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Marquez-Molins J, Cheng J, Corell-Sierra J, Juarez-Gonzalez VT, Villalba-Bermell P, Annacondia ML, Gomez G, Martinez G. Hop stunt viroid infection induces heterochromatin reorganization. THE NEW PHYTOLOGIST 2024; 243:2351-2367. [PMID: 39030826 DOI: 10.1111/nph.19986] [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: 03/02/2024] [Accepted: 06/26/2024] [Indexed: 07/22/2024]
Abstract
Viroids are pathogenic noncoding RNAs that completely rely on their host molecular machinery to accomplish their life cycle. Several interactions between viroids and their host molecular machinery have been identified, including interference with epigenetic mechanisms such as DNA methylation. Despite this, whether viroids influence changes in other epigenetic marks such as histone modifications remained unknown. Epigenetic regulation is particularly important during pathogenesis processes because it might be a key regulator of the dynamism of the defense response. Here we have analyzed the changes taking place in Cucumis sativus (cucumber) facultative and constitutive heterochromatin during hop stunt viroid (HSVd) infection using chromatin immunoprecipitation (ChIP) of the two main heterochromatic marks: H3K9me2 and H3K27me3. We find that HSVd infection is associated with changes in both H3K27me3 and H3K9me2, with a tendency to decrease the levels of repressive epigenetic marks through infection progression. These epigenetic changes are connected to the transcriptional regulation of their expected targets, genes, and transposable elements. Indeed, several genes related to the defense response are targets of both epigenetic marks. Our results highlight another host regulatory mechanism affected by viroid infection, providing further information about the complexity of the multiple layers of interactions between pathogens/viroids and hosts/plants.
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Affiliation(s)
- Joan Marquez-Molins
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Jinping Cheng
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
| | - Julia Corell-Sierra
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Vasti Thamara Juarez-Gonzalez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
| | - Pascual Villalba-Bermell
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Maria Luz Annacondia
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, 1871, Denmark
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
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2
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Ge T, Brickner JH. Inheritance of epigenetic transcriptional memory. Curr Opin Genet Dev 2024; 85:102174. [PMID: 38430840 PMCID: PMC10947848 DOI: 10.1016/j.gde.2024.102174] [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: 11/09/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Epigenetic memory allows organisms to stably alter their transcriptional program in response to developmental or environmental stimuli. Such transcriptional programs are mediated by heritable regulation of the function of enhancers and promoters. Memory involves read-write systems that enable self-propagation and mitotic inheritance of cis-acting epigenetic marks to induce stable changes in transcription. Also, in response to environmental cues, cells can induce epigenetic transcriptional memory to poise inducible genes for faster induction in the future. Here, we discuss modes of epigenetic inheritance and the molecular basis of epigenetic transcriptional memory.
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Affiliation(s)
- Tiffany Ge
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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3
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Godwin J, Govindasamy M, Nedounsejian K, March E, Halton R, Bourbousse C, Wolff L, Fort A, Krzyszton M, López Corrales J, Swiezewski S, Barneche F, Schubert D, Farrona S. The UBP5 histone H2A deubiquitinase counteracts PRCs-mediated repression to regulate Arabidopsis development. Nat Commun 2024; 15:667. [PMID: 38253560 PMCID: PMC10803359 DOI: 10.1038/s41467-023-44546-8] [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: 11/15/2022] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Polycomb Repressive Complexes (PRCs) control gene expression through the incorporation of H2Aub and H3K27me3. In recent years, there is increasing evidence of the complexity of PRCs' interaction networks and the interplay of these interactors with PRCs in epigenome reshaping, which is fundamental to understand gene regulatory mechanisms. Here, we identified UBIQUITIN SPECIFIC PROTEASE 5 (UBP5) as a chromatin player able to counteract the deposition of the two PRCs' epigenetic hallmarks in Arabidopsis thaliana. We demonstrated that UBP5 is a plant developmental regulator based on functional analyses of ubp5-CRISPR Cas9 mutant plants. UBP5 promotes H2A monoubiquitination erasure, leading to transcriptional de-repression. Furthermore, preferential association of UBP5 at PRC2 recruiting motifs and local H3K27me3 gaining in ubp5 mutant plants suggest the existence of functional interplays between UBP5 and PRC2 in regulating epigenome dynamics. In summary, acting as an antagonist of the pivotal epigenetic repressive marks H2Aub and H3K27me3, UBP5 provides novel insights to disentangle the complex regulation of PRCs' activities.
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Affiliation(s)
- James Godwin
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Mohan Govindasamy
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Kiruba Nedounsejian
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Eduardo March
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Ronan Halton
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Clara Bourbousse
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léa Wolff
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Antoine Fort
- Dept. of Veterinary and Microbial Sciences, Technological University of The Shannon: Midlands, Athlone, Co., Roscommon, Ireland
| | - Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw, 02-106, Poland
| | - Jesús López Corrales
- Molecular Parasitology Laboratory (MPL), Centre for One Health and Ryan Institute, School of Natural Sciences, University of Galway, Galway, H91 DK59, Ireland
| | - Szymon Swiezewski
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw, 02-106, Poland
| | - Fredy Barneche
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Daniel Schubert
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Sara Farrona
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland.
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4
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Shankar N, Sunkara P, Nath U. A double-negative feedback loop between miR319c and JAW-TCPs establishes growth pattern in incipient leaf primordia in Arabidopsis thaliana. PLoS Genet 2023; 19:e1010978. [PMID: 37769020 PMCID: PMC10564139 DOI: 10.1371/journal.pgen.1010978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/10/2023] [Accepted: 09/17/2023] [Indexed: 09/30/2023] Open
Abstract
The microRNA miR319 and its target JAW-TCP transcription factors regulate the proliferation-to-differentiation transition of leaf pavement cells in diverse plant species. In young Arabidopsis leaf primordia, JAW-TCPs are detected towards the distal region whereas the major mRNA319-encoding gene MIR319C, is expressed at the base. Little is known about how this complementary expression pattern of MIR319C and JAW-TCPs is generated. Here, we show that MIR319C is initially expressed uniformly throughout the incipient primordia and is later abruptly down-regulated at the distal region, with concomitant distal appearance of JAW-TCPs, when leaves grow to ~100 μm long. Loss of JAW-TCPs causes distal extension of the MIR319C expression domain, whereas ectopic TCP activity restricts MIR319C more proximally. JAW-TCPs are recruited to and are capable of depositing histone H3K27me3 repressive marks on the MIR319C chromatin. JAW-TCPs fail to repress MIR319C in transgenic seedlings where the TCP-binding cis-elements on MIR319C are mutated, causing miR319 gain-of-function-like phenotype in the embryonic leaves. Based on these results, we propose a model for growth patterning in leaf primordia wherein MIR319C and JAW-TCPs repress each other and divide the uniformly growing primordia into distal differentiation zone and proximal proliferation domain.
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Affiliation(s)
- Naveen Shankar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Preethi Sunkara
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Utpal Nath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
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5
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Sahu A, Singh R, Verma PK. Plant BBR/BPC transcription factors: unlocking multilayered regulation in development, stress and immunity. PLANTA 2023; 258:31. [PMID: 37368167 DOI: 10.1007/s00425-023-04188-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/17/2023] [Indexed: 06/28/2023]
Abstract
MAIN CONCLUSION This review provides a detailed structural and functional understanding of BBR/BPC TF, their conservation across the plant lineage, and their comparative study with animal GAFs. Plant-specific Barley B Recombinant/Basic PentaCysteine (BBR/BPC) transcription factor (TF) family binds to "GA" repeats similar to animal GAGA Factors (GAFs). These GAGA binding proteins are among the few TFs that regulate the genes at multiple steps by modulating the chromatin structure. The hallmark of the BBR/BPC TF family is the presence of a conserved C-terminal region with five cysteine residues. In this review, we present: first, the structural distinct yet functional similar relation of plant BBR/BPC TF with animal GAFs, second, the conservation of BBR/BPC across the plant lineage, third, their role in planta, fourth, their potential interacting partners and structural insights. We conclude that BBR/BPC TFs have multifaceted roles in plants. Besides the earliest identified function in homeotic gene regulation and developmental processes, presently BBR/BPC TFs were identified in hormone signaling, stress, circadian oscillation, and sex determination processes. Understanding how plants' development and stress processes are coordinated is central to divulging the growth-immunity trade-off regulation. The BBR/BPC TFs may hold keys to divulge the interactions between development and immunity. Moreover, the conservation of BBR/BPC across plant lineage makes it an evolutionary vital gene family. Consequently, BBR/BPCs are prospective to attract the increasing attention of the scientific communities as they are probably at the crossroads of diverse fundamental processes.
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Affiliation(s)
- Anubhav Sahu
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ritu Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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6
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Kong C, Zhao G, Gao L, Kong X, Wang D, Liu X, Jia J. Epigenetic Landscape Is Largely Shaped by Diversiform Transposons in Aegilops tauschii. Int J Mol Sci 2023; 24:9349. [PMID: 37298301 PMCID: PMC10253722 DOI: 10.3390/ijms24119349] [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: 04/18/2023] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Transposons (TEs) account for more than 80% of the wheat genome, the highest among all known crop species. They play an important role in shaping the elaborate genomic landscape, which is the key to the speciation of wheat. In this study, we analyzed the association between TEs, chromatin states, and chromatin accessibility in Aegilops tauschii, the D genome donor of bread wheat. We found that TEs contributed to the complex but orderly epigenetic landscape as chromatin states showed diverse distributions on TEs of different orders or superfamilies. TEs also contributed to the chromatin state and openness of potential regulatory elements, affecting the expression of TE-related genes. Some TE superfamilies, such as hAT-Ac, carry active/open chromatin regions. In addition, the histone mark H3K9ac was found to be associated with the accessibility shaped by TEs. These results suggest the role of diversiform TEs in shaping the epigenetic landscape and in gene expression regulation in Aegilops tauschii. This has positive implications for understanding the transposon roles in Aegilops tauschii or the wheat D genome.
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Affiliation(s)
- Chuizheng Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.K.); (G.Z.); (L.G.); (X.K.)
| | - Guangyao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.K.); (G.Z.); (L.G.); (X.K.)
| | - Lifeng Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.K.); (G.Z.); (L.G.); (X.K.)
| | - Xiuying Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.K.); (G.Z.); (L.G.); (X.K.)
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China;
| | - Xu Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.K.); (G.Z.); (L.G.); (X.K.)
| | - Jizeng Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.K.); (G.Z.); (L.G.); (X.K.)
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China;
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7
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Sano N, Malabarba J, Chen Z, Gaillard S, Windels D, Verdier J. Chromatin dynamics associated with seed desiccation tolerance/sensitivity at early germination in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:1059493. [PMID: 36507374 PMCID: PMC9729785 DOI: 10.3389/fpls.2022.1059493] [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: 10/01/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Desiccation tolerance (DT) has contributed greatly to the adaptation of land plants to severe water-deficient conditions. DT is mostly observed in reproductive parts in flowering plants such as seeds. The seed DT is lost at early post germination stage but is temporally re-inducible in 1 mm radicles during the so-called DT window following a PEG treatment before being permanently silenced in 5 mm radicles of germinating seeds. The molecular mechanisms that activate/reactivate/silence DT in developing and germinating seeds have not yet been elucidated. Here, we analyzed chromatin dynamics related to re-inducibility of DT before and after the DT window at early germination in Medicago truncatula radicles to determine if DT-associated genes were transcriptionally regulated at the chromatin levels. Comparative transcriptome analysis of these radicles identified 948 genes as DT re-induction-related genes, positively correlated with DT re-induction. ATAC-Seq analyses revealed that the chromatin state of genomic regions containing these genes was clearly modulated by PEG treatment and affected by growth stages with opened chromatin in 1 mm radicles with PEG (R1P); intermediate openness in 1 mm radicles without PEG (R1); and condensed chromatin in 5 mm radicles without PEG (R5). In contrast, we also showed that the 103 genes negatively correlated with the re-induction of DT did not show any transcriptional regulation at the chromatin level. Additionally, ChIP-Seq analyses for repressive marks H2AK119ub and H3K27me3 detected a prominent signal of H3K27me3 on the DT re-induction-related gene sequences at R5 but not in R1 and R1P. Moreover, no clear H2AK119ub marks was observed on the DT re-induction-related gene sequences at both developmental radicle stages, suggesting that silencing of DT process after germination will be mainly due to H3K27me3 marks by the action of the PRC2 complex, without involvement of PRC1 complex. The dynamic of chromatin changes associated with H3K27me3 were also confirmed on seed-specific genes encoding potential DT-related proteins such as LEAs, oleosins and transcriptional factors. However, several transcriptional factors did not show a clear link between their decrease of chromatin openness and H3K27me3 levels, suggesting that their accessibility may also be regulated by additional factors, such as other histone modifications. Finally, in order to make these comprehensive genome-wide analyses of transcript and chromatin dynamics useful to the scientific community working on early germination and DT, we generated a dedicated genome browser containing all these data and publicly available at https://iris.angers.inrae.fr/mtseedepiatlas/jbrowse/?data=Mtruncatula.
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8
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Yadav N, Nagar P, Rakhi R, Kumar A, Rai A, Mustafiz A. Transcript profiling of Polycomb gene family in Oryza sativa indicates their abiotic stress-specific response. Funct Integr Genomics 2022; 22:1211-1227. [PMID: 36197542 DOI: 10.1007/s10142-022-00906-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/16/2022] [Accepted: 09/27/2022] [Indexed: 11/27/2022]
Abstract
The precise regulation of gene expression is required for the determination of cell fate, differentiation, and developmental programs in eukaryotes. The Polycomb Group (PcG) genes are the key transcriptional regulators that constitute the repressive system, with two major protein complexes, Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2). Previous studies have demonstrated the significance of these proteins in regulation of normal growth and development processes. However, the role of PcG in adaptation of crops to abiotic stress is still not well understood. The present study aimed to a comprehensive genome-wide identification of the PcG gene family in one of the economically important staple crops, Oryza sativa. Here, a total of 14 PcG genes have been identified, which were distributed over eight chromosomes. Protein structure analysis revealed that both the complexes have distinct domain and motifs that are conserved within the complexes. In silico promoter analysis showed that PcG gene promoters have abundance of abiotic stress-responsive elements. RNA-seq based expression analysis revealed that PcG genes are differentially expressed in different tissues and responded variably in different environmental stress. Validation of gene expression by qRT-PCR showed that most of the genes were upregulated at 1-h time point in shoot tissue and at 24-h time point in root tissue under the drought and salinity stress conditions. These findings provide important and extensive information on the PcG family of O. sativa, which will pave the path for understanding their role in stress signaling in plants.
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Affiliation(s)
- Nikita Yadav
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, 110021, India
| | - Preeti Nagar
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, 110021, India
| | - R Rakhi
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, 110021, India
| | - Ashish Kumar
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, 110021, India
| | - Archita Rai
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, 110021, India
| | - Ananda Mustafiz
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, 110021, India.
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9
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Dasgupta P, Prasad P, Bag SK, Chaudhuri S. Dynamicity of histone H3K27ac and H3K27me3 modifications regulate the cold-responsive gene expression in Oryza sativa L. ssp. indica. Genomics 2022; 114:110433. [PMID: 35863676 DOI: 10.1016/j.ygeno.2022.110433] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/15/2022] [Accepted: 07/10/2022] [Indexed: 11/29/2022]
Abstract
Cultivated in tropical and subtropical regions, Oryza sativa L. ssp. indica is largely affected by cold-stress, especially at the seedling stage. The present model of the stress-responsive regulatory network in plants entails the role of genetic and epigenetic factors in stress-responsive gene expression. Despite extensive transcriptomic studies, the regulation of various epigenetic factors in plants cold-stress response is less explored. The present study addresses the effect of genome-wide changes of H3K27 modifications on gene expression in IR64 rice, during cold-stress. Our results suggest a positive correlation between the changes in H3K27 modifications and stress-responsive gene activation in indica rice. Cold-induced enrichment of H3K27 acetylation promotes nucleosomal rearrangement, thereby facilitating the accessibility of the transcriptional machinery at the stress-responsive loci for transcription activation. Although H3K27ac exhibits uniform distribution throughout the loci of enriched genes; occupancy of H3K27me3 is biased to intergenic regions. Integration of the ChIP-seq data with transcriptome indicated that upregulation of stress-responsive TFs, photosynthesis-TCA-related, water-deficit genes, redox and JA signalling components, was associated with differential changes of H3K27ac and H3K27me3 levels. Furthermore, cold-induced upregulation of histone acetyltransferases and downregulation of DNA methyltransferases was noted through the antagonistic switch of H3K27ac and H3K27me3. Moreover, motif analysis of H3K27ac and H3K27me3 enriched regions are associated with putative stress responsive transcription factors binding sites, GAGA element and histone H3K27demethylase. Collectively our analysis suggests that differential expression of various chromatin and DNA modifiers coupled with increased H3K27ac and depleted H3K27me3 increases DNA accessibility, thereby promoting transcription of the cold-responsive genes in indica rice.
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Affiliation(s)
- Pratiti Dasgupta
- Division of Plant Biology, Bose Institute, Unified Academic Campus, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, WB, India
| | - Priti Prasad
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
| | - Sumit K Bag
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, Unified Academic Campus, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, WB, India.
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10
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Kumari P, Khan S, Wani IA, Gupta R, Verma S, Alam P, Alaklabi A. Unravelling the Role of Epigenetic Modifications in Development and Reproduction of Angiosperms: A Critical Appraisal. Front Genet 2022; 13:819941. [PMID: 35664328 PMCID: PMC9157814 DOI: 10.3389/fgene.2022.819941] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 12/28/2022] Open
Abstract
Epigenetics are the heritable changes in gene expression patterns which occur without altering DNA sequence. These changes are reversible and do not change the sequence of the DNA but can alter the way in which the DNA sequences are read. Epigenetic modifications are induced by DNA methylation, histone modification, and RNA-mediated mechanisms which alter the gene expression, primarily at the transcriptional level. Such alterations do control genome activity through transcriptional silencing of transposable elements thereby contributing toward genome stability. Plants being sessile in nature are highly susceptible to the extremes of changing environmental conditions. This increases the likelihood of epigenetic modifications within the composite network of genes that affect the developmental changes of a plant species. Genetic and epigenetic reprogramming enhances the growth and development, imparts phenotypic plasticity, and also ensures flowering under stress conditions without changing the genotype for several generations. Epigenetic modifications hold an immense significance during the development of male and female gametophytes, fertilization, embryogenesis, fruit formation, and seed germination. In this review, we focus on the mechanism of epigenetic modifications and their dynamic role in maintaining the genomic integrity during plant development and reproduction.
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Affiliation(s)
- Priyanka Kumari
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Sajid Khan
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Ishfaq Ahmad Wani
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Renu Gupta
- Division of Soil Sciences & Agricultural Chemistry, Faculty of Agriculture Sher e Kashmir University of Agricultural Sciences and Technology, Chatha, India
| | - Susheel Verma
- Department of Botany, University of Jammu, Jammu, India
- *Correspondence: Susheel Verma,
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University (PSAU), Alkharj, Saudi Arabia
| | - Abdullah Alaklabi
- Department of Biology, College of Science, University of Bisha, Bisha, Saudi Arabia
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11
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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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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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Volynkin VA, Likhovskoi VV, Vasylyk IA, Rybachenko NA, Lushchay EA, Gorislavets SM, Volodin VA, Risovannaya VI, Potokina EK. Introgressions of Vitis rotundifolia Michx. to obtain grapevine genotypes with complex resistance to biotic and abiotic stresses. Vavilovskii Zhurnal Genet Selektsii 2021; 25:693-700. [PMID: 34950841 PMCID: PMC8649748 DOI: 10.18699/vj21.079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/19/2022] Open
Abstract
Vitis rotundifolia Michx. is one of the species of the family Vitaceae, with resistance to both biotic and abiotic stresses. The present study reports new scientif ic knowledge about the inheritance of resistance to downy mildew, powdery mildew and frost by V. vinifera varieties from V. rotundifolia. Recombinant lines of three hybrid populations from the crossing of the maternal genotype ♀M. 31-77-10 with V. rotundifolia hybrids were used as the object of the study. As a result of laboratory screening, more than 40 % of recombinants of the ♀M. 31-77-10 × × [DRX-M5-734 + DRX-M5-753 + DRX-M5-790] population showed a high degree of frost resistance (-24 °C), while 6 % of transgressive recombinants were characterized by a very high degree of resistance (-27 °С). The maternal genotype ♀M. 31-77-10 does not carry alleles of resistance to powdery mildew at the Run1 locus and in the f ield suffers from powdery mildew much more than the paternal genotypes. The prevalence of powdery mildew on vegetative organs in the three recombinant populations over the years varies on average between 3.2-17.1, 0.3-17.7 and 0.6-5.2 %, respectively. As a result, almost all recombinant genotypes that received a resistant allele from the paternal genome are highly resistant to powdery mildew.
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Affiliation(s)
- V A Volynkin
- All-Russian National Research Institute of Viticulture and Winemaking "Magarach" of the Russian Academy of Sciences, Yalta, Russia
| | - V V Likhovskoi
- All-Russian National Research Institute of Viticulture and Winemaking "Magarach" of the Russian Academy of Sciences, Yalta, Russia
| | - I A Vasylyk
- All-Russian National Research Institute of Viticulture and Winemaking "Magarach" of the Russian Academy of Sciences, Yalta, Russia
| | - N A Rybachenko
- All-Russian National Research Institute of Viticulture and Winemaking "Magarach" of the Russian Academy of Sciences, Yalta, Russia
| | - E A Lushchay
- All-Russian National Research Institute of Viticulture and Winemaking "Magarach" of the Russian Academy of Sciences, Yalta, Russia
| | - S M Gorislavets
- All-Russian National Research Institute of Viticulture and Winemaking "Magarach" of the Russian Academy of Sciences, Yalta, Russia
| | - V A Volodin
- All-Russian National Research Institute of Viticulture and Winemaking "Magarach" of the Russian Academy of Sciences, Yalta, Russia
| | - V I Risovannaya
- All-Russian National Research Institute of Viticulture and Winemaking "Magarach" of the Russian Academy of Sciences, Yalta, Russia
| | - E K Potokina
- All-Russian National Research Institute of Viticulture and Winemaking "Magarach" of the Russian Academy of Sciences, Yalta, Russia
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