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Mol Cell. 2014 Aug 7;55(3):383-96. doi: 10.1016/j.molcel.2014.06.011. Epub 2014 Jul 10.

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

Author information

1
CNRS, Institut des Sciences du Végétal, Saclay Plant Sciences, 91198 Gif-sur-Yvette and Université Paris Diderot-Paris 7, 75013 Paris, France.
2
Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, SPS Saclay Plant Sciences, 91405 Orsay, France.
3
Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, SPS Saclay Plant Sciences, 91405 Orsay, France; Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia. Electronic address: moussa.benhamed@u-psud.fr.
4
CNRS, Institut des Sciences du Végétal, Saclay Plant Sciences, 91198 Gif-sur-Yvette and Université Paris Diderot-Paris 7, 75013 Paris, France. Electronic address: crespi@isv.cnrs-gif.fr.

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.

PMID:
25018019
DOI:
10.1016/j.molcel.2014.06.011
[Indexed for MEDLINE]
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