Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs
Abstract
The transcriptomes of eukaryotic cells are incredibly complex. Individual non-coding RNAs dwarf the number of protein-coding genes, and include classes that are well understood as well as classes for which the nature, extent and functional roles are obscure. Deep sequencing of small RNAs (<200 nucleotides) from human HeLa and HepG2 cells revealed a remarkable breadth of species. These arose both from within annotated genes and from unannotated intergenic regions. Overall, small RNAs tended to align with CAGE (cap-analysis of gene expression) tags, which mark the 5′ ends of capped, long RNA transcripts. Many small RNAs, including the previously described promoter-associated small RNAs, appeared to possess cap structures. Members of an extensive class of both small RNAs and CAGE tags were distributed across internal exons of annotated protein coding and non-coding genes, sometimes crossing exon–exon junctions. Here we show that processing of mature mRNAs through an as yet unknown mechanism may generate complex populations of both long and short RNAs whose apparently capped 5′ ends coincide. Supplying synthetic promoter-associated small RNAs corresponding to the c-MYC transcriptional start site reduced MYC messenger RNA abundance. The studies presented here expand the catalogue of cellular small RNAs and demonstrate a biological impact for at least one class of non-canonical small RNAs.
Additional Information
© 2009 Macmillan Publishers Limited. Received 16 September 2008; Accepted 02 January 2009; Published 25 January 2009. We thank L. Cardone, D. Rebolini, M. Kramer, and W. R. McCombie for Illumina sequencing. We wish to thank J. Brosius, J. Schmitz and T. Rozhdestvensky for their help with the small RNA cloning protocol and J. Dumais for technical assistance. K.F.-T. was in part supported by the Schering Foundation. This work was supported in part by grants from the NIH and was performed as part of the ENCODE consortium (G.J.H. and T.R.G.). G.J.H is an investigator of the Howard Hughes Medical Institute. Author Contributions: K.F.-T. and P.K. performed experiments in collaboration with E.D., V.S., R.D. and A.T.W. P.K., S.F., R.S. and G.A. performed data analysis. G.J.H. and T.R.G. planned experiments and wrote the paper. Competing interests: R.D. is an employee of Affymetrix, which manufactures the tiling arrays used in the study.Attached Files
Accepted Version - nihms127518.pdf
Supplemental Material - 41586_2009_BFnature07759_MOESM295_ESM.ppt
Supplemental Material - 41586_2009_BFnature07759_MOESM296_ESM.ppt
Supplemental Material - 41586_2009_BFnature07759_MOESM297_ESM.ppt
Supplemental Material - 41586_2009_BFnature07759_MOESM298_ESM.ppt
Supplemental Material - 41586_2009_BFnature07759_MOESM299_ESM.ppt
Supplemental Material - 41586_2009_BFnature07759_MOESM300_ESM.pdf
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Additional details
- PMCID
- PMC2719882
- Eprint ID
- 102592
- DOI
- 10.1038/nature07759
- Resolver ID
- CaltechAUTHORS:20200416-155025982
- Schering Foundation
- NIH
- Howard Hughes Medical Institute (HHMI)
- Created
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2020-04-16Created from EPrint's datestamp field
- Updated
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2021-11-16Created from EPrint's last_modified field