1
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Obermeyer S, Kapoor H, Markusch H, Grasser KD. Transcript elongation by RNA polymerase II in plants: factors, regulation and impact on gene expression. Plant J 2024; 118:645-656. [PMID: 36703573 DOI: 10.1111/tpj.16115] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Transcriptional elongation by RNA polymerase II (RNAPII) through chromatin is a dynamic and highly regulated step of eukaryotic gene expression. A combination of transcript elongation factors (TEFs) including modulators of RNAPII activity and histone chaperones facilitate efficient transcription on nucleosomal templates. Biochemical and genetic analyses, primarily performed in Arabidopsis, provided insight into the contribution of TEFs to establish gene expression patterns during plant growth and development. In addition to summarising the role of TEFs in plant gene expression, we emphasise in our review recent advances in the field. Thus, mechanisms are presented how aberrant intragenic transcript initiation is suppressed by repressing transcriptional start sites within coding sequences. We also discuss how transcriptional interference of ongoing transcription with neighbouring genes is prevented. Moreover, it appears that plants make no use of promoter-proximal RNAPII pausing in the way mammals do, but there are nucleosome-defined mechanism(s) that determine the efficiency of mRNA synthesis by RNAPII. Accordingly, a still growing number of processes related to plant growth, development and responses to changing environmental conditions prove to be regulated at the level of transcriptional elongation.
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Affiliation(s)
- Simon Obermeyer
- Cell Biology and Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Henna Kapoor
- Cell Biology and Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Hanna Markusch
- Cell Biology and Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology and Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
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2
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Simon L, Probst AV. Maintenance and dynamic reprogramming of chromatin organization during development. Plant J 2024; 118:657-670. [PMID: 36700345 DOI: 10.1111/tpj.16119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 06/17/2023]
Abstract
Controlled transcription of genes is critical for cell differentiation and development. Gene expression regulation therefore involves a multilayered control from nucleosome composition in histone variants and their post-translational modifications to higher-order folding of chromatin fibers and chromatin interactions in nuclear space. Recent technological advances have allowed gaining insight into these mechanisms, the interplay between local and higher-order chromatin organization, and the dynamic changes that occur during stress response and developmental transitions. In this review, we will discuss chromatin organization from the nucleosome to its three-dimensional structure in the nucleus, and consider how these different layers of organization are maintained during the cell cycle or rapidly reprogrammed during development.
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Affiliation(s)
- Lauriane Simon
- 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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3
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Li J, Gu W, Yang Z, Chen J, Yi F, Li T, Li J, Zhou Y, Guo Y, Song W, Lai J, Zhao H. ZmELP1, an Elongator complex subunit, is required for the maintenance of histone acetylation and RNA Pol II phosphorylation in maize kernels. Plant Biotechnol J 2024; 22:1251-1268. [PMID: 38098341 PMCID: PMC11022810 DOI: 10.1111/pbi.14262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 01/26/2024]
Abstract
The Elongator complex was originally identified as an interactor of hyperphosphorylated RNA polymerase II (RNAPII) in yeast and has histone acetyltransferase (HAT) activity. However, the genome-wide regulatory roles of Elongator on transcriptional elongation and histone acetylation remain unclear. We characterized a maize miniature seed mutant, mn7 and map-based cloning revealed that Mn7 encodes one of the subunits of the Elongator complex, ZmELP1. ZmELP1 deficiency causes marked reductions in the kernel size and weight. Molecular analyses showed that ZmELP1 interacts with ZmELP3, which is required for H3K14 acetylation (H3K14ac), and Elongator complex subunits interact with RNA polymerase II (RNAPII) C-terminal domain (CTD). Genome-wide analyses indicated that loss of ZmELP1 leads to a significant decrease in the deposition of H3K14ac and the CTD of phosphorylated RNAPII on Ser2 (Ser2P). These chromatin changes positively correlate with global transcriptomic changes. ZmELP1 mutation alters the expression of genes involved in transcriptional regulation and kernel development. We also showed that the decrease of Ser2P depends on the deposition of Elongator complex-mediated H3K14ac. Taken together, our results reveal an important role of ZmELP1 in the H3K14ac-dependent transcriptional elongation, which is critical for kernel development.
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Affiliation(s)
- Jianrui Li
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Wei Gu
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
- Crop Breeding, Cultivation Research Institution/CIMMYT‐China Specialty Maize Research Center, Shanghai Engineering Research Center of Specialty Maize, Shanghai Key Laboratory of Agricultural Genetics and BreedingShanghai Academy of Agricultural SciencesShanghaiChina
| | - Zhijia Yang
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jian Chen
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Fei Yi
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
- Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Tong Li
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jingrui Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yue Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Weibin Song
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Haiming Zhao
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
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4
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Chen Y, Guo P, Dong Z. The role of histone acetylation in transcriptional regulation and seed development. Plant Physiol 2024; 194:1962-1979. [PMID: 37979164 DOI: 10.1093/plphys/kiad614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/09/2023] [Accepted: 10/29/2023] [Indexed: 11/20/2023]
Abstract
Histone acetylation is highly conserved across eukaryotes and has been linked to gene activation since its discovery nearly 60 years ago. Over the past decades, histone acetylation has been evidenced to play crucial roles in plant development and response to various environmental cues. Emerging data indicate that histone acetylation is one of the defining features of "open chromatin," while the role of histone acetylation in transcription remains controversial. In this review, we briefly describe the discovery of histone acetylation, the mechanism of histone acetylation regulating transcription in yeast and mammals, and summarize the research progress of plant histone acetylation. Furthermore, we also emphasize the effect of histone acetylation on seed development and its potential use in plant breeding. A comprehensive knowledge of histone acetylation might provide new and more flexible research perspectives to enhance crop yield and stress resistance.
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Affiliation(s)
- Yan Chen
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Peiguo Guo
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
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5
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Crawford T, Siebler L, Sulkowska A, Nowack B, Jiang L, Pan Y, Lämke J, Kappel C, Bäurle I. The Mediator kinase module enhances polymerase activity to regulate transcriptional memory after heat stress in Arabidopsis. EMBO J 2024; 43:437-461. [PMID: 38228917 PMCID: PMC10897291 DOI: 10.1038/s44318-023-00024-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/18/2024] Open
Abstract
Plants are often exposed to recurring adverse environmental conditions in the wild. Acclimation to high temperatures entails transcriptional responses, which prime plants to better withstand subsequent stress events. Heat stress (HS)-induced transcriptional memory results in more efficient re-induction of transcription upon recurrence of heat stress. Here, we identified CDK8 and MED12, two subunits of the kinase module of the transcription co-regulator complex, Mediator, as promoters of heat stress memory and associated histone modifications in Arabidopsis. CDK8 is recruited to heat-stress memory genes by HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2). Like HSFA2, CDK8 is largely dispensable for the initial gene induction upon HS, and its function in transcriptional memory is thus independent of primary gene activation. In addition to the promoter and transcriptional start region of target genes, CDK8 also binds their 3'-region, where it may promote elongation, termination, or rapid re-initiation of RNA polymerase II (Pol II) complexes during transcriptional memory bursts. Our work presents a complex role for the Mediator kinase module during transcriptional memory in multicellular eukaryotes, through interactions with transcription factors, chromatin modifications, and promotion of Pol II efficiency.
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Affiliation(s)
- Tim Crawford
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Lara Siebler
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Bryan Nowack
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Li Jiang
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Yufeng Pan
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jörn Lämke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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6
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Hisanaga T, Wu S, Schafran P, Axelsson E, Akimcheva S, Dolan L, Li F, Berger F. The ancestral chromatin landscape of land plants. New Phytol 2023; 240:2085-2101. [PMID: 37823324 PMCID: PMC10952607 DOI: 10.1111/nph.19311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/29/2023] [Indexed: 10/13/2023]
Abstract
Recent studies have shown that correlations between chromatin modifications and transcription vary among eukaryotes. This is the case for marked differences between the chromatin of the moss Physcomitrium patens and the liverwort Marchantia polymorpha. Mosses and liverworts diverged from hornworts, altogether forming the lineage of bryophytes that shared a common ancestor with land plants. We aimed to describe chromatin in hornworts to establish synapomorphies across bryophytes and approach a definition of the ancestral chromatin organization of land plants. We used genomic methods to define the 3D organization of chromatin and map the chromatin landscape of the model hornwort Anthoceros agrestis. We report that nearly half of the hornwort transposons were associated with facultative heterochromatin and euchromatin and formed the center of topologically associated domains delimited by protein coding genes. Transposons were scattered across autosomes, which contrasted with the dense compartments of constitutive heterochromatin surrounding the centromeres in flowering plants. Most of the features observed in hornworts are also present in liverworts or in mosses but are distinct from flowering plants. Hence, the ancestral genome of bryophytes was likely a patchwork of units of euchromatin interspersed within facultative and constitutive heterochromatin. We propose this genome organization was ancestral to land plants.
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Affiliation(s)
- Tetsuya Hisanaga
- Gregor Mendel InstituteAustrian Academy of Sciences, Vienna BioCenterDr. Bohr‐Gasse 3Vienna1030Austria
| | - Shuangyang Wu
- Gregor Mendel InstituteAustrian Academy of Sciences, Vienna BioCenterDr. Bohr‐Gasse 3Vienna1030Austria
| | | | - Elin Axelsson
- Gregor Mendel InstituteAustrian Academy of Sciences, Vienna BioCenterDr. Bohr‐Gasse 3Vienna1030Austria
| | - Svetlana Akimcheva
- Gregor Mendel InstituteAustrian Academy of Sciences, Vienna BioCenterDr. Bohr‐Gasse 3Vienna1030Austria
| | - Liam Dolan
- Gregor Mendel InstituteAustrian Academy of Sciences, Vienna BioCenterDr. Bohr‐Gasse 3Vienna1030Austria
| | - Fay‐Wei Li
- Boyce Thompson InstituteIthacaNY14853USA
- Plant Biology SectionCornell UniversityIthacaNY14853USA
| | - Frédéric Berger
- Gregor Mendel InstituteAustrian Academy of Sciences, Vienna BioCenterDr. Bohr‐Gasse 3Vienna1030Austria
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7
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Jamge B, Lorković ZJ, Axelsson E, Osakabe A, Shukla V, Yelagandula R, Akimcheva S, Kuehn AL, Berger F. Histone variants shape chromatin states in Arabidopsis. eLife 2023; 12:RP87714. [PMID: 37467143 PMCID: PMC10393023 DOI: 10.7554/elife.87714] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
How different intrinsic sequence variations and regulatory modifications of histones combine in nucleosomes remain unclear. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in the Arabidopsis thaliana genome. We showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role of the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of constitutive heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks.
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Affiliation(s)
- Bhagyshree Jamge
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Vienna BioCenterViennaAustria
| | - Zdravko J Lorković
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Akihisa Osakabe
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-kuTokyoJapan
- PRESTO, Japan Science and Technology Agency, HonchoKawaguchiJapan
| | - Vikas Shukla
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Vienna BioCenterViennaAustria
| | - Ramesh Yelagandula
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Institute of Molecular Biotechnology, IMBA, Dr. Bohr-Gasse 3ViennaAustria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Annika Luisa Kuehn
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
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8
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Marquardt S, Petrillo E, Manavella PA. Cotranscriptional RNA processing and modification in plants. Plant Cell 2023; 35:1654-1670. [PMID: 36259932 PMCID: PMC10226594 DOI: 10.1093/plcell/koac309] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/14/2022] [Indexed: 05/30/2023]
Abstract
The activities of RNA polymerases shape the epigenetic landscape of genomes with profound consequences for genome integrity and gene expression. A fundamental event during the regulation of eukaryotic gene expression is the coordination between transcription and RNA processing. Most primary RNAs mature through various RNA processing and modification events to become fully functional. While pioneering results positioned RNA maturation steps after transcription ends, the coupling between the maturation of diverse RNA species and their transcription is becoming increasingly evident in plants. In this review, we discuss recent advances in our understanding of the crosstalk between RNA Polymerase II, IV, and V transcription and nascent RNA processing of both coding and noncoding RNAs.
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Affiliation(s)
- Sebastian Marquardt
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Ezequiel Petrillo
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, C1428EHA, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
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9
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Jin Y, Ivanov M, Dittrich AN, Nelson AD, Marquardt S. LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis. EMBO J 2023:e110921. [PMID: 37051749 DOI: 10.15252/embj.2022110921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 04/14/2023] Open
Abstract
How the noncoding genome affects cellular functions is a key biological question. A particular challenge is to distinguish the effects of noncoding DNA elements from long noncoding RNAs (lncRNAs) that coincide at the same loci. Here, we identified the flowering-associated intergenic lncRNA (FLAIL) in Arabidopsis through early flowering flail mutants. Expression of FLAIL RNA from a different chromosomal location in combination with strand-specific RNA knockdown characterized FLAIL as a trans-acting RNA molecule. FLAIL directly binds to differentially expressed target genes that control flowering via RNA-DNA interactions through conserved sequence motifs. FLAIL interacts with protein and RNA components of the spliceosome to affect target mRNA expression through co-transcriptional alternative splicing (AS) and linked chromatin regulation. In the absence of FLAIL, splicing defects at the direct FLAIL target flowering gene LACCASE 8 (LAC8) correlated with reduced mRNA expression. Double mutant analyses support a model where FLAIL-mediated splicing of LAC8 promotes its mRNA expression and represses flowering. Our study suggests lncRNAs as accessory components of the spliceosome that regulate AS and gene expression to impact organismal development.
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Affiliation(s)
- Yu Jin
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Maxim Ivanov
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Sebastian Marquardt
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
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10
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Zhong Z, Wang Y, Wang M, Yang F, Thomas QA, Xue Y, Zhang Y, Liu W, Jami-Alahmadi Y, Xu L, Feng S, Marquardt S, Wohlschlegel JA, Ausin I, Jacobsen SE. Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis. Nat Commun 2022; 13:6970. [PMID: 36379930 PMCID: PMC9666630 DOI: 10.1038/s41467-022-34648-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display a preference for the HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefers the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated histone deposition for proper epigenetic regulation of the genome.
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Affiliation(s)
- Zhenhui Zhong
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Yafei Wang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ming Wang
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Fan Yang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Quentin Angelo Thomas
- grid.5254.60000 0001 0674 042XCopenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Yan Xue
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Yaxin Zhang
- grid.256111.00000 0004 1760 2876Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Wanlu Liu
- grid.512487.dZhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400 Zhejiang China
| | - Yasaman Jami-Alahmadi
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA 90095 USA
| | - Linhao Xu
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, 06466 Germany
| | - Suhua Feng
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, CA 90095 USA
| | - Sebastian Marquardt
- grid.5254.60000 0001 0674 042XCopenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - James A. Wohlschlegel
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA 90095 USA
| | - Israel Ausin
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Steven E. Jacobsen
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095 USA
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11
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Zhou Q, Sun Y, Zhao X, Yu Y, Cheng W, Lu L, Chu Z, Chen X. Bromodomain-containing factor GTE4 regulates Arabidopsis immune response. BMC Biol 2022; 20:256. [DOI: 10.1186/s12915-022-01454-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/31/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Plants are continuously challenged with biotic stress from environmental pathogens, and precise regulation of defense responses is critical for plant survival. Defense systems require considerable amounts of energy and resources, impairing plant growth, and plant hormones controlling transcriptional regulation play essential roles in establishing the appropriate balance between defense response to pathogens and growth. Chromatin regulators modulating gene transcription are broadly involved in regulating stress-responsive genes. However, which chromatin factors are involved in coordinating hormone signaling and immune responses in plants, and their functional mechanisms, remains unclear. Here, we identified a role of bromodomain-containing protein GTE4 in negatively regulating defense responses in Arabidopsis thaliana.
Results
GTE4 mainly functions as activator of gene expression upon infection with Pseudomonas syringe. Genome-wide profiling of GTE4 occupancy shows that GTE4 tends to bind to active genes, including ribosome biogenesis related genes and maintains their high expression levels during pathogen infection. However, GTE4 is also able to repress gene expression. GTE4 binds to and represses jasmonate biosynthesis gene OPR3. Disruption of GTE4 results in overaccumulation of jasmonic acid (JA) and enhanced JA-responsive gene expression. Unexpectedly, over-accumulated JA content in gte4 mutant is coupled with downregulation of JA-mediated immune defense genes and upregulation of salicylic acid (SA)-mediated immune defense genes, and enhanced resistance to Pseudomonas, likely through a noncanonical pathway.
Conclusions
Overall, we identified a new role of the chromatin factor GTE4 as negative regulator of plant immune response through inhibition of JA biosynthesis, which in turn noncanonically activates the defense system against Pseudomonas. These findings provide new knowledge of chromatic regulation of plant hormone signaling during defense responses.
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12
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Bhatia G, Prall W, Sharma B, Gregory BD. Covalent RNA modifications and their budding crosstalk with plant epigenetic processes. Curr Opin Plant Biol 2022; 69:102287. [PMID: 35988352 DOI: 10.1016/j.pbi.2022.102287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/29/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Our recent cognizance of diverse RNA classes undergoing dynamic covalent chemical modifications (or epitranscriptomic marks) in plants has provided fresh insight into the underlying molecular mechanisms of gene expression regulation. Comparatively, epigenetic marks comprising heritable modifications of DNA and histones have been extensively studied in plants and their impact on plant gene expression is quite established. Based on our growing knowledge of the plant epitranscriptome and epigenome, it is logical to explore how the two regulatory layers intermingle to intricately determine gene expression levels underlying key biological processes such as development and response to stress. Herein, we focus on the emerging evidence of crosstalk between the plant epitranscriptome with epigenetic regulation involving DNA modification, histone modification, and non-coding RNAs.
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Affiliation(s)
- Garima Bhatia
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, Philadelphia, PA 19104, USA
| | - Wil Prall
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, Philadelphia, PA 19104, USA
| | - Bishwas Sharma
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, Philadelphia, PA 19104, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, Philadelphia, PA 19104, USA.
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13
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Oya S, Takahashi M, Takashima K, Kakutani T, Inagaki S. Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation. Nat Commun 2022; 13:4521. [PMID: 35953471 PMCID: PMC9372134 DOI: 10.1038/s41467-022-32165-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 06/01/2021] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Mono-, di-, and trimethylation of histone H3 lysine 4 (H3K4me1/2/3) are associated with transcription, yet it remains controversial whether H3K4me1/2/3 promote or result from transcription. Our previous characterizations of Arabidopsis H3K4 demethylases suggest roles for H3K4me1 in transcription. However, the control of H3K4me1 remains unexplored in Arabidopsis, in which no methyltransferase for H3K4me1 has been identified. Here, we identify three Arabidopsis methyltransferases that direct H3K4me1. Analyses of their genome-wide localization using ChIP-seq and machine learning reveal that one of the enzymes cooperates with the transcription machinery, while the other two are associated with specific histone modifications and DNA sequences. Importantly, these two types of localization patterns are also found for the other H3K4 methyltransferases in Arabidopsis and mice. These results suggest that H3K4me1/2/3 are established and maintained via interplay with transcription as well as inputs from other chromatin features, presumably enabling elaborate gene control. Methylation of histone H3 lysine 4 is associated with transcription. Here the authors describe three Arabidopsis methyltransferases that direct H3K4me1 and propose that one methyltransferase works co-transcriptionally while the others are recruited to genomic and epigenomic features.
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Affiliation(s)
- Satoyo Oya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | | | | | - Tetsuji Kakutani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. .,National Institute of Genetics, Mishima, Japan.
| | - Soichi Inagaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. .,PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
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14
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Hu H, Du J. Structure and mechanism of histone methylation dynamics in Arabidopsis. Curr Opin Plant Biol 2022; 67:102211. [PMID: 35452951 DOI: 10.1016/j.pbi.2022.102211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Histone methylation plays a central role in regulating chromatin state and gene expression in Arabidopsis and is involved in a variety of physiological and developmental processes. Dynamic regulation of histone methylation relies on both histone methyltransferase "writer" and histone demethylases "eraser" proteins. In this review, we focus on the four major histone methylation modifications in Arabidopsis H3, H3K4, H3K9, H3K27, and H3K36, and summarize current knowledge of the dynamic regulation of these modifications, with an emphasis on the biochemical and structural perspectives of histone methyltransferases and demethylases.
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Affiliation(s)
- Hongmiao Hu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
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15
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Lapin D, Johanndrees O, Wu Z, Li X, Parker JE. Molecular innovations in plant TIR-based immunity signaling. Plant Cell 2022; 34:1479-1496. [PMID: 35143666 PMCID: PMC9153377 DOI: 10.1093/plcell/koac035] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/27/2022] [Indexed: 05/19/2023]
Abstract
A protein domain (Toll and Interleukin-1 receptor [TIR]-like) with homology to animal TIRs mediates immune signaling in prokaryotes and eukaryotes. Here, we present an overview of TIR evolution and the molecular versatility of TIR domains in different protein architectures for host protection against microbial attack. Plant TIR-based signaling emerges as being central to the potentiation and effectiveness of host defenses triggered by intracellular and cell-surface immune receptors. Equally relevant for plant fitness are mechanisms that limit potent TIR signaling in healthy tissues but maintain preparedness for infection. We propose that seed plants evolved a specialized protein module to selectively translate TIR enzymatic activities to defense outputs, overlaying a more general function of TIRs.
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Affiliation(s)
- Dmitry Lapin
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
- Author for correspondence: (D.L.), (J.E.P.)
| | - Oliver Johanndrees
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Zhongshou Wu
- Michael Smith Labs and Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Labs and Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Duesseldorf 40225, Germany
- Author for correspondence: (D.L.), (J.E.P.)
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16
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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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17
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Szádeczky-Kardoss I, Szaker H, Verma R, Darkó É, Pettkó-Szandtner A, Silhavy D, Csorba T. Elongation factor TFIIS is essential for heat stress adaptation in plants. Nucleic Acids Res 2022; 50:1927-1950. [PMID: 35100405 PMCID: PMC8886746 DOI: 10.1093/nar/gkac020] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 06/03/2021] [Revised: 12/11/2021] [Accepted: 01/06/2022] [Indexed: 12/22/2022] Open
Abstract
Elongation factor TFIIS (transcription factor IIS) is structurally and biochemically probably the best characterized elongation cofactor of RNA polymerase II. However, little is known about TFIIS regulation or its roles during stress responses. Here, we show that, although TFIIS seems unnecessary under optimal conditions in Arabidopsis, its absence renders plants supersensitive to heat; tfIIs mutants die even when exposed to sublethal high temperature. TFIIS activity is required for thermal adaptation throughout the whole life cycle of plants, ensuring both survival and reproductive success. By employing a transcriptome analysis, we unravel that the absence of TFIIS makes transcriptional reprogramming sluggish, and affects expression and alternative splicing pattern of hundreds of heat-regulated transcripts. Transcriptome changes indirectly cause proteotoxic stress and deterioration of cellular pathways, including photosynthesis, which finally leads to lethality. Contrary to expectations of being constantly present to support transcription, we show that TFIIS is dynamically regulated. TFIIS accumulation during heat occurs in evolutionary distant species, including the unicellular alga Chlamydomonas reinhardtii, dicot Brassica napus and monocot Hordeum vulgare, suggesting that the vital role of TFIIS in stress adaptation of plants is conserved.
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Affiliation(s)
- István Szádeczky-Kardoss
- Genetics and Biotechnology Institute, MATE University, Szent-Györgyi A. u. 4, 2100 Gödöllő, Hungary
| | - Henrik Mihály Szaker
- Genetics and Biotechnology Institute, MATE University, Szent-Györgyi A. u. 4, 2100 Gödöllő, Hungary
- Faculty of Natural Sciences, Eötvös Lóránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62., 6726 Szeged, Hungary
| | - Radhika Verma
- Genetics and Biotechnology Institute, MATE University, Szent-Györgyi A. u. 4, 2100 Gödöllő, Hungary
- Doctorate School of Biological Sciences, MATE University, Pater Karoly u. 1, 2100 Gödöllő, Hungary
| | - Éva Darkó
- Agricultural Institute, Centre for Agricultural Research, Brunszvik u. 2., 2462 Martonvásár, Hungary
| | | | - Dániel Silhavy
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62., 6726 Szeged, Hungary
| | - Tibor Csorba
- Genetics and Biotechnology Institute, MATE University, Szent-Györgyi A. u. 4, 2100 Gödöllő, Hungary
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18
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Abstract
Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene.
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Affiliation(s)
- Andrzej T Wierzbicki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Todd Blevins
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France;
| | - Szymon Swiezewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland;
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19
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Friedrich T, Oberkofler V, Trindade I, Altmann S, Brzezinka K, Lämke J, Gorka M, Kappel C, Sokolowska E, Skirycz A, Graf A, Bäurle I. Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis. Nat Commun 2021; 12:3426. [PMID: 34103516 PMCID: PMC8187452 DOI: 10.1038/s41467-021-23786-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/13/2021] [Indexed: 02/05/2023] Open
Abstract
Adaptive plasticity in stress responses is a key element of plant survival strategies. For instance, moderate heat stress (HS) primes a plant to acquire thermotolerance, which allows subsequent survival of more severe HS conditions. Acquired thermotolerance is actively maintained over several days (HS memory) and involves the sustained induction of memory-related genes. Here we show that FORGETTER3/ HEAT SHOCK TRANSCRIPTION FACTOR A3 (FGT3/HSFA3) is specifically required for physiological HS memory and maintaining high memory-gene expression during the days following a HS exposure. HSFA3 mediates HS memory by direct transcriptional activation of memory-related genes after return to normal growth temperatures. HSFA3 binds HSFA2, and in vivo both proteins form heteromeric complexes with additional HSFs. Our results indicate that only complexes containing both HSFA2 and HSFA3 efficiently promote transcriptional memory by positively influencing histone H3 lysine 4 (H3K4) hyper-methylation. In summary, our work defines the major HSF complex controlling transcriptional memory and elucidates the in vivo dynamics of HSF complexes during somatic stress memory.
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Affiliation(s)
- Thomas Friedrich
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Vicky Oberkofler
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Inês Trindade
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Simone Altmann
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany ,grid.8241.f0000 0004 0397 2876Present Address: School of Life Sciences, University of Dundee, Dundee, UK
| | - Krzysztof Brzezinka
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jörn Lämke
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michal Gorka
- grid.418390.70000 0004 0491 976XMax-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Christian Kappel
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ewelina Sokolowska
- grid.418390.70000 0004 0491 976XMax-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Aleksandra Skirycz
- grid.418390.70000 0004 0491 976XMax-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Alexander Graf
- grid.418390.70000 0004 0491 976XMax-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Isabel Bäurle
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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20
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Inagaki S, Takahashi M, Takashima K, Oya S, Kakutani T. Chromatin-based mechanisms to coordinate convergent overlapping transcription. Nat Plants 2021; 7:295-302. [PMID: 33649596 DOI: 10.1038/s41477-021-00868-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
In eukaryotic genomes, the transcription units of genes often overlap with other protein-coding and/or noncoding transcription units1,2. In such intertwined genomes, the coordinated transcription of nearby or overlapping genes would be important to ensure the integrity of genome function3-6; however, the mechanisms underlying this coordination are largely unknown. Here, we show in Arabidopsis thaliana that genes with convergent orientation of transcription are major sources of antisense transcripts and that these genes transcribed on both strands are regulated by a putative Lysine-Specific Demethylase 1 family histone demethylase, FLOWERING LOCUS D (FLD)7,8. Our genome-wide chromatin profiling revealed that FLD, as well as its associating factor LUMINIDEPENDENS9, downregulates histone H3K4me1 in regions with convergent overlapping transcription. FLD localizes to actively transcribed genes, where it colocalizes with elongating RNA polymerase II phosphorylated at the Ser2 or Ser5 sites. Genome-wide transcription analyses suggest that FLD-mediated H3K4me1 removal negatively regulates the transcription of genes with high levels of antisense transcription. Furthermore, the effect of FLD on transcription dynamics is antagonized by DNA topoisomerase I. Our study reveals chromatin-based mechanisms to cope with overlapping transcription, which may occur by modulating DNA topology. This global mechanism to cope with overlapping transcription could be co-opted for specific epigenetic processes, such as cellular memory of responses to the environment10.
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Affiliation(s)
- Soichi Inagaki
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Tokyo, Japan.
- National Institute of Genetics, Mishima, Japan.
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Shonankokusaimura, Hayama, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
| | | | | | - Satoyo Oya
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Tokyo, Japan
| | - Tetsuji Kakutani
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Tokyo, Japan
- National Institute of Genetics, Mishima, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Shonankokusaimura, Hayama, Japan
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21
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Gowthaman U, García-Pichardo D, Jin Y, Schwarz I, Marquardt S. DNA Processing in the Context of Noncoding Transcription. Trends Biochem Sci 2020; 45:1009-1021. [DOI: 10.1016/j.tibs.2020.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/17/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022]
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22
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Tognacca RS, Kubaczka MG, Servi L, Rodríguez FS, Godoy Herz MA, Petrillo E. Light in the transcription landscape: chromatin, RNA polymerase II and splicing throughout Arabidopsis thaliana's life cycle. Transcription 2020; 11:117-133. [PMID: 32748694 DOI: 10.1080/21541264.2020.1796473] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plants have a high level of developmental plasticity that allows them to respond and adapt to changes in the environment. Among the environmental cues, light controls almost every aspect of A. thaliana's life cycle, including seed maturation, seed germination, seedling de-etiolation and flowering time. Light signals induce massive reprogramming of gene expression, producing changes in RNA polymerase II transcription, alternative splicing, and chromatin state. Since splicing reactions occur mainly while transcription takes place, the regulation of RNAPII transcription has repercussions in the splicing outcomes. This cotranscriptional nature allows a functional coupling between transcription and splicing, in which properties of the splicing reactions are affected by the transcriptional process. Chromatin landscapes influence both transcription and splicing. In this review, we highlight, summarize and discuss recent progress in the field to gain a comprehensive insight on the cross-regulation between chromatin state, RNAPII transcription and splicing decisions in plants, with a special focus on light-triggered responses. We also introduce several examples of transcription and splicing factors that could be acting as coupling factors in plants. Unravelling how these connected regulatory networks operate, can help in the design of better crops with higher productivity and tolerance.
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Affiliation(s)
- Rocío S Tognacca
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - M Guillermina Kubaczka
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Lucas Servi
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Florencia S Rodríguez
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina.,Departamento De Biodiversidad Y Biología Experimental, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Micaela A Godoy Herz
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Ezequiel Petrillo
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
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