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Baile F, Merini W, Hidalgo I, Calonje M. EAR domain-containing transcription factors trigger PRC2-mediated chromatin marking in Arabidopsis. Plant Cell 2021; 33:2701-2715. [PMID: 34003929 PMCID: PMC8408475 DOI: 10.1093/plcell/koab139] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Gómez-Zambrano Á, Merini W, Calonje M. The repressive role of Arabidopsis H2A.Z in transcriptional regulation depends on AtBMI1 activity. Nat Commun 2019; 10:2828. [PMID: 31249301 PMCID: PMC6597585 DOI: 10.1038/s41467-019-10773-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 05/31/2019] [Indexed: 11/24/2022] Open
Abstract
H2A.Z variant has emerged as a critical player in regulating plant responses to environment; however, the mechanism by which H2A.Z mediates this regulation remains unclear. In Arabidopsis, H2A.Z has been proposed to have opposite effects on transcription depending on its localization within the gene. These opposite roles have been assigned by correlating gene expression and H2A.Z enrichment analyses but without considering the impact of possible H2A.Z post-translational modifications. Here, we show that H2A.Z can be monoubiquitinated by the PRC1 components AtBMI1A/B/C. The incorporation of this modification is required for H2A.Z-mediated transcriptional repression through a mechanism that does not require PRC2 activity. Our data suggest that the dual role of H2A.Z in regulating gene expression depends on the modification that it carries, while the levels of H2A.Z within genes depend on the transcriptional activity. Arabidopsis H2A.Z plays an important role in regulating gene expression in response to stressors; however, the underlying mechanism is still puzzling. Here, the authors show that monoubiquitination of H2A.Z by AtBMI1 is required for H2A.Z-mediated transcriptional repression.
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Affiliation(s)
- Ángeles Gómez-Zambrano
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-University of Seville), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Wiam Merini
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-University of Seville), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-University of Seville), Avenida Américo Vespucio 49, 41092, Seville, Spain.
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Merini W, Romero-Campero FJ, Gomez-Zambrano A, Zhou Y, Turck F, Calonje M. The Arabidopsis Polycomb Repressive Complex 1 (PRC1) Components AtBMI1A, B, and C Impact Gene Networks throughout All Stages of Plant Development. Plant Physiol 2017; 173:627-641. [PMID: 27837089 PMCID: PMC5210725 DOI: 10.1104/pp.16.01259] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/02/2016] [Indexed: 05/04/2023]
Abstract
Polycomb Group regulation in Arabidopsis (Arabidopsis thaliana) is required to maintain cell differentiation and allow developmental phase transitions. This is achieved by the activity of three PcG repressive complex 2s (PRC2s) and the participation of a yet poorly defined PRC1. Previous results showed that apparent PRC1 components perform discrete roles during plant development, suggesting the existence of PRC1 variants; however, it is not clear in how many processes these components participate. We show that AtBMI1 proteins are required to promote all developmental phase transitions and to control cell proliferation during organ growth and development, expanding their proposed range of action. While AtBMI1 function during germination is closely linked to B3 domain transcription factors VAL1/2 possibly in combination with GT-box binding factors, other AtBMI1 regulatory networks require participation of different factor combinations. Conversely, EMF1 and LHP1 bind many H3K27me3 positive genes up-regulated in atbmi1a/b/c mutants; however, loss of their function affects expression of a different subset, suggesting that even if EMF1, LHP1, and AtBMI1 exist in a common PRC1 variant, their role in repression depends on the functional context.
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Affiliation(s)
- Wiam Merini
- Institute of Plant Biochemistry and Photosynthesis, 41092 Seville, Spain (W.M., A.G.-Z., M.C.)
- Department of Computer Science and Artificial Intelligence, University of Seville, 41012 Seville, Spain (F.J.R.-C.); and
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, 50829 Cologne, Germany (F.T.)
| | - Francisco J Romero-Campero
- Institute of Plant Biochemistry and Photosynthesis, 41092 Seville, Spain (W.M., A.G.-Z., M.C.)
- Department of Computer Science and Artificial Intelligence, University of Seville, 41012 Seville, Spain (F.J.R.-C.); and
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, 50829 Cologne, Germany (F.T.)
| | - Angeles Gomez-Zambrano
- Institute of Plant Biochemistry and Photosynthesis, 41092 Seville, Spain (W.M., A.G.-Z., M.C.)
- Department of Computer Science and Artificial Intelligence, University of Seville, 41012 Seville, Spain (F.J.R.-C.); and
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, 50829 Cologne, Germany (F.T.)
| | - Yue Zhou
- Institute of Plant Biochemistry and Photosynthesis, 41092 Seville, Spain (W.M., A.G.-Z., M.C.)
- Department of Computer Science and Artificial Intelligence, University of Seville, 41012 Seville, Spain (F.J.R.-C.); and
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, 50829 Cologne, Germany (F.T.)
| | - Franziska Turck
- Institute of Plant Biochemistry and Photosynthesis, 41092 Seville, Spain (W.M., A.G.-Z., M.C.)
- Department of Computer Science and Artificial Intelligence, University of Seville, 41012 Seville, Spain (F.J.R.-C.); and
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, 50829 Cologne, Germany (F.T.)
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis, 41092 Seville, Spain (W.M., A.G.-Z., M.C.);
- Department of Computer Science and Artificial Intelligence, University of Seville, 41012 Seville, Spain (F.J.R.-C.); and
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, 50829 Cologne, Germany (F.T.)
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Picó S, Ortiz-Marchena MI, Merini W, Calonje M. Deciphering the Role of POLYCOMB REPRESSIVE COMPLEX1 Variants in Regulating the Acquisition of Flowering Competence in Arabidopsis. Plant Physiol 2015; 168:1286-97. [PMID: 25897002 PMCID: PMC4528732 DOI: 10.1104/pp.15.00073] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/16/2015] [Indexed: 05/18/2023]
Abstract
Polycomb group (PcG) proteins play important roles in regulating developmental phase transitions in plants; however, little is known about the role of the PcG machinery in regulating the transition from juvenile to adult phase. Here, we show that Arabidopsis (Arabidopsis thaliana) B lymphoma Moloney murine leukemia virus insertion region1 homolog (BMI1) POLYCOMB REPRESSIVE COMPLEX1 (PRC1) components participate in the repression of microRNA156 (miR156). Loss of AtBMI1 function leads to the up-regulation of the primary transcript of MIR156A and MIR156C at the time the levels of miR156 should decline, resulting in an extended juvenile phase and delayed flowering. Conversely, the PRC1 component EMBRYONIC FLOWER (EMF1) participates in the regulation of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE and MIR172 genes. Accordingly, plants impaired in EMF1 function displayed misexpression of these genes early in development, which contributes to a CONSTANS-independent up-regulation of FLOWERING LOCUS T (FT) leading to the earliest flowering phenotype described in Arabidopsis. Our findings show how the different regulatory roles of two functional PRC1 variants coordinate the acquisition of flowering competence and help to reach the threshold of FT necessary to flower. Furthermore, we show how two central regulatory mechanisms, such as PcG and microRNA, assemble to achieve a developmental outcome.
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Affiliation(s)
- Sara Picó
- Institute of Plant Biochemistry and Photosynthesis, Instituto de Bioquímica Vegetal y Fotosíntesis-Consejo Superior de Investigaciones Científicas-University of Seville, Isla de La Cartuja, 41092 Seville, Spain
| | - M Isabel Ortiz-Marchena
- Institute of Plant Biochemistry and Photosynthesis, Instituto de Bioquímica Vegetal y Fotosíntesis-Consejo Superior de Investigaciones Científicas-University of Seville, Isla de La Cartuja, 41092 Seville, Spain
| | - Wiam Merini
- Institute of Plant Biochemistry and Photosynthesis, Instituto de Bioquímica Vegetal y Fotosíntesis-Consejo Superior de Investigaciones Científicas-University of Seville, Isla de La Cartuja, 41092 Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis, Instituto de Bioquímica Vegetal y Fotosíntesis-Consejo Superior de Investigaciones Científicas-University of Seville, Isla de La Cartuja, 41092 Seville, Spain
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Abstract
Polycomb group (PcG) proteins constitute a major epigenetic mechanism for gene repression throughout the plant life. For a long time, the PcG mechanism has been proposed to follow a hierarchical recruitment of PcG repressive complexes (PRCs) to target genes in which the binding of PRC2 and the incorporation of H3 lysine 27 trimethyl marks led to recruitment of PRC1, which in turn mediated H2A monoubiquitination. However, recent studies have turned this model upside-down by showing that PRC1 activity can be required for PRC2 recruitment and H3K27me3 marking. Here, we review the current knowledge on plant PRC1 composition and mechanisms of repression, as well as its role during plant development.
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Affiliation(s)
- Wiam Merini
- Institute of Plant Biochemistry and Photosynthesis, IBVF-CSIC-University of Seville, Avenida América Vespucio, 49, Isla de La Cartuja, 41092, Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis, IBVF-CSIC-University of Seville, Avenida América Vespucio, 49, Isla de La Cartuja, 41092, Seville, Spain
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