Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs

Fejes-Toth, K., Sotirova, V., Sachidanandam, R., Assaf, G., Hannon, G. J., Kapranov, P., Foissac, S., Willingham, A. T., Duttagupta, R., Dumais, E., Gingeras, T. R. (February 2009) Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature, 457 (7232). pp. 1028-1032. ISSN 0028-0836

URL: http://www.ncbi.nlm.nih.gov/pubmed/19169241
DOI: 10.1038/nature07759

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(1). 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(2), which mark the 5 ' ends of capped, long RNA transcripts. Many small RNAs, including the previously described promoter- associated small RNAs3, 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 noncoding 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.

Item Type: Paper
Uncontrolled Keywords: GENE-EXPRESSION gene expression HUMAN GENOME human genome CELLS cells IDENTIFICATION identification TRANSCRIPTION transcription REVEAL MAPS maps
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > sRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:
Communities: CSHL labs > Gingeras lab
CSHL labs > Hannon lab
Depositing User: CSHL Librarian
Date: February 2009
Date Deposited: 08 Mar 2012 15:03
Last Modified: 27 Mar 2014 19:34
PMCID: PMC2719882
Related URLs:
URI: http://repository.cshl.edu/id/eprint/25334

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