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Shade triggers posttranscriptional PHYTOCHROME-INTERACTING FACTOR-dependent increases in H3K4 trimethylation.

Robert H Calderon1,2,3, Jutta Dalton1,2, Yu Zhang1,2,4

  • 1Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720, USA.

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Plant phytochrome (phy)-PHYTOCHROME-INTERACTING FACTOR (PIF) signaling regulates gene expression. Epigenetic modifications like H3K4me3 may buffer light-induced gene expression changes, rather than cause them.

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Area of Science:

  • Plant molecular biology
  • Plant physiology
  • Epigenetics

Background:

  • The phytochrome (phy)-PHYTOCHROME-INTERACTING FACTOR (PIF) module senses light signals to regulate plant growth and development.
  • Plants respond to environmental light cues, including initial light exposure and shade light quality.
  • Previous work categorized light- and shade-responsive genes.

Purpose of the Study:

  • To investigate the role of epigenetic chromatin modifications in differential light and shade-induced gene expression.
  • To understand how these modifications regulate distinct gene expression patterns in Arabidopsis.

Main Methods:

  • Utilized RNA-sequencing (RNA-seq) for time-resolved transcript profiling.
  • Employed ChIP-sequencing (ChIP-seq) for time-resolved profiling of histone 3 lysine 4 trimethylation (H3K4me3).

Main Results:

  • Dark-to-light transition rapidly decreased both transcript levels and H3K4me3.
  • Light-to-shade transition rapidly increased transcript levels, preceding H3K4me3 increases.
  • H3K4me3 levels did not appear to be the primary cause of shade-induced gene expression changes.

Conclusions:

  • Epigenetic modification H3K4me3 may not be causal for shade-induced gene expression.
  • H3K4me3 might function to buffer rapid light/shade fluctuations in natural environments.
  • Findings offer insights into light signal transduction and epigenetic regulation in plants.