Review
Plant Sciences
Peilin Wang, Muhammad Ali Abid, Ghulam Qanmber, Muhammad Askari, Lili Zhou, Yuhan Song, Chengzhen Liang, Zhigang Meng, Waqas Malik, Yunxiao Wei, Yuan Wang, Hongmei Cheng, Rui Zhang
Summary: Light is the primary source of energy for plants and influences various physiological processes. Phytochrome-interacting factors (PIFs) are transcription factors that play important roles in seed germination, skotomorphogenesis, and developmental changes. Recent studies indicate that other molecular pathways also regulate PIF activity. Understanding the role of PIFs in crop improvement could lead to the development of climate-tolerant crops and increased crop yield.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2022)
Article
Developmental Biology
Qian-Qian Li, Zhan Zhang, Chao-Xing Zhang, Ya-Ling Wang, Chu-Bin Liu, Jia-Chen Wu, Mei-Ling Han, Qiu-Xia Wang, Dai-Yin Chao
Summary: Adventitious roots (ARs) exhibit high phenotypic plasticity in response to environmental stimuli. This study reveals that phytochrome-interacting factors (PIFs) play a central role in darkness-induced hypocotyl adventitious root (HAR) formation by inducing the expression of genes involved in auxin biosynthesis, auxin transport, and root primordium initiation.
Review
Biochemistry & Molecular Biology
Aishwarye Sharma, Harsha Samtani, Karishma Sahu, Arun Kumar Sharma, Jitendra Paul Khurana, Paramjit Khurana
Summary: Transcription factors are important in regulating plant responses to environmental changes. Fluctuations in necessary resources such as light, temperature, and water lead to gene reprogramming. Phytochrome-Interacting Factors (PIFs) are key transcription factors that regulate both developmental and external stimuli-based plant growth. This review focuses on identifying PIFs in various organisms, their regulation by different proteins, and their functions in diverse developmental pathways and external stimuli-induced plant responses. Recent advances in characterizing PIFs in crops like rice, maize, and tomato are also discussed, highlighting their potential as key regulators for enhancing agronomic traits.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Plant Sciences
Eduardo Gonzalez-Grandio, Simon Alamos, Yu Zhang, Jutta Dalton-Roesler, Krishna K. Niyogi, Hernan G. Garcia, Peter H. Quail
Summary: This study identifies rapidly light-responsive genes and their relationship with chromatin modifications, suggesting that light-induced transcriptional and chromatin-remodeling processes may be mechanistically intertwined.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Emily Biernat, Uzair Khan, Chhabi K. Govind
Summary: Nucleosomes are the repeating units of chromatin and hinder DNA-dependent processes. MNase digestion of chromatin followed by ChIP-seq can determine nucleosome occupancy, positioning, and the impact of chromatin interacting factors on chromatin accessibility.
Review
Plant Sciences
Andre M. Cordeiro, Luis Andrade, Catarina C. Monteiro, Guilherme Leitao, Philip A. Wigge, Nelson J. M. Saibo
Summary: Light regulates the function of PIFs in plant growth and yield, including their role in architecture, stress tolerance, and cell division elongation. Different crops have overlapping but distinct PIF functions. Therefore, understanding the molecular mechanisms of PIFs in plant development is crucial for improving crop productivity.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Na Li, Cunpei Bo, Yuanyuan Zhang, Lei Wang
Summary: Heat stress can induce leaf senescence in plants, with PIF4 and PIF5 proteins playing important roles in this process, possibly through hormone signaling pathways and other biological processes. Additionally, heat stress-induced leaf senescence is regulated by the circadian clock, with plants showing more active responses to this process during the day.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Plant Sciences
Quyen T. N. Hoang, Sharanya Tripathi, Jae-Yong Cho, Da-Min Choi, Ah-Young Shin, Suk-Yoon Kwon, Yun-Jeong Han, Jeong-Il Kim
Summary: This study investigated the functions of BdPIL1 and BdPIL3, two PIF-like genes in Brachypodium distachyon, and found that they interact with phytochromes in an active form-specific manner, affecting plant growth and development. Transgenic Brachypodium seedlings with RNAi constructs of BdPIL1 and BdPIL3 showed decreased coleoptile lengths, increased leaf growth, taller stature, and delayed flowering compared to wild-type plants, with downregulation of genes related to cell number regulation, floral induction, and chlorophyll biosynthesis. Additionally, the study revealed the DNA-binding ability of BdPIL1 and BdPIL3 to target promoters was inhibited in the presence of phytochromes, providing insights into the molecular mechanism underlying phytochrome-mediated PIF regulation in Brachypodium.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Sang Woo Lee, Dasom Choi, Heewon Moon, Sujeong Kim, Hajeong Kang, Inyup Paik, Enamul Huq, Dong-Hwan Kim
Summary: Light signaling through PIF factors regulates the expression of the QS gene, helping plants to utilize optimal amounts of starch during the night and prevent overconsumption before its biosynthesis during the upcoming day.
Article
Multidisciplinary Sciences
Masahito Ogawa, Fan-Suo Geng, David T. Humphreys, Esther Kristianto, Delicia Z. Sheng, Subhra P. Hui, Yuxi Zhang, Kotaro Sugimoto, Maki Nakayama, Dawei Zheng, Daniel Hesselson, Mark P. Hodson, Ozren Bogdanovic, Kazu Kikuchi
Summary: Our research identified Klf1 as a key transcriptional regulator of cardiomyocyte renewal in adult zebrafish hearts, supporting myocardial expansion through epigenetic reprogramming and rewiring of mitochondrial metabolism.
Article
Plant Sciences
Jihua Ding, Bo Zhang, Yue Li, Domenique Andre, Ove Nilsson
Summary: The phytochrome B (phyB) serves as a light and temperature sensor in the seasonally synchronized growth cycle of perennial plants. PHYB genes and their downstream PHYTOCHROME INTERACTING FACTOR (PIF) targets play different roles in regulating tree growth and shade avoidance. The PHYB-PIF8 regulon controls seasonal growth, while phyB coordinately regulates shade avoidance responses and seasonal growth cessation in Populus trees.
Review
Biochemistry & Molecular Biology
Ze-Ting Song, Jian-Xiang Liu, Jia-Jia Han
Summary: Plants rely on chromatin remodeling factors (CHRs) to maintain genome integrity and regulate gene expression levels in response to environmental stress, by modulating the composition and position of nucleosomes on chromatin. CHRs also play a role in RNA processing through interaction with other epigenetic mechanisms.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Review
Plant Sciences
Shah Saud, Zhenjie Shi, Liangbing Xiong, Subhan Danish, Rahul Datta, Imran Ahmad, Shah Fahad, Jan Banout
Summary: Phytochrome-interacting factor (PIF) is a type of basic helix-loop-helix transcription factor that plays a role in multiple biological processes in plants. It regulates plant growth and development, and also plays an important role in plant resistance to both abiotic and biotic stresses.
Review
Cell Biology
Jiaxin Long, Benjamin Carter, Emily T. Johnson, Joe Ogas
Summary: The enrichment of H2A.Z in plant chromatin is involved in dynamic gene expression, especially in response to differentiation and environmental changes. Recent research has revealed the mechanism of how plants achieve dynamic changes in H2A.Z enrichment and identified additional chromatin pathways related to transcriptional properties of H2A.Z-enriched chromatin.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Review
Plant Sciences
Koushik Halder, Abira Chaudhuri, Malik Z. Abdin, Manoj Majee, Asis Datta
Summary: The stress response of plants involves a complex network of signaling cascades that regulate transcriptional reprogramming to adapt to abiotic stress conditions. Changes in chromatin modification and DNA methylation have significant effects on the expression of stress-responsive genes. This review primarily focuses on chromatin restructuring under severe abiotic stresses, the crosstalk between epigenetic regulators, and the initial research on stress priming in plants.
Article
Biochemistry & Molecular Biology
Shelly A. Trigg, Yaamini R. Venkataraman, Mackenzie R. Gavery, Steven B. Roberts, Debashish Bhattacharya, Alan Downey-Wall, Jose M. Eirin-Lopez, Kevin M. Johnson, Katie E. Lotterhos, Jonathan B. Puritz, Hollie M. Putnam
Summary: This study compares three methods for quantifying DNA methylation and finds higher methylation in two coral species, primarily located in gene bodies and flanking regions. Each method has its advantages and disadvantages in detecting CpGs, and the relative genome size affects the number and location of CpGs detected by each method.
MOLECULAR ECOLOGY RESOURCES
(2022)
Review
Plant Sciences
Joseph Swift, Kathleen Greenham, Joseph R. Ecker, Gloria M. Coruzzi, C. Robertson McClung
Summary: This review discusses the spatiotemporal nature of gene regulation in plants, highlighting the ways in which plant tissues are time sensitive. It explores how the study of plant cell identity can reveal developmental trajectories, the evidence showing plant cell types maintain their own local time through tissue-specific regulation of the circadian clock, and what determines the speed of environmental signaling responses. The review sheds light on how these different scales of time-based responses can act with tissue and cell-type specificity to elicit changes in whole plant systems.
Article
Multidisciplinary Sciences
Elizabeth T. Montano, Jason F. Nideffer, Lauren Brumage, Marcella Erb, Julia Busch, Lynley Fernandez, Alan I. Derman, John Paul Davis, Elena Estrada, Sharon Fu, Danielle Le, Aishwarya Vuppala, Cassidy Tran, Elaine Luterstein, Shivani Lakkaraju, Sriya Panchagnula, Caroline Ren, Jennifer Doan, Sharon Tran, Jamielyn Soriano, Yuya Fujita, Pranathi Gutala, Quinn Fujii, Minda Lee, Anthony Bui, Carleen Villarreal, Samuel R. Shing, Sean Kim, Danielle Freeman, Vipula Racha, Alicia Ho, Prianka Kumar, Kian Falah, Thomas Dawson, Eray Enustun, Amy Prichard, Ana Gomez, Kanika Khanna, Shelly Trigg, Kit Pogliano, Joe Pogliano
Summary: The study identified novel gene clusters in Streptomyces strains that have the potential to produce new antibiotics. Additionally, it isolated and analyzed bacteriophages with antibacterial activity, as well as predicted the host ranges of these phages based on the CRISPR-Cas systems present in the strains.
Article
Multidisciplinary Sciences
Magdalena E. Potok, Zhenhui Zhong, Colette L. Picard, Qikun Liu, Truman Do, Cassidy E. Jacobsen, Ocean Sakr, Bilguudei Naranbaatar, Ruwan Thilakaratne, Zhanna Khnkoyan, Megan Purl, Harrison Cheng, Helena Vervaet, Suhua Feng, Shima Rayatpisheh, James A. Wohlschlegel, Ronan C. O'Malley, Joseph R. Ecker, Steven E. Jacobsen
Summary: ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) and ATXR6 are essential for maintaining genomic stability and regulating DNA damage response and transposable elements in Arabidopsis. Reduction of ATXR5/6 activity leads to tissue-specific derepression of transposable elements, decompaction of chromocenters, and accumulation of excess DNA from heterochromatin. This study provides a comprehensive characterization of the atxr5/6 mutant, revealing the tissue-specific phenotypes and the role of ATXR6 in female germline development.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Correction
Genetics & Heredity
Bjorn C. Willige, Mark Zander, Chan Yul Yoo, Amy Phan, Renee M. M. Garza, Shelly A. A. Wanamaker, Yupeng He, Joseph R. R. Nery, Huaming Chen, Meng Chen, Joseph R. R. Ecker, Joanne Chory
Article
Multidisciplinary Sciences
Youra Hwang, Soeun Han, Chan Yul Yoo, Liu Hong, Chenjiang You, Brandon H. Le, Hui Shi, Shangwei Zhong, Ute Hoecker, Xuemei Chen, Meng Chen
Summary: Light activates plastid photosynthesis genes by inhibiting PIFs and generating a nucleus-to-plastid signal. Four sigma factors act as anterograde signals to activate plastid photosynthesis genes.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Samuel R. Major, Matthew J. Harke, Roberto Cruz-Flores, Arun K. Dhar, Andrea G. Bodnar, Shelly A. Wanamaker
Summary: Timely detection of pathogens is crucial for disease control, especially in high-density populations where quarantine is limited. Standard molecular tests have sensitivity but delayed results. We demonstrated the adaptability of a CRISPR-based assay for detecting shrimp viruses, showing similar sensitivity and accuracy to real-time PCR. These assays can specifically target the viruses without false positives.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Qing Sang, Lusheng Fan, Tianxiang Liu, Yongjian Qiu, Juan Du, Beixin Mo, Meng Chen, Xuemei Chen
Summary: MicroRNAs play important roles in the temperature plasticity of plants, and the miR156/SPL9 module is a key factor in regulating thermomorphogenesis by controlling auxin sensitivity.
NATURE COMMUNICATIONS
(2023)
Correction
Multidisciplinary Sciences
Shelly A. A. Wanamaker, Paul McElhany, Michael Maher, Danielle Perez, D. Shallin Busch, Krista M. M. Nichols
SCIENTIFIC REPORTS
(2023)
Editorial Material
Plant Sciences
Marcel Quint, Carolin Delker, Sureshkumar Balasubramanian, Martin Balcerowicz, Jorge J. Casal, Christian Danve M. Castroverde, Meng Chen, Xuemei Chen, Ive De Smet, Christian Fankhauser, Keara A. Franklin, Karen J. Halliday, Scott Hayes, Danhua Jiang, Jae-Hoon Jung, Eirini Kaiserli, S. Vinod Kumar, Daniel Maag, Eunkyoo Oh, Chung-Mo Park, Steven Penfield, Giorgio Perrella, Salome Prat, Rodrigo S. Reis, Philip A. Wigge, Bjorn C. Willige, Martijn van Zanten
TRENDS IN PLANT SCIENCE
(2023)
Editorial Material
Biochemical Research Methods
Tatsuya Nobori, Joseph R. Ecker
Summary: While progress has been made in understanding plant responses to pathogen attacks at the tissue or major cell type scale, a comprehensive understanding of individual cell responses is still lacking. Zhu et al. used single-cell transcriptome analysis to reveal the heterogeneous responses of plant cells during bacterial pathogen confrontation.
CELL REPORTS METHODS
(2023)
Article
Plant Sciences
Tatsuya Nobori, Marina Oliva, Ryan Lister, Joseph R. Ecker
Summary: PHYTOMap is a multiplexed fluorescence in situ hybridization method that allows for single-cell and spatial analysis of gene expression in whole-mount plant tissue, without the need for transgenes and at a low cost. This study demonstrates the successful application of PHYTOMap in identifying major cell types in Arabidopsis roots and its potential to accelerate the spatial mapping of marker genes in complex plant tissue.