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

Handle URI:
http://hdl.handle.net/10754/563684
Title:
Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop
Authors:
Ariel, Federico D.; Jégu, Teddy; Latrasse, David; Romero-Barrios, Natali; Christ, Aurélie; Benhamed, Moussa ( 0000-0002-4181-1702 ) ; Crespi, Martín D.
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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Center for Desert Agriculture; Chromatin and development Research Group
Publisher:
Elsevier BV
Journal:
Molecular Cell
Issue Date:
Aug-2014
DOI:
10.1016/j.molcel.2014.06.011
PubMed ID:
25018019
Type:
Article
ISSN:
10972765
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.
Appears in Collections:
Articles; Bioscience Program; Desert Agriculture Initiative; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorAriel, Federico D.en
dc.contributor.authorJégu, Teddyen
dc.contributor.authorLatrasse, Daviden
dc.contributor.authorRomero-Barrios, Natalien
dc.contributor.authorChrist, Aurélieen
dc.contributor.authorBenhamed, Moussaen
dc.contributor.authorCrespi, Martín D.en
dc.date.accessioned2015-08-03T12:06:16Zen
dc.date.available2015-08-03T12:06:16Zen
dc.date.issued2014-08en
dc.identifier.issn10972765en
dc.identifier.pmid25018019en
dc.identifier.doi10.1016/j.molcel.2014.06.011en
dc.identifier.urihttp://hdl.handle.net/10754/563684en
dc.description.abstractThe 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.en
dc.description.sponsorshipWe 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.en
dc.publisherElsevier BVen
dc.titleNoncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loopen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentBioscience Programen
dc.contributor.departmentCenter for Desert Agricultureen
dc.contributor.departmentChromatin and development Research Groupen
dc.identifier.journalMolecular Cellen
dc.contributor.institutionCNRS, Institut des Sciences du Végétal, Saclay Plant Sciences, 91198 Gif-sur-Yvette and Universite Paris Diderot-Paris 7, 75013 Paris, Franceen
dc.contributor.institutionInstitut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, SPS Saclay Plant Sciences, 91405 Orsay, Franceen
kaust.authorBenhamed, Moussaen
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