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

TitlePost-transcriptional processing generates a diversity of 5'-modified long and short RNAs.
Publication TypeJournal Article
Year of Publication2009
Corporate AuthorsAffymetrix ENCODE Transcriptome Project, Cold Spring Harbor Laboratory ENCODE Transcriptome Project
JournalNature
Volume457
Issue7232
Pagination1028-32
Date Published2009 Feb 19
ISSN1476-4687
Keywords5' Untranslated Regions, Cell Line, Tumor, Exons, Gene Expression Profiling, Genes, myc, Genome, Human, HeLa Cells, Humans, Models, Genetic, RNA, RNA Caps, RNA Processing, Post-Transcriptional, RNA, Untranslated, Transcription Initiation Site
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.

DOI10.1038/nature07759
Alternate JournalNature
PubMed ID19169241
PubMed Central IDPMC2719882
Grant ListU54 HG004557 / HG / NHGRI NIH HHS / United States
U54 HG004557-01 / HG / NHGRI NIH HHS / United States
/ / Howard Hughes Medical Institute / United States