skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: PIF transcription factors-versatile plant epigenome landscapers
Plants are exquisitely responsive to their local light and temperature environment utilizing these environmental cues to modulate their developmental pathways and adjust growth patterns. This responsiveness is primarily achieved by the intricate interplay between the photoreceptor phyB (phytochrome B) and PIF (PHYTOCHROME INTERACTING FACTORs) transcription factors (TFs), forming a pivotal signaling nexus. phyB and PIFs co-associate in photobodies (PBs) and depending on environmental conditions, PIFs can dissociate from PBs to orchestrate gene expression. Until recently, the mechanisms governing epigenome modifications subsequent to PIF binding to target genes remained elusive. This mini review sheds light on the emerging role of PIFs in mediating epigenome reprogramming by recruiting chromatin regulators (CRs). The formation of numerous different PIF-CR complexes enables precise temporal and spatial control over the gene regulatory networks (GRNs) governing plant-environment interactions. We refer to PIFs as epigenome landscapers, as while they do not directly reprogram the epigenome, they act as critical sequence-specific recruitment platforms for CRs. Intriguingly, in the absence of PIFs, the efficacy of epigenome reprogramming is largely compromised in light and temperature-controlled processes. We have thoroughly examined the composition and function of known PIF-CR complexes and will explore also unanswered questions regarding the precise of locations PIF-mediated epigenome reprogramming within genes, nuclei, and plants.  more » « less
Award ID(s):
2339927
PAR ID:
10563234
Author(s) / Creator(s):
; ;
Publisher / Repository:
Frontiers Media SA
Date Published:
Journal Name:
Frontiers in Epigenetics and Epigenomics
Volume:
2
ISSN:
2813-706X
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; ; ; ; ; et al (, Nature Communications)
    Abstract Photoactivated phytochrome B (PHYB) binds to antagonistically acting PHYTOCHROME-INTERACTING transcription FACTORs (PIFs) to regulate hundreds of light responsive genes in Arabidopsis by promoting PIF degradation. However, whether PHYB directly controls the transactivation activity of PIFs remains ambiguous. Here we show that the prototypic PIF, PIF3, possesses a p53-like transcription activation domain (AD) consisting of a hydrophobic activator motif flanked by acidic residues. A PIF3mAD mutant, in which the activator motif is replaced with alanines, fails to activate PIF3 target genes in Arabidopsis , validating the functions of the PIF3 AD in vivo. Intriguingly, the N-terminal photosensory module of PHYB binds immediately adjacent to the PIF3 AD to repress PIF3’s transactivation activity, demonstrating a novel PHYB signaling mechanism through direct interference of the transactivation activity of PIF3. Our findings indicate that PHYB, likely also PHYA, controls the stability and activity of PIFs via structurally separable dual signaling mechanisms. 
    more » « less
  2. ; ; ; ; (, Proceedings of the National Academy of Sciences)
    Light is a crucial environmental factor that impacts various aspects of plant development. Phytochromes, as light sensors, regulate myriads of downstream genes to mediate developmental reprogramming in response to changes in environmental conditions. CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is an E3 ligase for a number of substrates in light signaling, acting as a central repressor of photomorphogenesis. The interplay between phytochrome B (phyB) and COP1 forms an antagonistic regulatory module that triggers extensive gene expression reprogramming when exposed to light. Here, we uncover a role of COP1 in light-dependent chromatin remodeling through the regulation of VIL1 (VIN3-LIKE 1)/VERNALIZATION 5, a Polycomb protein. VIL1 directly interacts with phyB and regulates photomorphogenesis through the formation of repressive chromatin loops at downstream growth-promoting genes in response to light. Furthermore, we reveal that COP1 governs light-dependent formation of chromatin loop and limiting a repressive histone modification to fine-tune expressions of growth-promoting genes during photomorphogenesis through VIL1. 
    more » « less
  3. ; ; (, Journal of Experimental Botany)
    Abstract Light serves as a pivotal environmental cue regulating various aspects of plant growth and development, including seed germination, seedling de-etiolation, and shade avoidance. Within this regulatory framework, the basic helix–loop–helix transcription factors known as phytochrome-interacting factors (PIFs) play an essential role in orchestrating responses to light stimuli. Phytochromes, acting as red/far-red light receptors, initiate a cascade of events leading to the degradation of PIFs (except PIF7), thereby triggering transcriptional reprogramming to facilitate photomorphogenesis. Recent research has unveiled multiple post-translational modifications that regulate the abundance and/or activity of PIFs, including phosphorylation, dephosphorylation, ubiquitination, deubiquitination, and SUMOylation. Moreover, intriguing findings indicate that PIFs can influence chromatin modifications. These include modulation of histone 3 lysine 9 acetylation (H3K9ac), as well as occupancy of histone variants such as H2A.Z (associated with gene repression) and H3.3 (associated with gene activation), thereby intricately regulating downstream gene expression in response to environmental cues. This review summarizes recent advances in understanding the role of PIFs in regulating various signaling pathways, with a major focus on photomorphogenesis. 
    more » « less
  4. ; ; ; ; ; ; ; ; (, Plant physiology and biochemistry)
    Plant phytochromes are well-studied photoreceptors that sense red and far-red light, regulating photomorpho- genic development. Molecular signaling mechanisms of phytochrome A (phyA) and phyB largely overlap, especially in regulation of PHYTOCHROME-INTERACTING FACTORs (PIFs) and E3 ligase complexes composed of CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSORs OF phyA-105 (SPAs). However, the differences in their molecular signaling mechanisms remain unclear. Constitutively active mutants of phyB (YVB) and NLS-fused phyA (YVA:NLS) mediate light-independent seedling development, leading to constitutive photomorphogenic (cop) phenotypes in their transgenic Arabidopsis plants. Interestingly, YVB interacted with PIF3 independently of light, but YVA showed little interaction. In this study, we investigated distinct signaling mechanisms underlying the similar cop phenotypes given by YVB and YVA:NLS. Our findings indicated that YVA efficiently inactivate the COP1/SPA complex, leading to accumulation of ELONGATED HYPOCOTYL 5 (HY5) and subsequent expression of its target genes HY5 and HYH. YVB induced light-independent PIF3 and PIF1 degra- dation, in addition to HY5 accumulation. Moreover, co-expression of PIF3 in the YVB plant significantly attenuated the cop phenotypes, but minimal effects were observed in the YVA:NLS plant. In particular, PIF3 negatively regulated the interaction between YVB and COP1, which decreased HY5 accumulation in the YVB plant co-expressing PIF3. Furthermore, when transferred from light to dark, PIF3 was highly accumulated in phyB-5, whereas HY5 is degraded faster in phyA-201 compared to that in Ler. Collectively, our results suggest HY5 accumulation as the molecular bases for the cop phenotypes and also indicate that phyB is more important for regulating PIF3, whereas phyA effectively inactivates the COP1/SPA complex relative to PIF3 degradation. 
    more » « less
  5. ; ; ; ; ; (, Nature Communications)
    Photoactivation of the plant photoreceptor and thermosensor phytochrome B (PHYB) triggers its condensation into subnuclear membraneless organelles named photobodies (PBs). However, the function of PBs in PHYB signaling remains frustratingly elusive. Here, we found that PHYB recruits PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) to PBs. Surprisingly, PHYB exerts opposing roles in degrading and stabilizing PIF5. Perturbing PB size by overproducing PHYB provoked a biphasic PIF5 response: while a moderate increase in PHYB enhanced PIF5 degradation, further elevating the PHYB level stabilized PIF5 by retaining more of it in enlarged PBs. Conversely, reducing PB size by dim light, which enhanced PB dynamics and nucleoplasmic PHYB and PIF5, switched the balance towards PIF5 degradation. Together, these results reveal that PB formation spatially segregates two antagonistic PHYB signaling actions – PIF5 stabilization in PBs and PIF5 degradation in the surrounding nucleoplasm – which could enable an environmentally sensitive, counterbalancing mechanism to titrate nucleoplasmic PIF5 and environmental responses. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email