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González-Grandío E, Álamos S, Zhang Y, Dalton-Roesler J, Niyogi KK, García HG, Quail PH. Chromatin Changes in Phytochrome Interacting Factor-Regulated Genes Parallel Their Rapid Transcriptional Response to Light. Front Plant Sci 2022; 13:803441. [PMID: 35251080 PMCID: PMC8891703 DOI: 10.3389/fpls.2022.803441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/27/2022] [Indexed: 05/11/2023]
Abstract
As sessile organisms, plants must adapt to a changing environment, sensing variations in resource availability and modifying their development in response. Light is one of the most important resources for plants, and its perception by sensory photoreceptors (e.g., phytochromes) and subsequent transduction into long-term transcriptional reprogramming have been well characterized. Chromatin changes have been shown to be involved in photomorphogenesis. However, the initial short-term transcriptional changes produced by light and what factors enable these rapid changes are not well studied. Here, we define rapidly light-responsive, Phytochrome Interacting Factor (PIF) direct-target genes (LRP-DTGs). We found that a majority of these genes also show rapid changes in Histone 3 Lysine-9 acetylation (H3K9ac) in response to the light signal. Detailed time-course analysis of transcript and chromatin changes showed that, for light-repressed genes, H3K9 deacetylation parallels light-triggered transcriptional repression, while for light-induced genes, H3K9 acetylation appeared to somewhat precede light-activated transcript accumulation. However, direct, real-time imaging of transcript elongation in the nucleus revealed that, in fact, transcriptional induction actually parallels H3K9 acetylation. Collectively, the data raise the possibility that light-induced transcriptional and chromatin-remodeling processes are mechanistically intertwined. Histone modifying proteins involved in long term light responses do not seem to have a role in this fast response, indicating that different factors might act at different stages of the light response. This work not only advances our understanding of plant responses to light, but also unveils a system in which rapid chromatin changes in reaction to an external signal can be studied under natural conditions.
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Affiliation(s)
- Eduardo González-Grandío
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
- *Correspondence: Eduardo González-Grandío,
| | - Simón Álamos
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, United States
| | - Yu Zhang
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
| | - Jutta Dalton-Roesler
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
| | - Krishna K. Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Hernán G. García
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
- Department of Physics, University of California, Berkeley, Berkeley, CA, United States
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, United States
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA, United States
| | - Peter H. Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
- Peter H. Quail,
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Leivar P, Martín G, Soy J, Dalton-Roesler J, Quail PH, Monte E. Phytochrome-imposed inhibition of PIF7 activity shapes photoperiodic growth in Arabidopsis together with PIF1, 3, 4 and 5. Physiol Plant 2020; 169:452-466. [PMID: 32412656 DOI: 10.1111/ppl.13123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 05/29/2023]
Abstract
Under photoperiodic conditions, Arabidopsis thaliana seedling growth is inhibited in long days (LDs), but promoted under the extended nights of short days (SDs). This behavior is partly implemented by phytochrome (phy)-imposed oscillations in the abundance of the growth-promoting, phy-interacting bHLH transcription factors PHY-INTERACTING FACTOR 1 (PIF1), PIF3, PIF4 and PIF5 (PIF quartet or PIFq). However, the observation that a pifq mutant is still stimulated to elongate when given a phy-inactivating end-of-day far-red pulse (EODFR), suggests that additional factors are involved in the phy-mediated suppression of growth during the subsequent dark period. Here, by combining growth-analysis of pif7 single- and higher-order mutants with gene expression analysis under SD, LD, SD-EODFR, and LD-EODFR, we show that PIF7 promotes growth during the dark hours of SD, by regulating growth-related gene expression. Interestingly, the relative contribution of PIF7 in promoting growth is stronger under EODFR, whereas PIF3 role is more important under SD, suggesting that PIF7 is a prominent target of phy-suppression. Indeed, we show that phy imposes phosphorylation and inactivation of PIF7 during the light hours in SD, and prevents full dephosphorylation during the night. This repression can be lifted with an EODFR, which correlates with increased PIF7-mediated gene expression and elongation. In addition, our results suggest that PIF7 function might involve heterodimerization with PIF3. Furthermore, our data indicate that a pifqpif7 quintuple mutant is largely insensitive to photoperiod for hypocotyl elongation. Collectively, the data suggest that PIF7, together with the PIFq, is required for the photoperiodic regulation of seasonal growth.
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Affiliation(s)
- Pablo Leivar
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
| | - Guiomar Martín
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Judit Soy
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Jutta Dalton-Roesler
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
- United States Department of Agriculture, Plant Gene Expression Center, Albany, CA, USA
| | - Peter H Quail
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
- United States Department of Agriculture, Plant Gene Expression Center, Albany, CA, USA
| | - Elena Monte
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
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