Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation

Alexander Sherstnev, Céline Duc, Christian Cole, Vasiliki Zacharaki, Csaba Hornyik, Fatih Ozsolak, Patrice M. Milos, Geoffrey J. Barton (Lead / Corresponding author), Gordon G. Simpson (Lead / Corresponding author)

    Research output: Contribution to journalArticle

    94 Citations (Scopus)

    Abstract

    It has recently been shown that RNA 3'-end formation plays a more widespread role in controlling gene expression than previously thought. To examine the impact of regulated 3'-end formation genome-wide, we applied direct RNA sequencing to A. thaliana. Here we show the authentic transcriptome in unprecedented detail and describe the effects of 3'-end formation on genome organization. We reveal extreme heterogeneity in RNA 3' ends, discover previously unrecognized noncoding RNAs and propose widespread reannotation of the genome. We explain the origin of most poly(A)+ antisense RNAs and identify cis elements that control 3'-end formation in different registers. These findings are essential to understanding what the genome actually encodes, how it is organized and how regulated 3'-end formation affects these processes.
    Original languageEnglish
    Pages (from-to)845-852
    Number of pages8
    JournalNature Structural & Molecular Biology
    Volume19
    Issue number8
    Early online date22 Jul 2012
    DOIs
    Publication statusPublished - Aug 2012

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