Meta-Analysis of the Transcriptome Reveals a Core Set of Shade-Avoidance Genes in Arabidopsis

Photochemistry and Photobiology
Romina SellaroJorge J Casal

Abstract

The presence of neighboring vegetation modifies the light input perceived by photo-sensory receptors, initiating a signaling cascade that adjusts plant growth and physiology. Thousands of genes can change their expression during this process, but the structure of the transcriptional circuit is poorly understood. Here we present a meta-analysis of transcriptome data from Arabidopsis thaliana exposed to neighbor signals in different contexts, including organs where growth is promoted or inhibited by these signals. We identified a small set of genes that consistently and dynamically respond to neighbor light signals. This group is also affected by light during de-etiolation and day/night cycles. Among these genes, many of those with positive response to neighbor signals are binding targets of PHYTOCHROME-INTERACTING FACTORS (PIFs) and function as transcriptional regulators themselves, but none of these features is observed among those with negative response to neighbor signals. Changes. in neighbor signals can mimic the transcriptional signature of auxin, gibberellins, brassinosteroid, abscisic acid, ethylene, jasmonic acid and cytokinin but in a context-dependent manner. We propose the existence of a small core set of genes invol...Continue Reading

References

May 1, 1996·Plant Physiology·S Abel, A Theologis
Aug 16, 1996·Science·M J BennettK A Feldmann
Dec 20, 2000·Trends in Plant Science·P Hedden, A L Phillips
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Nov 15, 2003·The Plant Cell·Patricia LariguetChristian Fankhauser
Dec 3, 2003·Plant Physiology·Paul Francis DevlinSteve A Kay
Apr 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jennifer M GagneRichard D Vierstra
May 17, 2005·Annals of Botany·Keara A Franklin, Garry C Whitelam
Jan 13, 2006·Plant Physiology·Toshitsugu NakanoHideaki Shinshi
Oct 28, 2006·Annual Review of Plant Biology·John M Christie
Dec 1, 2007·The Plant Journal : for Cell and Molecular Biology·Séverine LorrainChristian Fankhauser
Apr 19, 2008·Cold Spring Harbor Symposia on Quantitative Biology·T C MocklerJ Chory
Oct 24, 2009·The EMBO Journal·Patricia HornitschekChristian Fankhauser
May 25, 2010·Trends in Plant Science·Agepati S RaghavendraErwin Grill
Jul 30, 2010·Plant Physiology·Romina SellaroJorge José Casal
Sep 14, 2010·Trends in Plant Science·Pablo Leivar, Peter H Quail
Aug 19, 2011·The Plant Journal : for Cell and Molecular Biology·Romina SellaroJorge J Casal
Apr 18, 2012·Genes & Development·Lin LiJoanne Chory
Apr 28, 2012·The Plant Journal : for Cell and Molecular Biology·Patricia HornitschekChristian Fankhauser
May 15, 2012·The Arabidopsis Book·Jorge J Casal
Oct 23, 2012·Trends in Plant Science·Charlotte M M GommersRonald Pierik
Feb 5, 2013·Annual Review of Plant Biology·Jorge J Casal
Mar 19, 2013·The Plant Journal : for Cell and Molecular Biology·Shivakumar SreeramuluGuido Sessa
May 8, 2013·The Plant Journal : for Cell and Molecular Biology·Manuel PacínJorge J Casal

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Citations

Sep 21, 2017·Frontiers in Plant Science·Chuanwei Yang, Lin Li
Jul 30, 2019·Frontiers in Plant Science·Lin Ma, Gang Li
Oct 17, 2017·Journal of Experimental Botany·María José IglesiasJorge José Casal
Oct 3, 2018·Proceedings of the National Academy of Sciences of the United States of America·Mieke de WitChristian Fankhauser
Apr 29, 2021·The New Phytologist·Sofía Romero-MontepaoneJorge J Casal

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