed the study, performed the experiments and the data analysis. S.F. and D.L. performed additional bioinformatics analyses. C.H. and S.R. assisted with the development of the Helicos analysis pipeline. S.W.K., A.P.M. and B.J. performed the northern blot and RPA validation experiments. C.B. and S.E.A. contributed to the validation experiments.

Corresponding authors

Correspondence to Philipp Kapranov or Patrice M. Milos.

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Competing interests

P.K., F.O., D.L., C.H. and P.M.M. are employees and stockholders of Helicos BioSciences Corporation. S.F. is an employee of Integromics, S.L.

Supplementary information

Supplementary Information

This file contains Supplementary Text, Supplementary Methods and Materials, References, Supplementary Tables S1 –S2, Supplementary Figures S1-S8 and Supplementary Data for Human Expressed Sequence Tags. (PDF 2599 kb)

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Kapranov, P., Ozsolak, F., Kim, S. et al. New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism. Nature 466, 642–646 (2010). https://doi.org/10.1038/nature09190

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