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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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Pollak B, Cerda A, Delmans M, Álamos S, Moyano T, West A, Gutiérrez RA, Patron NJ, Federici F, Haseloff J. Loop assembly: a simple and open system for recursive fabrication of DNA circuits. New Phytol 2019; 222:628-640. [PMID: 30521109 DOI: 10.1111/nph.15625] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 09/20/2018] [Indexed: 06/09/2023]
Abstract
High-efficiency methods for DNA assembly have enabled the routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customization, elaborate vector sets or serial manipulations for the different stages of assembly. We have developed Loop assembly based on a recursive approach to DNA fabrication. The system makes use of two Type IIS restriction endonucleases and corresponding vector sets for efficient and parallel assembly of large DNA circuits. Standardized level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly enables efficient and versatile DNA fabrication for plant transformation. We show the construction of plasmids up to 16 genes and 38 kb with high efficiency (> 80%). We have characterized Loop assembly on over 200 different DNA constructs and validated the fidelity of the method by high-throughput Illumina plasmid sequencing. Our method provides a simple generalized solution for DNA construction with standardized parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.
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Affiliation(s)
- Bernardo Pollak
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Ariel Cerda
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Simón Álamos
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Tomás Moyano
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Anthony West
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Nicola J Patron
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Fernán Federici
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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