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    Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

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    Type
    Article
    Authors
    Ariel, Federico D.
    Jégu, Teddy
    Latrasse, David cc
    Romero-Barrios, Natali
    Christ, Aurélie
    Benhamed, Moussa cc
    Crespi, Martín D.
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Chromatin and development Research Group
    Desert Agriculture Initiative
    Plant Science
    Plant Science Program
    Date
    2014-08
    Permanent link to this record
    http://hdl.handle.net/10754/563684
    
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    Abstract
    The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes. © 2014 Elsevier Inc.
    Citation
    Ariel, F., Jegu, T., Latrasse, D., Romero-Barrios, N., Christ, A., Benhamed, M., & Crespi, M. (2014). Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop. Molecular Cell, 55(3), 383–396. doi:10.1016/j.molcel.2014.06.011
    Sponsors
    We thank Herve Vaucheret for rdd seeds, Francois Roudier for clf and swn seeds, and both of them for constructive discussions, as well as Allison Mallory for careful reading of the manuscript. We also thank Craig Pikaard for NRPE1-FLAG-transformed seeds and Koji Goto for LHP1-GFP-transformed seeds. F.A. is an EMBO postdoc fellow; N.R.-B. and T.J. are Paris-Sud University PhD fellows. This work was funded by LABEX Saclay Plant Sciences and the France-Brazilian COFECUB Exchange program.
    Publisher
    Elsevier BV
    Journal
    Molecular Cell
    DOI
    10.1016/j.molcel.2014.06.011
    PubMed ID
    25018019
    ae974a485f413a2113503eed53cd6c53
    10.1016/j.molcel.2014.06.011
    Scopus Count
    Collections
    Articles; Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Plant Science Program; Desert Agriculture Initiative

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