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Xu F, Zhang D, Le L, Pu L. Polycomb and trithorax: Their yin-yang dynamics in plants. MOLECULAR PLANT 2024; 17:845-847. [PMID: 38783605 DOI: 10.1016/j.molp.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Affiliation(s)
- Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Daolei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; School of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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2
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Xu F, Dong H, Guo W, Le L, Jing Y, Fletcher JC, Sun J, Pu L. The trxG protein ULT1 regulates Arabidopsis organ size by interacting with TCP14/15 to antagonize the LIM peptidase DA1 for H3K4me3 on target genes. PLANT COMMUNICATIONS 2024; 5:100819. [PMID: 38217289 PMCID: PMC11009162 DOI: 10.1016/j.xplc.2024.100819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/18/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
Plant organ size is an important agronomic trait that makes a significant contribution to plant yield. Despite its central importance, the genetic and molecular mechanisms underlying organ size control remain to be fully clarified. Here, we report that the trithorax group protein ULTRAPETALA1 (ULT1) interacts with the TEOSINTE BRANCHED1/CYCLOIDEA/PCF14/15 (TCP14/15) transcription factors by antagonizing the LIN-11, ISL-1, and MEC-3 (LIM) peptidase DA1, thereby regulating organ size in Arabidopsis. Loss of ULT1 function significantly increases rosette leaf, petal, silique, and seed size, whereas overexpression of ULT1 results in reduced organ size. ULT1 associates with TCP14 and TCP15 to co-regulate cell size by affecting cellular endoreduplication. Transcriptome analysis revealed that ULT1 and TCP14/15 regulate common target genes involved in endoreduplication and leaf development. ULT1 can be recruited by TCP14/15 to promote lysine 4 of histone H3 trimethylation at target genes, activating their expression to determine final cell size. Furthermore, we found that ULT1 influences the interaction of DA1 and TCP14/15 and antagonizes the effect of DA1 on TCP14/15 degradation. Collectively, our findings reveal a novel epigenetic mechanism underlying the regulation of organ size in Arabidopsis.
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Affiliation(s)
- Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huixue Dong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yexing Jing
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jennifer C Fletcher
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Plant Gene Expression Center, United States Department of Agriculture - Agricultural Research Service, Albany, CA 94710, USA
| | - Jiaqiang Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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3
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Amiard S, Feit L, Vanrobays E, Simon L, Le Goff S, Loizeau L, Wolff L, Butter F, Bourbousse C, Barneche F, Tatout C, Probst AV. The TELOMERE REPEAT BINDING proteins TRB4 and TRB5 function as transcriptional activators of PRC2-controlled genes to regulate plant development. PLANT COMMUNICATIONS 2024:100890. [PMID: 38566416 DOI: 10.1016/j.xplc.2024.100890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 02/07/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Plant-specific transcriptional regulators called TELOMERE REPEAT BINDING proteins (TRBs) combine two DNA-binding domains, the GH1 domain, which binds to linker DNA and is shared with H1 histones, and the Myb/SANT domain, which specifically recognizes the telobox DNA-binding site motif. TRB1, TRB2, and TRB3 proteins recruit Polycomb group complex 2 (PRC2) to deposit H3K27me3 and JMJ14 to remove H3K4me3 at gene promoters containing telobox motifs to repress transcription. Here, we demonstrate that TRB4 and TRB5, two related paralogs belonging to a separate TRB clade conserved in spermatophytes, regulate the transcription of several hundred genes involved in developmental responses to environmental cues. TRB4 binds to several thousand sites in the genome, mainly at transcription start sites and promoter regions of transcriptionally active and H3K4me3-marked genes, but, unlike TRB1, it is not enriched at H3K27me3-marked gene bodies. However, TRB4 can physically interact with the catalytic components of PRC2, SWINGER, and CURLY LEAF (CLF). Unexpectedly, we show that TRB4 and TRB5 are required for distinctive phenotypic traits observed in clf mutant plants and thus function as transcriptional activators of several hundred CLF-controlled genes, including key flowering genes. We further demonstrate that TRB4 shares multiple target genes with TRB1 and physically and genetically interacts with members of both TRB clades. Collectively, these results reveal that TRB proteins engage in both positive and negative interactions with other members of the family to regulate plant development through both PRC2-dependent and -independent mechanisms.
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Affiliation(s)
- Simon Amiard
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France.
| | - Léa Feit
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Emmanuel Vanrobays
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Lauriane Simon
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Samuel Le Goff
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Loriane Loizeau
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Léa Wolff
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Falk Butter
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Clara Bourbousse
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Fredy Barneche
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Christophe Tatout
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Aline V Probst
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France.
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4
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Gao Z, He Y. Molecular epigenetic understanding of winter memory in Arabidopsis. PLANT PHYSIOLOGY 2024; 194:1952-1961. [PMID: 37950890 DOI: 10.1093/plphys/kiad597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 10/13/2023] [Accepted: 11/03/2023] [Indexed: 11/13/2023]
Affiliation(s)
- Zheng Gao
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yuehui He
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
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Qiu C, Wang T, Wang H, Tao Z, Wang C, Ma J, Li S, Zhao Y, Liu J, Li P. SISTER OF FCA physically associates with SKB1 to regulate flowering time in Arabidopsis thaliana. BMC PLANT BIOLOGY 2024; 24:188. [PMID: 38486139 PMCID: PMC10941358 DOI: 10.1186/s12870-024-04887-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/07/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND Proper flowering time is important for the growth and development of plants, and both too early and too late flowering impose strong negative influences on plant adaptation and seed yield. Thus, it is vitally important to study the mechanism underlying flowering time control in plants. In a previous study by the authors, genome-wide association analysis was used to screen the candidate gene SISTER OF FCA (SSF) that regulates FLOWERING LOCUS C (FLC), a central gene encoding a flowering suppressor in Arabidopsis thaliana. RESULTS SSF physically interacts with Protein arginine methyltransferase 5 (PRMT5, SKB1). Subcellular co-localization analysis showed that SSF and SKB1 interact in the nucleus. Genetically, SSF and SKB1 exist in the same regulatory pathway that controls FLC expression. Furthermore, RNA-sequencing analysis showed that both SSF and SKB1 regulate certain common pathways. CONCLUSIONS This study shows that PRMT5 interacts with SSF, thus controlling FLC expression and facilitating flowering time control.
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Affiliation(s)
- Chunhong Qiu
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Tengyue Wang
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hui Wang
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zhen Tao
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chuanhong Wang
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Jing Ma
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Shuai Li
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yibing Zhao
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Jifang Liu
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Peijin Li
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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Wang G, Huang L, Zhuang S, Han F, Huang Q, Hao M, Lin G, Chen L, Shen B, Li F, Li X, Chen C, Gao Y, Mock T, Liang J. Resting cell formation in the marine diatom Thalassiosira pseudonana. THE NEW PHYTOLOGIST 2024. [PMID: 38402560 DOI: 10.1111/nph.19646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/08/2024] [Indexed: 02/26/2024]
Abstract
Resting cells represent a survival strategy employed by diatoms to endure prolonged periods of unfavourable conditions. In the oceans, many diatoms sink at the end of their blooming season and therefore need to endure cold and dark conditions in the deeper layers of the water column. How they survive these conditions is largely unknown. We conducted an integrative analysis encompassing methods from histology, physiology, biochemistry, and genetics to reveal the biological mechanism of resting-cell formation in the model diatom Thalassiosira pseudonana. Resting-cell formation was triggered by a decrease in light and temperature with subsequent catabolism of storage compounds. Resting cells were characterised by an acidic and viscous cytoplasm and altered morphology of the chloroplast ultrastructure. The formation of resting cells in T. pseudonana is an energy demanding process required for a biophysical alteration of the cytosol and chloroplasts to endure the unfavourable conditions of the deeper ocean as photosynthetic organisms. However, most resting cells (> 90%) germinate upon return to favorable growth conditions.
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Affiliation(s)
- Guangning Wang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Lu Huang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Shanshan Zhuang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Fang Han
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Qianqian Huang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Mengyuan Hao
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Guifang Lin
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Longnan Chen
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Biying Shen
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Feng Li
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Xuesong Li
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Changping Chen
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yahui Gao
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
- State Key Laboratory of Marine Environment Science, Xiamen University, Xiamen, 361102, Fujian, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia (UEA), Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Junrong Liang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
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Lee SW, Nugroho ABD, Park M, Moon H, Kim J, Kim DH. Identification of vernalization-related genes and cold memory element (CME) required for vernalization response in radish (Raphanus sativus L.). PLANT MOLECULAR BIOLOGY 2024; 114:5. [PMID: 38227117 DOI: 10.1007/s11103-023-01412-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Abstract
Floral transition is accelerated by exposure to long-term cold like winter in plants, which is called as vernalization. Acceleration of floral transition by vernalization is observed in a diversity of biennial and perennial plants including Brassicaceae family plants. Scientific efforts to understand molecular mechanism underlying vernalization-mediated floral transition have been intensively focused in model plant Arabidopsis thaliana. To get a better understanding on floral transition by vernalization in radish (Raphanus sativus L.), we investigated transcriptomic changes taking place during vernalization in radish. Thousands of genes were differentially regulated along time course of vernalization compared to non-vernalization (NV) sample. Twelve major clusters of DEGs were identified based on distinctive expression profiles during vernalization. Radish FLC homologs were shown to exert an inhibition of floral transition when transformed into Arabidopsis plants. In addition, DNA region containing RY motifs located within a Raphanus sativus FLC homolog, RsFLC1 was found to be required for repression of RsFLC1 by vernalization. Transgenic plants harboring disrupted RY motifs were impaired in the enrichment of H3K27me3 on RsFLC1 chromatin, thus resulting in the delayed flowering in Arabidopsis. Taken together, we report transcriptomic profiles of radish during vernalization and demonstrate the requirement of RY motif for vernalization-mediated repression of RsFLC homologs in radish (Raphanus sativus L.).
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Affiliation(s)
- Sang Woo Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | | | | | - Heewon Moon
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Jun Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Dong-Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea.
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8
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Yuan HY, Kagale S, Ferrie AMR. Multifaceted roles of transcription factors during plant embryogenesis. FRONTIERS IN PLANT SCIENCE 2024; 14:1322728. [PMID: 38235196 PMCID: PMC10791896 DOI: 10.3389/fpls.2023.1322728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Transcription factors (TFs) are diverse groups of regulatory proteins. Through their specific binding domains, TFs bind to their target genes and regulate their expression, therefore TFs play important roles in various growth and developmental processes. Plant embryogenesis is a highly regulated and intricate process during which embryos arise from various sources and undergo development; it can be further divided into zygotic embryogenesis (ZE) and somatic embryogenesis (SE). TFs play a crucial role in the process of plant embryogenesis with a number of them acting as master regulators in both ZE and SE. In this review, we focus on the master TFs involved in embryogenesis such as BABY BOOM (BBM) from the APETALA2/Ethylene-Responsive Factor (AP2/ERF) family, WUSCHEL and WUSCHEL-related homeobox (WOX) from the homeobox family, LEAFY COTYLEDON 2 (LEC2) from the B3 family, AGAMOUS-Like 15 (AGL15) from the MADS family and LEAFY COTYLEDON 1 (LEC1) from the Nuclear Factor Y (NF-Y) family. We aim to present the recent progress pertaining to the diverse roles these master TFs play in both ZE and SE in Arabidopsis, as well as other plant species including crops. We also discuss future perspectives in this context.
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Affiliation(s)
| | | | - Alison M. R. Ferrie
- Aquatic and Crop Resource Development Research Center, National Research Council Canada, Saskatoon, SK, Canada
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Wu H, Galli M, Spears CJ, Zhan J, Liu P, Yadegari R, Dannenhoffer JM, Gallavotti A, Becraft PW. NAKED ENDOSPERM1, NAKED ENDOSPERM2, and OPAQUE2 interact to regulate gene networks in maize endosperm development. THE PLANT CELL 2023; 36:19-39. [PMID: 37795691 PMCID: PMC10734603 DOI: 10.1093/plcell/koad247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 10/06/2023]
Abstract
NAKED ENDOSPERM1 (NKD1), NKD2, and OPAQUE2 (O2) are transcription factors important for cell patterning and nutrient storage in maize (Zea mays) endosperm. To study the complex regulatory interrelationships among these 3 factors in coregulating gene networks, we developed a set of nkd1, nkd2, and o2 homozygous lines, including all combinations of mutant and wild-type genes. Among the 8 genotypes tested, we observed diverse phenotypes and gene interactions affecting cell patterning, starch content, and storage proteins. From ∼8 to ∼16 d after pollination, maize endosperm undergoes a transition from cellular development to nutrient accumulation for grain filling. Gene network analysis showed that NKD1, NKD2, and O2 dynamically regulate a hierarchical gene network during this period, directing cellular development early and then transitioning to constrain cellular development while promoting the biosynthesis and storage of starch, proteins, and lipids. Genetic interactions regulating this network are also dynamic. The assay for transposase-accessible chromatin using sequencing (ATAC-seq) showed that O2 influences the global regulatory landscape, decreasing NKD1 and NKD2 target site accessibility, while NKD1 and NKD2 increase O2 target site accessibility. In summary, interactions of NKD1, NKD2, and O2 dynamically affect the hierarchical gene network and regulatory landscape during the transition from cellular development to grain filling in maize endosperm.
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Affiliation(s)
- Hao Wu
- Genetics, Development and Cell Biology Department, Iowa State University, Ames, IA 50011, USA
| | - Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08901-8520, USA
| | - Carla J Spears
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Junpeng Zhan
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Ramin Yadegari
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08901-8520, USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ
| | - Philip W Becraft
- Genetics, Development and Cell Biology Department, Iowa State University, Ames, IA 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
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10
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Li J, Li Q, Wang W, Zhang X, Chu C, Tang X, Zhu B, Xiong L, Zhao Y, Zhou D. DELLA-mediated gene repression is maintained by chromatin modification in rice. EMBO J 2023; 42:e114220. [PMID: 37691541 PMCID: PMC10620761 DOI: 10.15252/embj.2023114220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
DELLA proteins are master regulators of gibberellic acid (GA) signaling through their effects on gene expression. Enhanced DELLA accumulation in rice and wheat varieties has greatly contributed to grain yield increases during the green revolution. However, the molecular basis of DELLA-mediated gene repression remains elusive. In this work, we show that the rice DELLA protein SLENDER RICE1 (SLR1) forms a tripartite complex with Polycomb-repressive complex 2 (PRC2) and the histone deacetylase HDA702 to repress downstream genes by establishing a silent chromatin state. The slr1 mutation and GA signaling resulted in dissociation of PRC2 and HDA702 from GA-inducible genes. Loss-of-function or downregulation of the chromatin regulators impaired SLR1-dependent histone modification and gene repression. Time-resolved analysis of GA signaling revealed that GA-induced transcriptional activation was associated with a rapid increase of H3K9ac followed by H3K27me3 removal. Collectively, these results establish a general epigenetic mechanism for DELLA-mediated gene repression and reveal details of the chromatin dynamics during transcriptional activation stimulated by GA signaling.
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Affiliation(s)
- Junjie Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Qi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Wentao Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Xinran Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Chen Chu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Xintian Tang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Bo Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Dao‐Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Institute of Plant Science Paris‐Saclay (IPS2), CNRS, INRAEUniversity Paris‐SaclayOrsayFrance
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11
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Hisanaga T, Romani F, Wu S, Kowar T, Wu Y, Lintermann R, Fridrich A, Cho CH, Chaumier T, Jamge B, Montgomery SA, Axelsson E, Akimcheva S, Dierschke T, Bowman JL, Fujiwara T, Hirooka S, Miyagishima SY, Dolan L, Tirichine L, Schubert D, Berger F. The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes. Curr Biol 2023; 33:4367-4380.e9. [PMID: 37738971 DOI: 10.1016/j.cub.2023.08.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 06/19/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023]
Abstract
The mobility of transposable elements (TEs) contributes to evolution of genomes. Their uncontrolled activity causes genomic instability; therefore, expression of TEs is silenced by host genomes. TEs are marked with DNA and H3K9 methylation, which are associated with silencing in flowering plants, animals, and fungi. However, in distantly related groups of eukaryotes, TEs are marked by H3K27me3 deposited by the Polycomb repressive complex 2 (PRC2), an epigenetic mark associated with gene silencing in flowering plants and animals. The direct silencing of TEs by PRC2 has so far only been shown in one species of ciliates. To test if PRC2 silences TEs in a broader range of eukaryotes, we generated mutants with reduced PRC2 activity and analyzed the role of PRC2 in extant species along the lineage of Archaeplastida and in the diatom P. tricornutum. In this diatom and the red alga C. merolae, a greater proportion of TEs than genes were repressed by PRC2, whereas a greater proportion of genes than TEs were repressed by PRC2 in bryophytes. In flowering plants, TEs contained potential cis-elements recognized by transcription factors and associated with neighbor genes as transcriptional units repressed by PRC2. Thus, silencing of TEs by PRC2 is observed not only in Archaeplastida but also in diatoms and ciliates, suggesting that PRC2 deposited H3K27me3 to silence TEs in the last common ancestor of eukaryotes. We hypothesize that during the evolution of Archaeplastida, TE fragments marked with H3K27me3 were selected to shape transcriptional regulation, controlling networks of genes regulated by PRC2.
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Affiliation(s)
- Tetsuya Hisanaga
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Shuangyang Wu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Teresa Kowar
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Yue Wu
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Ruth Lintermann
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Arie Fridrich
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Chung Hyun Cho
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea
| | | | - Bhagyshree Jamge
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Sean A Montgomery
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia; ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Liam Dolan
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Daniel Schubert
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany.
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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12
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Chen Y, Hung FY, Sugimoto K. Epigenomic reprogramming in plant regeneration: Locate before you modify. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102415. [PMID: 37437389 DOI: 10.1016/j.pbi.2023.102415] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/04/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023]
Abstract
Plants possess remarkable abilities for regeneration, and this developmental capability is strongly influenced by environmental conditions. Previous research has highlighted the positive effects of wound signaling and warm temperature on plant regeneration, and recent studies suggest that light and nutrient signals also influence the regenerative efficiencies. Several epigenetic factors, such as histone acetyl-transferases (HATs), POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), and H2A variants, play crucial roles in regulating the expression of genes implicated in plant regeneration. However, how these epigenetic factors recognize specific genomic regions to regulate regeneration genes is still unclear. In this article, we describe the latest studies of epigenetic regulation and discuss the functional coordination between transcription factors and epigenetic modifiers in plant regeneration.
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Affiliation(s)
- Yu Chen
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Fu-Yu Hung
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan.
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan.
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13
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Franco-Echevarría E, Nielsen M, Schulten A, Cheema J, Morgan TE, Bienz M, Dean C. Distinct accessory roles of Arabidopsis VEL proteins in Polycomb silencing. Genes Dev 2023; 37:801-817. [PMID: 37734835 PMCID: PMC7615239 DOI: 10.1101/gad.350814.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/31/2023] [Indexed: 09/23/2023]
Abstract
Polycomb repressive complex 2 (PRC2) mediates epigenetic silencing of target genes in animals and plants. In Arabidopsis, PRC2 is required for the cold-induced epigenetic silencing of the FLC floral repressor locus to align flowering with spring. During this process, PRC2 relies on VEL accessory factors, including the constitutively expressed VRN5 and the cold-induced VIN3. The VEL proteins are physically associated with PRC2, but their individual functions remain unclear. Here, we show an intimate association between recombinant VRN5 and multiple components within a reconstituted PRC2, dependent on a compact conformation of VRN5 central domains. Key residues mediating this compact conformation are conserved among VRN5 orthologs across the plant kingdom. In contrast, VIN3 interacts with VAL1, a transcriptional repressor that binds directly to FLC These associations differentially affect their role in H3K27me deposition: Both proteins are required for H3K27me3, but only VRN5 is necessary for H3K27me2. Although originally defined as vernalization regulators, VIN3 and VRN5 coassociate with many targets in the Arabidopsis genome that are modified with H3K27me3. Our work therefore reveals the distinct accessory roles for VEL proteins in conferring cold-induced silencing on FLC, with broad relevance for PRC2 targets generally.
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Affiliation(s)
- Elsa Franco-Echevarría
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Mathias Nielsen
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Anna Schulten
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Jitender Cheema
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Tomos E Morgan
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Mariann Bienz
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Caroline Dean
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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14
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Wang L, Xue M, Zhang H, Ma L, Jiang D. TONSOKU is required for the maintenance of repressive chromatin modifications in Arabidopsis. Cell Rep 2023; 42:112738. [PMID: 37393621 DOI: 10.1016/j.celrep.2023.112738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/17/2023] [Accepted: 06/17/2023] [Indexed: 07/04/2023] Open
Abstract
The stability of eukaryotic genomes relies on the faithful transmission of DNA sequences and the maintenance of chromatin states through DNA replication. Plant TONSOKU (TSK) and its animal ortholog TONSOKU-like (TONSL) act as readers for newly synthesized histones and preserve DNA integrity via facilitating DNA repair at post-replicative chromatin. However, whether TSK/TONSL regulate the maintenance of chromatin states remains elusive. Here, we show that TSK is dispensable for global histone and nucleosome accumulation but necessary for maintaining repressive chromatin modifications, including H3K9me2, H2A.W, H3K27me3, and DNA methylation. TSK physically interacts with H3K9 methyltransferases and Polycomb proteins. Moreover, TSK mutation strongly enhances defects in Polycomb pathway mutants. TSK is intended to only associate with nascent chromatin until it starts to mature. We propose that TSK ensures the preservation of chromatin states by supporting the recruitment of chromatin modifiers to post-replicative chromatin in a critical short window of time following DNA replication.
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Affiliation(s)
- Lin Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mande Xue
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huairen Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Lijun Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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15
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Yin X, Romero-Campero FJ, Yang M, Baile F, Cao Y, Shu J, Luo L, Wang D, Sun S, Yan P, Gong Z, Mo X, Qin G, Calonje M, Zhou Y. Binding by the Polycomb complex component BMI1 and H2A monoubiquitination shape local and long-range interactions in the Arabidopsis genome. THE PLANT CELL 2023; 35:2484-2503. [PMID: 37070946 PMCID: PMC10291032 DOI: 10.1093/plcell/koad112] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Three-dimensional (3D) chromatin organization is highly dynamic during development and seems to play a crucial role in regulating gene expression. Self-interacting domains, commonly called topologically associating domains (TADs) or compartment domains (CDs), have been proposed as the basic structural units of chromatin organization. Surprisingly, although these units have been found in several plant species, they escaped detection in Arabidopsis (Arabidopsis thaliana). Here, we show that the Arabidopsis genome is partitioned into contiguous CDs with different epigenetic features, which are required to maintain appropriate intra-CD and long-range interactions. Consistent with this notion, the histone-modifying Polycomb group machinery is involved in 3D chromatin organization. Yet, while it is clear that Polycomb repressive complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) helps establish local and long-range chromatin interactions in plants, the implications of PRC1-mediated histone H2A monoubiquitination on lysine 121 (H2AK121ub) are unclear. We found that PRC1, together with PRC2, maintains intra-CD interactions, but it also hinders the formation of H3K4me3-enriched local chromatin loops when acting independently of PRC2. Moreover, the loss of PRC1 or PRC2 activity differentially affects long-range chromatin interactions, and these 3D changes differentially affect gene expression. Our results suggest that H2AK121ub helps prevent the formation of transposable element/H3K27me1-rich long loops and serves as a docking point for H3K27me3 incorporation.
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Affiliation(s)
- Xiaochang Yin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Francisco J Romero-Campero
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092 Seville, Spain
- Department of Computer Science and Artificial Intelligence, University of Sevilla, Avenida Reina Mercedes s/n, Seville 41012, Spain
| | - Minqi Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Fernando Baile
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092 Seville, Spain
| | - Yuxin Cao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jiayue Shu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Lingxiao Luo
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Dingyue Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shang Sun
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Peng Yan
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Zhiyun Gong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Xiaorong Mo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092 Seville, Spain
| | - Yue Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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16
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Han Y, Georgii E, Priego-Cubero S, Wurm CJ, Hüther P, Huber G, Koller R, Becker C, Durner J, Lindermayr C. Arabidopsis histone deacetylase HD2A and HD2B regulate seed dormancy by repressing DELAY OF GERMINATION 1. FRONTIERS IN PLANT SCIENCE 2023; 14:1124899. [PMID: 37313253 PMCID: PMC10258333 DOI: 10.3389/fpls.2023.1124899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/06/2023] [Indexed: 06/15/2023]
Abstract
Seed dormancy is a crucial developmental transition that affects the adaption and survival of plants. Arabidopsis DELAY OF GERMINATION 1 (DOG1) is known as a master regulator of seed dormancy. However, although several upstream factors of DOG1 have been reported, the exact regulation of DOG1 is not fully understood. Histone acetylation is an important regulatory layer, controlled by histone acetyltransferases and histone deacetylases. Histone acetylation strongly correlates with transcriptionally active chromatin, whereas heterochromatin is generally characterized by hypoacetylated histones. Here we describe that loss of function of two plant-specific histone deacetylases, HD2A and HD2B, resulted in enhanced seed dormancy in Arabidopsis. Interestingly, the silencing of HD2A and HD2B caused hyperacetylation of the DOG1 locus and promoted the expression of DOG1 during seed maturation and imbibition. Knockout of DOG1 could rescue the seed dormancy and partly rescue the disturbed development phenotype of hd2ahd2b. Transcriptomic analysis of the hd2ahd2b line shows that many genes involved in seed development were impaired. Moreover, we demonstrated that HSI2 and HSL1 interact with HD2A and HD2B. In sum, these results suggest that HSI2 and HSL1 might recruit HD2A and HD2B to DOG1 to negatively regulate DOG1 expression and to reduce seed dormancy, consequently, affecting seed development during seed maturation and promoting seed germination during imbibition.
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Affiliation(s)
- Yongtao Han
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
| | - Elisabeth Georgii
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
| | | | - Christoph J. Wurm
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
| | - Patrick Hüther
- Genetics, LMU Biocenter, Ludwig-Maximilians-Universität München, München, Germany
| | - Gregor Huber
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Claude Becker
- Genetics, LMU Biocenter, Ludwig-Maximilians-Universität München, München, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
- Chair of Biochemical Plant Pathology, Technische Universität München, Freising, Germany
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center, Helmholtz Zentrum München, Member of the German Center for Lung Research, München, Germany
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17
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Wang M, Zhong Z, Gallego-Bartolomé J, Feng S, Shih YH, Liu M, Zhou J, Richey JC, Ng C, Jami-Alahmadi Y, Wohlschlegel J, Wu K, Jacobsen SE. Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14. Nat Commun 2023; 14:1736. [PMID: 36977663 PMCID: PMC10049986 DOI: 10.1038/s41467-023-37263-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Arabidopsis telomeric repeat binding factors (TRBs) can bind telomeric DNA sequences to protect telomeres from degradation. TRBs can also recruit Polycomb Repressive Complex 2 (PRC2) to deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain target loci. Here, we demonstrate that TRBs also associate and colocalize with JUMONJI14 (JMJ14) and trigger H3K4me3 demethylation at some loci. The trb1/2/3 triple mutant and the jmj14-1 mutant show an increased level of H3K4me3 over TRB and JMJ14 binding sites, resulting in up-regulation of their target genes. Furthermore, tethering TRBs to the promoter region of genes with an artificial zinc finger (TRB-ZF) successfully triggers target gene silencing, as well as H3K27me3 deposition, and H3K4me3 removal. Interestingly, JMJ14 is predominantly recruited to ZF off-target sites with low levels of H3K4me3, which is accompanied with TRB-ZFs triggered H3K4me3 removal at these loci. These results suggest that TRB proteins coordinate PRC2 and JMJ14 activities to repress target genes via H3K27me3 deposition and H3K4me3 removal.
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Affiliation(s)
- Ming Wang
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Zhenhui Zhong
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Javier Gallego-Bartolomé
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, 46022, Valencia, Spain
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Yuan-Hsin Shih
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Mukun Liu
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Jessica Zhou
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - John Curtis Richey
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Charmaine Ng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Howard Hughes Medical Institute (HHMI), University of California at Los Angeles, Los Angeles, CA, 90095, USA.
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18
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Baud S, Corso M, Debeaujon I, Dubreucq B, Job D, Marion-Poll A, Miquel M, North H, Rajjou L, Lepiniec L. Recent progress in molecular genetics and omics-driven research in seed biology. C R Biol 2023; 345:61-110. [PMID: 36847120 DOI: 10.5802/crbiol.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 01/11/2023]
Abstract
Elucidating the mechanisms that control seed development, metabolism, and physiology is a fundamental issue in biology. Michel Caboche had long been a catalyst for seed biology research in France up until his untimely passing away last year. To honour his memory, we have updated a review written under his coordination in 2010 entitled "Arabidopsis seed secrets unravelled after a decade of genetic and omics-driven research". This review encompassed different molecular aspects of seed development, reserve accumulation, dormancy and germination, that are studied in the lab created by M. Caboche. We have extended the scope of this review to highlight original experimental approaches implemented in the field over the past decade such as omics approaches aimed at investigating the control of gene expression, protein modifications, primary and specialized metabolites at the tissue or even cellular level, as well as seed biodiversity and the impact of the environment on seed quality.
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19
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Liang N, Cheng D, Zhao L, Lu H, Xu L, Bi Y. Identification of the Genes Encoding B3 Domain-Containing Proteins Related to Vernalization of Beta vulgaris. Genes (Basel) 2022; 13:genes13122217. [PMID: 36553484 PMCID: PMC9778101 DOI: 10.3390/genes13122217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Vernalization is the process of exposure to low temperatures, which is crucial for the transition from vegetative to reproductive growth of plants. In this study, the global landscape vernalization-related mRNAs and long noncoding RNAs (lncRNAs) were identified in Beta vulgaris. A total of 22,159 differentially expressed mRNAs and 4418 differentially expressed lncRNAs were uncovered between the vernalized and nonvernalized samples. Various regulatory proteins, such as zinc finger CCCH domain-containing proteins, F-box proteins, flowering-time-related proteins FY and FPA, PHD finger protein EHD3 and B3 domain proteins were identified. Intriguingly, a novel vernalization-related lncRNA-mRNA target-gene co-expression regulatory network and the candidate vernalization genes, VRN1, VRN1-like, VAL1 and VAL2, encoding B3 domain-containing proteins were also unveiled. The results of this study pave the way for further illumination of the molecular mechanisms underlying the vernalization of B. vulgaris.
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Affiliation(s)
- Naiguo Liang
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
- Correspondence:
| | - Dayou Cheng
- School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Li Zhao
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
| | - Hedong Lu
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
| | - Lei Xu
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
| | - Yanhong Bi
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
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20
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Liang Z, Yuan L, Xiong X, Hao Y, Song X, Zhu T, Yu Y, Fu W, Lei Y, Xu J, Liu J, Li JF, Li C. The transcriptional repressors VAL1 and VAL2 mediate genome-wide recruitment of the CHD3 chromatin remodeler PICKLE in Arabidopsis. THE PLANT CELL 2022; 34:3915-3935. [PMID: 35866997 PMCID: PMC9516181 DOI: 10.1093/plcell/koac217] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 05/30/2023]
Abstract
PICKLE (PKL) is a chromodomain helicase DNA-binding domain 3 (CHD3) chromatin remodeler that plays essential roles in controlling the gene expression patterns that determine developmental identity in plants, but the molecular mechanisms through which PKL is recruited to its target genes remain elusive. Here, we define a cis-motif and trans-acting factors mechanism that governs the genomic occupancy profile of PKL in Arabidopsis thaliana. We show that two homologous trans-factors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 physically interact with PKL in vivo, localize extensively to PKL-occupied regions in the genome, and promote efficient PKL recruitment at thousands of target genes, including those involved in seed maturation. Transcriptome analysis and genetic interaction studies reveal a close cooperation of VAL1/VAL2 and PKL in regulating gene expression and developmental fate. We demonstrate that this recruitment operates at two master regulatory genes, ABSCISIC ACID INSENSITIVE3 and AGAMOUS-LIKE 15, to repress the seed maturation program and ensure the seed-to-seedling transition. Together, our work unveils a general rule through which the CHD3 chromatin remodeler PKL binds to its target chromatin in plants.
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Affiliation(s)
- Zhenwei Liang
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Liangbing Yuan
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xiangyu Xiong
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuanhao Hao
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xin Song
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Tao Zhu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yaoguang Yu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wei Fu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yawen Lei
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jianqu Xu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jun Liu
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jian-Feng Li
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
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21
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Mikulski P, Wolff P, Lu T, Nielsen M, Echevarria EF, Zhu D, Questa JI, Saalbach G, Martins C, Dean C. VAL1 acts as an assembly platform co-ordinating co-transcriptional repression and chromatin regulation at Arabidopsis FLC. Nat Commun 2022; 13:5542. [PMID: 36130923 PMCID: PMC9492735 DOI: 10.1038/s41467-022-32897-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/23/2022] [Indexed: 12/04/2022] Open
Abstract
Polycomb (PcG) silencing is crucial for development, but how targets are specified remains incompletely understood. The cold-induced Polycomb Repressive Complex 2 (PRC2) silencing of Arabidopsis thaliana FLOWERING LOCUS C (FLC) provides an excellent system to elucidate PcG regulation. Association of the DNA binding protein VAL1 to FLC PcG nucleation regionis an important step. VAL1 co-immunoprecipitates APOPTOSIS AND SPLICING ASSOCIATED PROTEIN (ASAP) complex and PRC1. Here, we show that ASAP and PRC1 are necessary for co-transcriptional repression and chromatin regulation at FLC. ASAP mutants affect FLC transcription in warm conditions, but the rate of FLC silencing in the cold is unaffected. PRC1-mediated H2Aub accumulation increases at the FLC nucleation region during cold, but unlike the PRC2-delivered H3K27me3, does not spread across the locus. H2Aub thus involved in the transition to epigenetic silencing at FLC, facilitating H3K27me3 accumulation and long-term epigenetic memory. Overall, our work highlights the importance of VAL1 as an assembly platform co-ordinating activities necessary for epigenetic silencing at FLC.
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Affiliation(s)
- Pawel Mikulski
- Cell and Developmental Biology, John Innes Centre, Norwich, UK. .,Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Philip Wolff
- Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Tiancong Lu
- Cell and Developmental Biology, John Innes Centre, Norwich, UK.,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mathias Nielsen
- Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | | | - Danling Zhu
- Cell and Developmental Biology, John Innes Centre, Norwich, UK.,SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Julia I Questa
- Cell and Developmental Biology, John Innes Centre, Norwich, UK.,Centre for Research in Agricultural Genomics, Barcelona, Spain
| | | | - Carlo Martins
- Biological Chemistry, John Innes Centre, Norwich, UK
| | - Caroline Dean
- Cell and Developmental Biology, John Innes Centre, Norwich, UK. .,MRC Laboratory of Molecular Biology, Cambridge, UK.
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22
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Chen C, Du X. LEAFY COTYLEDONs: Connecting different stages of plant development. FRONTIERS IN PLANT SCIENCE 2022; 13:916831. [PMID: 36119568 PMCID: PMC9470955 DOI: 10.3389/fpls.2022.916831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The life of higher plants progresses successively through embryonic, juvenile, adult, and reproductive stages. LEAFY COTYLEDON (LEC) transcription factors, first discovered in Arabidopsis thaliana several decades ago, play a key role in regulating plant embryonic development, seed maturation, and subsequent growth. Existing studies have demonstrated that LECs together with other transcription factors form a huge and complex regulatory network to regulate many aspects of plant growth and development and respond to environmental stresses. Here, we focus on the role that has received little attention about the LECs linking different developmental stages and generational cycles in plants. We summarize the current fragmented research progress on the LECs role and molecular mechanism in connecting embryonic and vegetative growth periods and the reproductive stage. Furthermore, the possibility of LECs controlling the maintenance and transition of plant growth stages through epigenetic modifications is discussed.
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23
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Tan FQ, Wang W, Li J, Lu Y, Zhu B, Hu F, Li Q, Zhao Y, Zhou DX. A coiled-coil protein associates Polycomb Repressive Complex 2 with KNOX/BELL transcription factors to maintain silencing of cell differentiation-promoting genes in the shoot apex. THE PLANT CELL 2022; 34:2969-2988. [PMID: 35512211 PMCID: PMC9338815 DOI: 10.1093/plcell/koac133] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 04/25/2022] [Indexed: 05/06/2023]
Abstract
Polycomb repressive complex 2 (PRC2), which mediates the deposition of H3K27me3 histone marks, is important for developmental decisions in animals and plants. In the shoot apical meristem (SAM), Three Amino acid Loop Extension family KNOTTED-LIKE HOMEOBOX /BEL-like (KNOX/BELL) transcription factors are key regulators of meristem cell pluripotency and differentiation. Here, we identified a PRC2-associated coiled-coil protein (PACP) that interacts with KNOX/BELL transcription factors in rice (Oryza sativa) shoot apex cells. A loss-of-function mutation of PACP resulted in differential gene expression similar to that observed in PRC2 gene knockdown plants, reduced H3K27me3 levels, and reduced genome-wide binding of the PRC2 core component EMF2b. The genomic binding of PACP displayed a similar distribution pattern to EMF2b, and genomic regions with high PACP- and EMF2b-binding signals were marked by high levels of H3K27me3. We show that PACP is required for the repression of cell differentiation-promoting genes targeted by a rice KNOX1 protein in the SAM. PACP is involved in the recruitment or stabilization of PRC2 to genes targeted by KNOX/BELL transcription factors to maintain H3K27me3 and gene repression in dividing cells of the shoot apex. Our results provide insight into PRC2-mediated maintenance of H3K27me3 and the mechanism by which KNOX/BELL proteins regulate SAM development.
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Affiliation(s)
| | | | - Junjie Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Lu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Bo Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangfang Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu Zhao
- Authors for correspondence: (Y.Z.); (D.X.Z.)
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24
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Interaction Analysis between the Arabidopsis Transcription Repressor VAL1 and Transcription Coregulators SIN3-LIKEs (SNLs). Int J Mol Sci 2022; 23:ijms23136987. [PMID: 35805982 PMCID: PMC9266683 DOI: 10.3390/ijms23136987] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 01/19/2023] Open
Abstract
VIVIPAROUS1/ABSCISIC ACID INSENSITIVE3-LIKE1 (VAL1) encodes a DNA-binding B3 domain protein and plays essential roles in seed maturation and flowering transition by repressing genes through epigenetic silencing in Arabidopsis. SWI-INDEPENDENT3 (SIN3)-LIKEs (SNLs), which encode scaffold proteins for the assembly of histone deacetylase complexes and have six SIN3 homologues (SNL1–SNL6) in Arabidopsis thaliana, directly repress gene expression to regulate seed maturation and flowering transition. However, it remains unclear whether VAL1 and SNLs work together in repressing the expression of related genes. In this study, yeast two-hybrid and firefly luciferase complementation imaging assays revealed that VAL1 interacts with SNLs, which can be attributed to its own zinc-finger CW (conserved Cys (C) and Trp (W) residues) domain and the PAH (Paired Amphipathic Helices) domains of SNLs. Furthermore, pull-down experiments confirmed that the CW domain of VAL1 interacts with both intact protein and the PAH domains of SNLs proteins, and the co-immunoprecipitation assays also confirmed the interaction between VAL1 and SNLs. In addition, quantitative real-time PCR (qRT-PCR) analysis showed that VAL1 and SNLs were expressed in seedlings, and transient expression assays showed that VAL1 and SNLs were localized in the nucleus. Considered together, these results reveal that VAL1 physically interacts with SNLs both in vitro and in vivo, and suggest that VAL1 and SNLs may work together to repress the expression of genes related to seed maturation and flowering transition in Arabidopsis.
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25
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Mao D, Tao S, Li X, Gao D, Tang M, Liu C, Wu D, Bai L, He Z, Wang X, Yang L, Zhu Y, Zhang D, Zhang W, Chen C. The Harbinger transposon-derived gene PANDA epigenetically coordinates panicle number and grain size in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1154-1166. [PMID: 35239255 PMCID: PMC9129072 DOI: 10.1111/pbi.13799] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/27/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Transposons significantly contribute to genome fractions in many plants. Although numerous transposon-related mutations have been identified, the evidence regarding transposon-derived genes regulating crop yield and other agronomic traits is very limited. In this study, we characterized a rice Harbinger transposon-derived gene called PANICLE NUMBER AND GRAIN SIZE (PANDA), which epigenetically coordinates panicle number and grain size. Mutation of PANDA caused reduced panicle number but increased grain size in rice, while transgenic plants overexpressing this gene showed the opposite phenotypic change. The PANDA-encoding protein can bind to the core polycomb repressive complex 2 (PRC2) components OsMSI1 and OsFIE2, and regulates the deposition of H3K27me3 in the target genes, thereby epigenetically repressing their expression. Among the target genes, both OsMADS55 and OsEMF1 were negative regulators of panicle number but positive regulators of grain size, partly explaining the involvement of PANDA in balancing panicle number and grain size. Moreover, moderate overexpression of PANDA driven by its own promoter in the indica rice cultivar can increase grain yield. Thus, our findings present a novel insight into the epigenetic control of rice yield traits by a Harbinger transposon-derived gene and provide its potential application for rice yield improvement.
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Affiliation(s)
- Donghai Mao
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm EnhancementCollaborative Innovation Center for Modern Crop Production co‐sponsored by Province and Ministry (CIC‐MCP)Nanjing Agricultural UniversityNanjingChina
| | - Xin Li
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- University of Chinese Academy of SciencesBeijingChina
| | - Dongying Gao
- Small Grains and Potato Germplasm Research UnitUSDA ARSAberdeenIDUSA
| | - Mingfeng Tang
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Chengbing Liu
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research CenterChina Three Gorges UniversityYichangChina
| | - Dan Wu
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Liangli Bai
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- College of Life SciencesHunan Normal UniversityChangshaChina
| | - Zhankun He
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- College of AgronomyHunan Agriculture UniversityChangshaChina
| | - Xiaodong Wang
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lei Yang
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- Longping BranchGraduate School of Hunan UniversityChangshaChina
| | - Yuxing Zhu
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Dechun Zhang
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research CenterChina Three Gorges UniversityYichangChina
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementCollaborative Innovation Center for Modern Crop Production co‐sponsored by Province and Ministry (CIC‐MCP)Nanjing Agricultural UniversityNanjingChina
| | - Caiyan Chen
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
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26
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UvKmt2-Mediated H3K4 Trimethylation Is Required for Pathogenicity and Stress Response in Ustilaginoidea virens. J Fungi (Basel) 2022; 8:jof8060553. [PMID: 35736036 PMCID: PMC9225167 DOI: 10.3390/jof8060553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 02/04/2023] Open
Abstract
Epigenetic modification is important for cellular functions. Trimethylation of histone H3 lysine 4 (H3K4me3), which associates with transcriptional activation, is one of the important epigenetic modifications. In this study, the biological functions of UvKmt2-mediated H3K4me3 modification were characterized in Ustilaginoidea virens, which is the causal agent of the false smut disease, one of the most destructive diseases in rice. Phenotypic analyses of the ΔUvkmt2 mutant revealed that UvKMT2 is necessary for growth, conidiation, secondary spore formation, and virulence in U. virens. Immunoblotting and chromatin immunoprecipitation assay followed by sequencing (ChIP-seq) showed that UvKMT2 is required for the establishment of H3K4me3, which covers 1729 genes of the genome in U. virens. Further RNA-seq analysis demonstrated that UvKmt2-mediated H3K4me3 acts as an important role in transcriptional activation. In particular, H3K4me3 modification involves in the transcriptional regulation of conidiation-related and pathogenic genes, including two important mitogen-activated protein kinases UvHOG1 and UvPMK1. The down-regulation of UvHOG1 and UvPMK1 genes may be one of the main reasons for the reduced pathogenicity and stresses adaptability of the ∆Uvkmt2 mutant. Overall, H3K4me3, established by histone methyltransferase UvKMT2, contributes to fungal development, secondary spore formation, virulence, and various stress responses through transcriptional regulation in U. virens.
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27
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Nam JW, Lee HG, Do H, Kim HU, Seo PJ. Transcriptional regulation of triacylglycerol accumulation in plants under environmental stress conditions. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2905-2917. [PMID: 35560201 DOI: 10.1093/jxb/erab554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/15/2021] [Indexed: 06/15/2023]
Abstract
Triacylglycerol (TAG), a major energy reserve in lipid form, accumulates mainly in seeds. Although TAG concentrations are usually low in vegetative tissues because of the repression of seed maturation programs, these programs are derepressed upon the exposure of vegetative tissues to environmental stresses. Metabolic reprogramming of TAG accumulation is driven primarily by transcriptional regulation. A substantial proportion of transcription factors regulating seed TAG biosynthesis also participates in stress-induced TAG accumulation in vegetative tissues. TAG accumulation leads to the formation of lipid droplets and plastoglobules, which play important roles in plant tolerance to environmental stresses. Toxic lipid intermediates generated from environmental-stress-induced lipid membrane degradation are captured by TAG-containing lipid droplets and plastoglobules. This review summarizes recent advances in the transcriptional control of metabolic reprogramming underlying stress-induced TAG accumulation, and provides biological insight into the plant adaptive strategy, linking TAG biosynthesis with plant survival.
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Affiliation(s)
- Jeong-Won Nam
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Hong Gil Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Hyungju Do
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, South Korea
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, South Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
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28
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Chen Q, Zhang J, Li G. Dynamic epigenetic modifications in plant sugar signal transduction. TRENDS IN PLANT SCIENCE 2022; 27:379-390. [PMID: 34865981 DOI: 10.1016/j.tplants.2021.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/28/2021] [Accepted: 10/22/2021] [Indexed: 05/21/2023]
Abstract
In eukaryotes, dynamic chromatin states are closely related to changes in gene expression. Epigenetic modifications help plants adapt to their ever-changing environment by modulating gene expression via covalent modification at specific sites on DNA or histones. Sugars provide energy, but also function as signaling molecules to control plant growth and development. Various epigenetic modifications participate in sensing and transmitting sugar signals. Here we summarize recent progress in uncovering the epigenetic mechanisms involved in sugar signal transduction, including histone acetylation and deacetylation, histone methylation and demethylation, and DNA methylation. We also highlight changes in chromatin marks when crosstalk occurs between sugar signaling and the light, temperature, and phytohormone signaling pathways, and describe potential questions and approaches for future research.
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Affiliation(s)
- Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, Shandong, China; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Jing Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China.
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29
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Shwartz I, Yahav C, Kovetz N, Levy M, Israeli A, Bar M, Duval KL, Krall EG, Teboul N, Jiménez-Gómez JM, Deal RB, Ori N. The VIL gene CRAWLING ELEPHANT controls maturation and differentiation in tomato via polycomb silencing. PLoS Genet 2022; 18:e1009633. [PMID: 35255095 PMCID: PMC8939788 DOI: 10.1371/journal.pgen.1009633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 03/22/2022] [Accepted: 02/22/2022] [Indexed: 11/18/2022] Open
Abstract
VERNALIZATION INSENSITIVE 3-LIKE (VIL) proteins are PHD-finger proteins that recruit the repressor complex Polycomb Repressive Complex 2 (PRC2) to the promoters of target genes. Most known VIL targets are flowering repressor genes. Here, we show that the tomato VIL gene CRAWLING ELEPHANT (CREL) promotes differentiation throughout plant development by facilitating the trimethylation of Histone H3 on lysine 27 (H3K27me3). We identified the crel mutant in a screen for suppressors of the simple-leaf phenotype of entire (e), a mutant in the AUX/IAA gene ENTIRE/SlIAA9, involved in compound-leaf development in tomato. crel mutants have increased leaf complexity, and suppress the ectopic blade growth of e mutants. In addition, crel mutants are late flowering, and have delayed and aberrant stem, root and flower development. Consistent with a role for CREL in recruiting PRC2, crel mutants show drastically reduced H3K27me3 enrichment at approximately half of the 14,789 sites enriched in wild-type plants, along with upregulation of many underlying genes. Interestingly, this reduction in H3K27me3 across the genome in crel is also associated with gains in H3K27me3 at a smaller number of sites that normally have modest levels of the mark in wild-type plants, suggesting that PRC2 activity is no longer limiting in the absence of CREL. Our results uncover a wide role for CREL in plant and organ differentiation in tomato and suggest that CREL is required for targeting PRC2 activity to, and thus silencing, a specific subset of polycomb targets. Plants form organs continuously throughout their lives, and the number and shape of their organs is determined in a flexible manner according to the internal and external circumstances. Alongside this flexibility, plants maintain basic developmental programs to ensure proper functioning. Among the ways by which plants achieve flexible development is by tuning the pace of their maturation and differentiation, at both the plant and organ levels. One of the ways plants regulate the rate of maturation and differentiation is by changing gene expression. Here, we identified a gene that promotes plant and organ maturation and differentiation. This gene, CRAWLING ELEPHANT (CREL) acts by bringing a repressing complex to target genes. We show the importance of CREL in multiple developmental processes and in the expression of multiple genes throughout the tomato genome.
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Affiliation(s)
- Ido Shwartz
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Chen Yahav
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Neta Kovetz
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Matan Levy
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alon Israeli
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maya Bar
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Katherine L. Duval
- Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Ellen G. Krall
- Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Naama Teboul
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - José M. Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Roger B. Deal
- Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, Georgia, United States of America
- * E-mail: (RD); (NO)
| | - Naomi Ori
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- * E-mail: (RD); (NO)
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30
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Godwin J, Farrona S. The Importance of Networking: Plant Polycomb Repressive Complex 2 and Its Interactors. EPIGENOMES 2022; 6:epigenomes6010008. [PMID: 35323212 PMCID: PMC8948837 DOI: 10.3390/epigenomes6010008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) is arguably the best-known plant complex of the Polycomb Group (PcG) pathway, formed by a group of proteins that epigenetically represses gene expression. PRC2-mediated deposition of H3K27me3 has amply been studied in Arabidopsis and, more recently, data from other plant model species has also been published, allowing for an increasing knowledge of PRC2 activities and target genes. How PRC2 molecular functions are regulated and how PRC2 is recruited to discrete chromatin regions are questions that have brought more attention in recent years. A mechanism to modulate PRC2-mediated activity is through its interaction with other protein partners or accessory proteins. Current evidence for PRC2 interactors has demonstrated the complexity of its protein network and how far we are from fully understanding the impact of these interactions on the activities of PRC2 core subunits and on the formation of new PRC2 versions. This review presents a list of PRC2 interactors, emphasizing their mechanistic action upon PRC2 functions and their effects on transcriptional regulation.
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31
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miR172 Regulates WUS during Somatic Embryogenesis in Arabidopsis via AP2. Cells 2022; 11:cells11040718. [PMID: 35203367 PMCID: PMC8869827 DOI: 10.3390/cells11040718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023] Open
Abstract
In plants, the embryogenic transition of somatic cells requires the reprogramming of the cell transcriptome, which is under the control of genetic and epigenetic factors. Correspondingly, the extensive modulation of genes encoding transcription factors and miRNAs has been indicated as controlling the induction of somatic embryogenesis in Arabidopsis and other plants. Among the MIRNAs that have a differential expression during somatic embryogenesis, members of the MIRNA172 gene family have been identified, which implies a role of miR172 in controlling the embryogenic transition in Arabidopsis. In the present study, we found a disturbed expression of both MIRNA172 and candidate miR172-target genes, including AP2, TOE1, TOE2, TOE3, SMZ and SNZ, that negatively affected the embryogenic response of transgenic explants. Next, we examined the role of AP2 in the miR172-mediated mechanism that controls the embryogenic response. We found some evidence that by controlling AP2, miR172 might repress the WUS that has an important function in embryogenic induction. We showed that the mechanism of the miR172-AP2-controlled repression of WUS involves histone acetylation. We observed the upregulation of the WUS transcripts in an embryogenic culture that was overexpressing AP2 and treated with trichostatin A (TSA), which is an inhibitor of HDAC histone deacetylases. The increased expression of the WUS gene in the embryogenic culture of the hdac mutants further confirmed the role of histone acetylation in WUS control during somatic embryogenesis. A chromatin-immunoprecipitation analysis provided evidence about the contribution of HDA6/19-mediated histone deacetylation to AP2-controlled WUS repression during embryogenic induction. The upstream regulatory elements of the miR172-AP2-WUS pathway might involve the miR156-controlled SPL9/SPL10, which control the level of mature miR172 in an embryogenic culture.
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Jamge B, Berger F. Diversification of chromatin organization in eukaryotes. Curr Opin Cell Biol 2022; 74:1-6. [PMID: 34998094 DOI: 10.1016/j.ceb.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/24/2022]
Abstract
Our knowledge of the chromatin landscape and its regulation was originally discovered using yeast and a limited number of animals models. A wealth of studies in model plants now strongly demonstrates the conservation of certain features while illuminating the diversification of others. Here we summarize recent advances that describe specific features of chromatin organization of transcriptional units and specific regulation of heterochromatin in flowering plants. We highlight the importance of transcriptional regulation in plant chromatin organization and the need to investigate a more diverse range of species to understand the chromatin landscape in eukaryotes.
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Affiliation(s)
- Bhagyshree Jamge
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria.
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33
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Shankhwar S, Schwarz K, Katiyar R, Jung M, Maxeiner S, Südhof TC, Schmitz F. RIBEYE B-Domain Is Essential for RIBEYE A-Domain Stability and Assembly of Synaptic Ribbons. Front Mol Neurosci 2022; 15:838311. [PMID: 35153673 PMCID: PMC8831697 DOI: 10.3389/fnmol.2022.838311] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/03/2022] [Indexed: 01/17/2023] Open
Abstract
Synaptic ribbons are presynaptic specializations that define eponymous ribbon synapses. Synaptic ribbons are largely composed of RIBEYE, a protein containing an N-terminal A-domain and a carboxyterminal B-domain that is identical with CtBP2, a NAD(H)-binding transcriptional co-repressor. Previously we showed that synaptic ribbons are completely absent in RIBEYE knockout mice in which the RIBEYE A-domain-encoding exon had been deleted, but CtBP2 is still made, demonstrating that the A-domain is required for synaptic ribbon assembly. In the present study, we asked whether the RIBEYE B-domain also has an essential role in the assembly of synaptic ribbons. For this purpose, we made use of RIBEYE knockin mice in which the RIBEYE B-domain was replaced by a fluorescent protein domain, whereas the RIBEYE A-domain was retained unchanged. We found that replacing the RIBEYE B-domain with a fluorescent protein module destabilizes the resulting hybrid protein and causes a complete loss of synaptic ribbons. Our results thus demonstrate an essential role of the RIBEYE B-domain in enabling RIBEYE assembly into synaptic ribbons, reinforcing the notion that RIBEYE is the central organizer of synaptic ribbons.
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Affiliation(s)
- Soni Shankhwar
- Institute of Anatomy and Cell Biology, Saarland University, Medical School, Homburg, Germany
- *Correspondence: Soni Shankhwar Frank Schmitz
| | - Karin Schwarz
- Institute of Anatomy and Cell Biology, Saarland University, Medical School, Homburg, Germany
| | - Rashmi Katiyar
- Institute of Anatomy and Cell Biology, Saarland University, Medical School, Homburg, Germany
| | - Martin Jung
- Institute of Medical Biochemistry and Molecular Biology, Saarland University, Medical School, Homburg, Germany
| | - Stephan Maxeiner
- Institute of Anatomy and Cell Biology, Saarland University, Medical School, Homburg, Germany
| | - Thomas C. Südhof
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, United States
| | - Frank Schmitz
- Institute of Anatomy and Cell Biology, Saarland University, Medical School, Homburg, Germany
- *Correspondence: Soni Shankhwar Frank Schmitz
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34
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Vijayanathan M, Trejo-Arellano MG, Mozgová I. Polycomb Repressive Complex 2 in Eukaryotes-An Evolutionary Perspective. EPIGENOMES 2022; 6:3. [PMID: 35076495 PMCID: PMC8788455 DOI: 10.3390/epigenomes6010003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 12/23/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) represents a group of evolutionarily conserved multi-subunit complexes that repress gene transcription by introducing trimethylation of lysine 27 on histone 3 (H3K27me3). PRC2 activity is of key importance for cell identity specification and developmental phase transitions in animals and plants. The composition, biochemistry, and developmental function of PRC2 in animal and flowering plant model species are relatively well described. Recent evidence demonstrates the presence of PRC2 complexes in various eukaryotic supergroups, suggesting conservation of the complex and its function. Here, we provide an overview of the current understanding of PRC2-mediated repression in different representatives of eukaryotic supergroups with a focus on the green lineage. By comparison of PRC2 in different eukaryotes, we highlight the possible common and diverged features suggesting evolutionary implications and outline emerging questions and directions for future research of polycomb repression and its evolution.
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Affiliation(s)
- Mallika Vijayanathan
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
| | - María Guadalupe Trejo-Arellano
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
| | - Iva Mozgová
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
- Faculty of Science, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
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35
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Baile F, Gómez-Zambrano Á, Calonje M. Roles of Polycomb complexes in regulating gene expression and chromatin structure in plants. PLANT COMMUNICATIONS 2022; 3:100267. [PMID: 35059633 PMCID: PMC8760139 DOI: 10.1016/j.xplc.2021.100267] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/09/2021] [Accepted: 11/23/2021] [Indexed: 05/16/2023]
Abstract
The evolutionary conserved Polycomb Group (PcG) repressive system comprises two central protein complexes, PcG repressive complex 1 (PRC1) and PRC2. These complexes, through the incorporation of histone modifications on chromatin, have an essential role in the normal development of eukaryotes. In recent years, a significant effort has been made to characterize these complexes in the different kingdoms, and despite there being remarkable functional and mechanistic conservation, some key molecular principles have diverged. In this review, we discuss current views on the function of plant PcG complexes. We compare the composition of PcG complexes between animals and plants, highlight the role of recently identified plant PcG accessory proteins, and discuss newly revealed roles of known PcG partners. We also examine the mechanisms by which the repression is achieved and how these complexes are recruited to target genes. Finally, we consider the possible role of some plant PcG proteins in mediating local and long-range chromatin interactions and, thus, shaping chromatin 3D architecture.
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Affiliation(s)
- Fernando Baile
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092 Seville, Spain
| | - Ángeles Gómez-Zambrano
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092 Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092 Seville, Spain
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36
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Ding X, Jia X, Xiang Y, Jiang W. Histone Modification and Chromatin Remodeling During the Seed Life Cycle. FRONTIERS IN PLANT SCIENCE 2022; 13:865361. [PMID: 35548305 PMCID: PMC9083068 DOI: 10.3389/fpls.2022.865361] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/21/2022] [Indexed: 05/16/2023]
Abstract
Seeds are essential for the reproduction and dispersion of spermatophytes. The seed life cycle from seed development to seedling establishment proceeds through a series of defined stages regulated by distinctive physiological and biochemical mechanisms. The role of histone modification and chromatin remodeling in seed behavior has been intensively studied in recent years. In this review, we summarize progress in elucidating the regulatory network of these two kinds of epigenetic regulation during the seed life cycle, especially in two model plants, rice and Arabidopsis. Particular emphasis is placed on epigenetic effects on primary tissue formation (e.g., the organized development of embryo and endosperm), pivotal downstream gene expression (e.g., transcription of DOG1 in seed dormancy and repression of seed maturation genes in seed-to-seedling transition), and environmental responses (e.g., seed germination in response to different environmental cues). Future prospects for understanding of intricate interplay of epigenetic pathways and the epigenetic mechanisms in other commercial species are also proposed.
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Affiliation(s)
- Xiali Ding
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Xuhui Jia
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Yong Xiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Wenhui Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
- *Correspondence: Wenhui Jiang,
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37
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Fang H, Shao Y, Wu G. Reprogramming of Histone H3 Lysine Methylation During Plant Sexual Reproduction. FRONTIERS IN PLANT SCIENCE 2021; 12:782450. [PMID: 34917115 PMCID: PMC8669150 DOI: 10.3389/fpls.2021.782450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Plants undergo extensive reprogramming of chromatin status during sexual reproduction, a process vital to cell specification and pluri- or totipotency establishment. As a crucial way to regulate chromatin organization and transcriptional activity, histone modification can be reprogrammed during sporogenesis, gametogenesis, and embryogenesis in flowering plants. In this review, we first introduce enzymes required for writing, recognizing, and removing methylation marks on lysine residues in histone H3 tails, and describe their differential expression patterns in reproductive tissues, then we summarize their functions in the reprogramming of H3 lysine methylation and the corresponding chromatin re-organization during sexual reproduction in Arabidopsis, and finally we discuss the molecular significance of histone reprogramming in maintaining the pluri- or totipotency of gametes and the zygote, and in establishing novel cell fates throughout the plant life cycle. Despite rapid achievements in understanding the molecular mechanism and function of the reprogramming of chromatin status in plant development, the research in this area still remains a challenge. Technological breakthroughs in cell-specific epigenomic profiling in the future will ultimately provide a solution for this challenge.
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38
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Osadchuk K, Cheng CL, Irish EE. The integration of leaf-derived signals sets the timing of vegetative phase change in maize, a process coordinated by epigenetic remodeling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 312:111035. [PMID: 34620439 DOI: 10.1016/j.plantsci.2021.111035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/02/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
After germination, the maize shoot proceeds through a series of developmental stages before flowering. The first transition occurs during the vegetative phase where the shoot matures from the juvenile to the adult phase, called vegetative phase change (VPC). In maize, both phases exhibit easily-scored morphological characteristics, facilitating the elucidation of molecular mechanisms directing the characteristic gene expression patterns and resulting physiological features of each phase. miR156 expression is high during the juvenile phase, suppressing expression of squamosa promoter binding proteins/SBP-like transcription factors and miR172. The decline in miR156 and subsequent increase in miR172 expression marks the transition into the adult phase, where miR172 represses transcripts that confer juvenile traits. Leaf-derived signals attenuate miR156 expression and thus the duration of the juvenile phase. As found in other species, VPC in maize utilizes signals that consist of hormones, stress, and sugar to direct epigenetic modifiers. In this review we identify the intersection of leaf-derived signaling with components that contribute to the epigenetic changes which may, in turn, manage the distinct global gene expression patterns of each phase. In maize, published research regarding chromatin remodeling during VPC is minimal. Therefore, we identified epigenetic regulators in the maize genome and, using published gene expression data and research from other plant species, identify VPC candidates.
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Affiliation(s)
- Krista Osadchuk
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Chi-Lien Cheng
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Erin E Irish
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA.
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39
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Bieluszewski T, Xiao J, Yang Y, Wagner D. PRC2 activity, recruitment, and silencing: a comparative perspective. TRENDS IN PLANT SCIENCE 2021; 26:1186-1198. [PMID: 34294542 DOI: 10.1016/j.tplants.2021.06.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 06/08/2021] [Accepted: 06/16/2021] [Indexed: 05/22/2023]
Abstract
Polycomb repressive complex (PRC)-mediated gene silencing is vital for cell identity and development in both the plant and the animal kingdoms. It also modulates responses to stress. Two major protein complexes, PRC1 and PRC2, execute conserved nuclear functions in metazoans and plants through covalent modification of histones and by compacting chromatin. While a general requirement for Polycomb complexes in mitotically heritable gene repression in the context of chromatin is well established, recent studies have brought new insights into the regulation of Polycomb complex activity and recruitment. Here, we discuss these recent advances with emphasis on PRC2.
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Affiliation(s)
- Tomasz Bieluszewski
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Centre of Excellence for Plant and Microbial Science (CEPAMS), the John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yiman Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19103, USA.
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40
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Alizadeh M, Hoy R, Lu B, Song L. Team effort: Combinatorial control of seed maturation by transcription factors. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102091. [PMID: 34343847 DOI: 10.1016/j.pbi.2021.102091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/07/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Seed development is under tight spatiotemporal regulation. Here, we summarize how transcriptional regulation helps shape the major traits during seed maturation, which include storage reserve accumulation, dormancy, desiccation tolerance, and longevity. The regulation is rarely a solo task by an individual transcription factor (TF). Rather, it often involves coordinated recruitment or replacement of multiple TFs to achieve combinatorial regulation. We highlight recent progress on the transcriptional integration of activation and repression of seed maturation genes, and discuss potential research directions to further understand the TF networks of seed maturation.
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Affiliation(s)
- Milad Alizadeh
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Ryan Hoy
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Bailan Lu
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Liang Song
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
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41
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Kim J, Bordiya Y, Kathare PK, Zhao B, Zong W, Huq E, Sung S. Phytochrome B triggers light-dependent chromatin remodelling through the PRC2-associated PHD finger protein VIL1. NATURE PLANTS 2021; 7:1213-1219. [PMID: 34354260 PMCID: PMC8448934 DOI: 10.1038/s41477-021-00986-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 07/12/2021] [Indexed: 05/16/2023]
Abstract
To compensate for a sessile nature, plants have developed sophisticated mechanisms to sense varying environmental conditions. Phytochromes (phys) are light and temperature sensors that regulate downstream genes to render plants responsive to environmental stimuli1-4. Here, we show that phyB directly triggers the formation of a repressive chromatin loop by physically interacting with VERNALIZATION INSENSITIVE 3-LIKE1/VERNALIZATION 5 (VIL1/VRN5), a component of Polycomb Repressive Complex 2 (PRC2)5,6, in a light-dependent manner. VIL1 and phyB cooperatively contribute to the repression of growth-promoting genes through the enrichment of Histone H3 Lys27 trimethylation (H3K27me3), a repressive histone modification. In addition, phyB and VIL1 mediate the formation of a chromatin loop to facilitate the repression of ATHB2. Our findings show that phyB directly utilizes chromatin remodelling to regulate the expression of target genes in a light-dependent manner.
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Affiliation(s)
- Junghyun Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Yogendra Bordiya
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Praveen Kumar Kathare
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Bo Zhao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Wei Zong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Enamul Huq
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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42
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Baile F, Merini W, Hidalgo I, Calonje M. EAR domain-containing transcription factors trigger PRC2-mediated chromatin marking in Arabidopsis. THE PLANT CELL 2021; 33:2701-2715. [PMID: 34003929 PMCID: PMC8408475 DOI: 10.1093/plcell/koab139] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 05/14/2021] [Indexed: 05/22/2023]
Abstract
Polycomb group (PcG) complexes ensure that every cell in an organism expresses the genes needed at a particular stage, time, or condition. However, it is still not fully understood how PcG complexes PcG-repressive complex 1 (PRC1) and PRC2 are recruited to target genes in plants. Recent findings in Arabidopsis thaliana support the notion that PRC2 recruitment is mediated by different transcription factors (TFs). However, it is unclear how all these TFs interact with PRC2 and whether they also recruit PRC1 activity. Here, by using a system to bind selected TFs to a synthetic promoter lacking the complexity of PcG target promoters in vivo, we show that while binding of the TF VIVIPAROUS1/ABSCISIC ACID-INSENSITIVE3-LIKE1 recapitulates PRC1 and PRC2 marking, the binding of other TFs only renders PRC2 marking. Interestingly, all these TFs contain an Ethylene-responsive element binding factor-associated Amphiphilic Repression (EAR) domain that triggers both HISTONE DEACETYLASE COMPLEX and PRC2 activities, connecting two different repressive mechanisms. Furthermore, we show that different TFs can have an additive effect on PRC2 activity, which may be required to maintain long-term repression of gene expression.
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Affiliation(s)
- Fernando Baile
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Wiam Merini
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Inés Hidalgo
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain
- Author for correspondence:
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43
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Fouracre JP, He J, Chen VJ, Sidoli S, Poethig RS. VAL genes regulate vegetative phase change via miR156-dependent and independent mechanisms. PLoS Genet 2021; 17:e1009626. [PMID: 34181637 PMCID: PMC8270478 DOI: 10.1371/journal.pgen.1009626] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/09/2021] [Accepted: 05/28/2021] [Indexed: 12/11/2022] Open
Abstract
How organisms control when to transition between different stages of development is a key question in biology. In plants, epigenetic silencing by Polycomb repressive complex 1 (PRC1) and PRC2 plays a crucial role in promoting developmental transitions, including from juvenile-to-adult phases of vegetative growth. PRC1/2 are known to repress the master regulator of vegetative phase change, miR156, leading to the transition to adult growth, but how this process is regulated temporally is unknown. Here we investigate whether transcription factors in the VIVIPAROUS/ABI3-LIKE (VAL) gene family provide the temporal signal for the epigenetic repression of miR156. Exploiting a novel val1 allele, we found that VAL1 and VAL2 redundantly regulate vegetative phase change by controlling the overall level, rather than temporal dynamics, of miR156 expression. Furthermore, we discovered that VAL1 and VAL2 also act independently of miR156 to control this important developmental transition. In combination, our results highlight the complexity of temporal regulation in plants. During their life-cycles multicellular organisms progress through a series of different developmental phases. The correct timing of the transitions between these phases is essential to ensure that development occurs at an appropriate rate and in the right order. In plants, vegetative phase change—the switch from a juvenile to an adult stage of vegetative growth prior to the onset of reproductive development–is a widely conserved transition associated with a number of phenotypic changes. It is therefore an excellent model to investigate the regulation of developmental timing. The timing of vegetative phase change is determined by a decline in the expression of a regulatory microRNA–miRNA156. However, what controls the temporal decline in miR156 expression is a major unknown in the field. In this study we tested whether members of the VAL gene family, known to be important for coordinating plant developmental transitions, are critical regulators of vegetative phase change. Using a series of genetic and biochemical approaches we found that VAL genes are important determinants of the timing of vegetative phase change. However, we discovered that VAL genes function largely to control the overall level, rather than temporal expression pattern, of miR156.
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Affiliation(s)
- Jim P. Fouracre
- Biology Department, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jia He
- Biology Department, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Victoria J. Chen
- Biology Department, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - R. Scott Poethig
- Biology Department, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Shen Q, Lin Y, Li Y, Wang G. Dynamics of H3K27me3 Modification on Plant Adaptation to Environmental Cues. PLANTS 2021; 10:plants10061165. [PMID: 34201297 PMCID: PMC8228231 DOI: 10.3390/plants10061165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022]
Abstract
Given their sessile nature, plants have evolved sophisticated regulatory networks to confer developmental plasticity for adaptation to fluctuating environments. Epigenetic codes, like tri-methylation of histone H3 on Lys27 (H3K27me3), are evidenced to account for this evolutionary benefit. Polycomb repressive complex 2 (PRC2) and PRC1 implement and maintain the H3K27me3-mediated gene repression in most eukaryotic cells. Plants take advantage of this epigenetic machinery to reprogram gene expression in development and environmental adaption. Recent studies have uncovered a number of new players involved in the establishment, erasure, and regulation of H3K27me3 mark in plants, particularly highlighting new roles in plants’ responses to environmental cues. Here, we review current knowledge on PRC2-H3K27me3 dynamics occurring during plant growth and development, including its writers, erasers, and readers, as well as targeting mechanisms, and summarize the emerging roles of H3K27me3 mark in plant adaptation to environmental stresses.
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Ruan J, Chen H, Zhu T, Yu Y, Lei Y, Yuan L, Liu J, Wang ZY, Kuang JF, Lu WJ, Huang S, Li C. Brassinosteroids repress the seed maturation program during the seed-to-seedling transition. PLANT PHYSIOLOGY 2021; 186:534-548. [PMID: 33620498 PMCID: PMC8154094 DOI: 10.1093/plphys/kiab089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 05/27/2023]
Abstract
In flowering plants, repression of the seed maturation program is essential for the transition from the seed to the vegetative phase, but the underlying mechanisms remain poorly understood. The B3-domain protein VIVIPAROUS1/ABSCISIC ACID-INSENSITIVE3-LIKE 1 (VAL1) is involved in repressing the seed maturation program. Here we uncovered a molecular network triggered by the plant hormone brassinosteroid (BR) that inhibits the seed maturation program during the seed-to-seedling transition in Arabidopsis (Arabidopsis thaliana). val1-2 mutant seedlings treated with a BR biosynthesis inhibitor form embryonic structures, whereas BR signaling gain-of-function mutations rescue the embryonic structure trait. Furthermore, the BR-activated transcription factors BRI1-EMS-SUPPRESSOR 1 and BRASSINAZOLE-RESISTANT 1 bind directly to the promoter of AGAMOUS-LIKE15 (AGL15), which encodes a transcription factor involved in activating the seed maturation program, and suppress its expression. Genetic analysis indicated that BR signaling is epistatic to AGL15 and represses the seed maturation program by downregulating AGL15. Finally, we showed that the BR-mediated pathway functions synergistically with the VAL1/2-mediated pathway to ensure the full repression of the seed maturation program. Together, our work uncovered a mechanism underlying the suppression of the seed maturation program, shedding light on how BR promotes seedling growth.
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Affiliation(s)
- Jiuxiao Ruan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Huhui Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Tao Zhu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yawen Lei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Liangbing Yuan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jun Liu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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