1
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Mahana Y, Ariyoshi M, Nozawa RS, Shibata S, Nagao K, Obuse C, Shirakawa M. Structural evidence for protein-protein interaction between the non-canonical methyl-CpG-binding domain of SETDB proteins and C11orf46. Structure 2024; 32:304-315.e5. [PMID: 38159574 DOI: 10.1016/j.str.2023.12.001] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/26/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
SETDB1 and SETDB2 mediate trimethylation of histone H3 lysine 9 (H3K9), an epigenetic hallmark of repressive chromatin. They contain a non-canonical methyl-CpG-binding domain (MBD) and bifurcated SET domain, implying interplay between H3K9 trimethylation and DNA methylation in SETDB functions. Here, we report the crystal structure of human SETDB2 MBD bound to the cysteine-rich domain of a zinc-binding protein, C11orf46. SETDB2 MBD comprises the conserved MBD core and a unique N-terminal extension. Although the MBD core has the conserved basic concave surface for DNA binding, it utilizes it for recognition of the cysteine-rich domain of C11orf46. This interaction involves the conserved arginine finger motif and the unique N-terminal extension of SETDB2 MBD, with a contribution from intermolecular β-sheet formation. Thus, the non-canonical MBD of SETDB1/2 seems to have lost methylated DNA-binding ability but gained a protein-protein interaction surface. Our findings provide insight into the molecular assembly of SETDB-associated repression complexes.
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Affiliation(s)
- Yutaka Mahana
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Mariko Ariyoshi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Ryu-Suke Nozawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Sachiko Shibata
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Koji Nagao
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan.
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2
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Wang S, Wang M, Ichino L, Boone BA, Zhong Z, Papareddy RK, Lin EK, Yun J, Feng S, Jacobsen SE. MBD2 couples DNA methylation to transposable element silencing during male gametogenesis. Nat Plants 2024; 10:13-24. [PMID: 38225352 PMCID: PMC10808059 DOI: 10.1038/s41477-023-01599-3] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/27/2023] [Indexed: 01/17/2024]
Abstract
DNA methylation is an essential component of transposable element (TE) silencing, yet the mechanism by which methylation causes transcriptional repression remains poorly understood1-5. Here we study the Arabidopsis thaliana Methyl-CpG Binding Domain (MBD) proteins MBD1, MBD2 and MBD4 and show that MBD2 acts as a TE repressor during male gametogenesis. MBD2 bound chromatin regions containing high levels of CG methylation, and MBD2 was capable of silencing the FWA gene when tethered to its promoter. MBD2 loss caused activation at a small subset of TEs in the vegetative cell of mature pollen without affecting DNA methylation levels, demonstrating that MBD2-mediated silencing acts strictly downstream of DNA methylation. TE activation in mbd2 became more significant in the mbd5 mbd6 and adcp1 mutant backgrounds, suggesting that MBD2 acts redundantly with other silencing pathways to repress TEs. Overall, our study identifies MBD2 as a methyl reader that acts downstream of DNA methylation to silence TEs during male gametogenesis.
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Affiliation(s)
- Shuya Wang
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ming Wang
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lucia Ichino
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brandon A Boone
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zhenhui Zhong
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ranjith K Papareddy
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Evan K Lin
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jaewon Yun
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Suhua Feng
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Steven E Jacobsen
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA.
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA.
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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3
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Boone BA, Ichino L, Wang S, Gardiner J, Yun J, Jami-Alahmadi Y, Sha J, Mendoza CP, Steelman BJ, van Aardenne A, Kira-Lucas S, Trentchev I, Wohlschlegel JA, Jacobsen SE. ACD15, ACD21, and SLN regulate the accumulation and mobility of MBD6 to silence genes and transposable elements. Sci Adv 2023; 9:eadi9036. [PMID: 37967186 PMCID: PMC10651127 DOI: 10.1126/sciadv.adi9036] [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: 05/24/2023] [Accepted: 10/13/2023] [Indexed: 11/17/2023]
Abstract
DNA methylation mediates silencing of transposable elements and genes in part via recruitment of the Arabidopsis MBD5/6 complex, which contains the methyl-CpG binding domain (MBD) proteins MBD5 and MBD6, and the J-domain containing protein SILENZIO (SLN). Here, we characterize two additional complex members: α-crystalline domain (ACD) containing proteins ACD15 and ACD21. We show that they are necessary for gene silencing, bridge SLN to the complex, and promote higher-order multimerization of MBD5/6 complexes within heterochromatin. These complexes are also highly dynamic, with the mobility of MBD5/6 complexes regulated by the activity of SLN. Using a dCas9 system, we demonstrate that tethering the ACDs to an ectopic site outside of heterochromatin can drive a massive accumulation of MBD5/6 complexes into large nuclear bodies. These results demonstrate that ACD15 and ACD21 are critical components of the gene-silencing MBD5/6 complex and act to drive the formation of higher-order, dynamic assemblies at CG methylation (meCG) sites.
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Affiliation(s)
- Brandon A. Boone
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Lucia Ichino
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Shuya Wang
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jason Gardiner
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jaewon Yun
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jihui Sha
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Cristy P. Mendoza
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bailey J. Steelman
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Aliya van Aardenne
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sophia Kira-Lucas
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Isabelle Trentchev
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - James A. Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Steven E. Jacobsen
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute (HHMI), University of California Los Angeles, Los Angeles, CA 90095, USA
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4
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Kovalchuk I. Role of Epigenetic Factors in Response to Stress and Establishment of Somatic Memory of Stress Exposure in Plants. Plants (Basel) 2023; 12:3667. [PMID: 37960024 PMCID: PMC10648063 DOI: 10.3390/plants12213667] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023]
Abstract
All species are well adapted to their environment. Stress causes a magnitude of biochemical and molecular responses in plants, leading to physiological or pathological changes. The response to various stresses is genetically predetermined, but is also controlled on the epigenetic level. Most plants are adapted to their environments through generations of exposure to all elements. Many plant species have the capacity to acclimate or adapt to certain stresses using the mechanism of priming. In most cases, priming is a somatic response allowing plants to deal with the same or similar stress more efficiently, with fewer resources diverted from growth and development. Priming likely relies on multiple mechanisms, but the differential expression of non-coding RNAs, changes in DNA methylation, histone modifications, and nucleosome repositioning play a crucial role. Specifically, we emphasize the role of BRM/CHR17, BRU1, FGT1, HFSA2, and H2A.Z proteins as positive regulators, and CAF-1, MOM1, DDM1, and SGS3 as potential negative regulators of somatic stress memory. In this review, we will discuss the role of epigenetic factors in response to stress, priming, and the somatic memory of stress exposures.
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Affiliation(s)
- Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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5
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Boone BA, Ichino L, Wang S, Gardiner J, Yun J, Jami-Alahmadi Y, Sha J, Mendoza CP, Steelman BJ, van Aardenne A, Kira-Lucas S, Trentchev I, Wohlschlegel JA, Jacobsen SE. ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements. bioRxiv 2023:2023.08.23.554494. [PMID: 37662299 PMCID: PMC10473691 DOI: 10.1101/2023.08.23.554494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
DNA methylation mediates silencing of transposable elements and genes in part via recruitment of the Arabidopsis MBD5/6 complex, which contains the methyl-CpG-binding domain (MBD) proteins MBD5 and MBD6, and the J-domain containing protein SILENZIO (SLN). Here we characterize two additional complex members: α-crystalline domain containing proteins ACD15 and ACD21. We show that they are necessary for gene silencing, bridge SLN to the complex, and promote higher order multimerization of MBD5/6 complexes within heterochromatin. These complexes are also highly dynamic, with the mobility of complex components regulated by the activity of SLN. Using a dCas9 system, we demonstrate that tethering the ACDs to an ectopic site outside of heterochromatin can drive massive accumulation of MBD5/6 complexes into large nuclear bodies. These results demonstrate that ACD15 and ACD21 are critical components of gene silencing complexes that act to drive the formation of higher order, dynamic assemblies.
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Affiliation(s)
- Brandon A. Boone
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- These authors contributed equally
| | - Lucia Ichino
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- These authors contributed equally
| | - Shuya Wang
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jason Gardiner
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Translational Plant Biology, Department of Biology, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - Jaewon Yun
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jihui Sha
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Cristy P. Mendoza
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bailey J. Steelman
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Aliya van Aardenne
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sophia Kira-Lucas
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Isabelle Trentchev
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - James A. Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Steven E. Jacobsen
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute (HHMI), UCLA; Los Angeles, CA 90095, USA
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6
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Zhou J, Lei X, Shafiq S, Zhang W, Li Q, Li K, Zhu J, Dong Z, He XJ, Sun Q. DDM1-mediated R-loop resolution and H2A.Z exclusion facilitates heterochromatin formation in Arabidopsis. Sci Adv 2023; 9:eadg2699. [PMID: 37566662 PMCID: PMC10421056 DOI: 10.1126/sciadv.adg2699] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/13/2023] [Indexed: 08/13/2023]
Abstract
Programmed constitutive heterochromatin silencing is essential for eukaryotic genome regulation, yet the initial step of this process is ambiguous. A large proportion of R-loops (RNA:DNA hybrids) had been unexpectedly identified within Arabidopsis pericentromeric heterochromatin with unknown functions. Through a genome-wide R-loop profiling screen, we find that DDM1 (decrease in DNA methylation 1) is the primary restrictor of pericentromeric R-loops via its RNA:DNA helicase activity. Low levels of pericentromeric R-loops resolved by DDM1 cotranscriptionally can facilitate constitutive heterochromatin silencing. Furthermore, we demonstrate that DDM1 physically excludes histone H2A variant H2A.Z and promotes H2A.W deposition for faithful heterochromatin initiation soon after R-loop clearance. The dual functions of DDM1 in R-loop resolution and H2A.Z eviction are essential for sperm nuclei structure maintenance in mature pollen. Our work unravels the cotranscriptional R-loop resolution coupled with accurate H2A variants deposition is the primary step of constitutive heterochromatin silencing in Arabidopsis, which might be conserved across eukaryotes.
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Affiliation(s)
- Jincong Zhou
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xue Lei
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Sarfraz Shafiq
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Qin Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jiafu Zhu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhicheng Dong
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xin-jian He
- National Institute of Biological Sciences, Beijing, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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7
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Liang J, Li X, Wen Y, Wu X, Wang H, Li D, Song F. Genome-Wide Characterization of the Methyl CpG Binding Domain-Containing Proteins in Watermelon and Functional Analysis of Their Roles in Disease Resistance Through Ectopic Overexpression in Arabidopsis thaliana. Front Plant Sci 2022; 13:886965. [PMID: 35615127 PMCID: PMC9125323 DOI: 10.3389/fpls.2022.886965] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Methyl-CPG-Binding Domain (MBD) proteins play important roles in plant growth, development, and stress responses. The present study characterized the MBD families in watermelon and other cucurbit plants regarding the gene numbers and structures, phylogenetic and syntenic relationships, evolution events, and conserved domain organization of the MBD proteins. The watermelon ClMBD proteins were found to be localized in nucleus, and ClMBD2 and ClMBD3 interacted with ClIDM2 and ClIDM3. ClMBD2 bound to DNA harboring methylated CG sites but not to DNA with methylated CHG and CHH sites in vitro. The ClMBD genes exhibited distinct expression patterns in watermelon plants after SA and MeJA treatment and after infection by fungal pathogens Fusarium oxysporum f.sp. niveum and Didymella bryoniae. Overexpression of ClMBD2, ClMBD3, or ClMBD5 in Arabidopsis resulted in attenuated resistance against Botrytis cinerea, accompanied by down-regulated expression of AtPDF1.2 and increased accumulation of H2O2 upon B. cinerea infection. Overexpression of ClMBD1 and ClMBD2 led to down-regulated expression of AtPR1 and decreased resistance while overexpression of ClMBD5 resulted in up-regulated expression of AtPR1 and increased resistance against Pseudomonas syringae pv. tomato DC3000. Transcriptome analysis revealed that overexpression of ClMBD2 in Arabidopsis up-regulated the expression of a small set of genes that negatively regulate Arabidopsis immunity. These data suggest the importance of some ClMBD genes in plant immunity and provide the possibility to improve plant immunity through modification of specific ClMBD genes.
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Affiliation(s)
- Jiayu Liang
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaodan Li
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ya Wen
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xinyi Wu
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Hui Wang
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Dayong Li
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fengming Song
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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8
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Mahana Y, Ohki I, Walinda E, Morimoto D, Sugase K, Shirakawa M. Structural Insights into Methylated DNA Recognition by the Methyl-CpG Binding Domain of MBD6 from Arabidopsis thaliana. ACS Omega 2022; 7:3212-3221. [PMID: 35128234 PMCID: PMC8811898 DOI: 10.1021/acsomega.1c04917] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/24/2021] [Indexed: 06/01/2023]
Abstract
Cytosine methylation is an epigenetic modification essential for formation of mature heterochromatin, gene silencing, and genomic stability. In plants, methylation occurs not only at cytosine bases in CpG but also in CpHpG and CpHpH contexts, where H denotes A, T, or C. Methyl-CpG binding domain (MBD) proteins, which recognize symmetrical methyl-CpG dinucleotides and act as gene repressors in mammalian cells, are also present in plant cells, although their structural and functional properties still remain poorly understood. To fill this gap, in this study, we determined the solution structure of the MBD domain of the MBD6 protein from Arabidopsis thaliana and investigated its binding properties to methylated DNA by binding assays and an in-depth NMR spectroscopic analysis. The AtMBD6 MBD domain folds into a canonical MBD structure in line with its binding specificity toward methyl-CpG and possesses a DNA binding interface similar to mammalian MBD domains. Intriguingly, however, the binding affinity of the AtMBD6 MBD domain toward methyl-CpG-containing DNA was found to be much lower than that of known mammalian MBD domains. The main difference arises from the absence of positively charged residues in AtMBD6 that supposedly interact with the DNA backbone as seen in mammalian MBD/methyl-CpG-containing DNA complexes. Taken together, we have established a structural basis for methyl-CpG recognition by AtMBD6 to develop a deeper understanding how MBD proteins work as mediators of epigenetic signals in plant cells.
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Affiliation(s)
- Yutaka Mahana
- Department
of Molecular Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Izuru Ohki
- Institute
for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Erik Walinda
- Graduate
School of Medicine, Kyoto University, Yoshida Konoe-Cho, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Daichi Morimoto
- Department
of Molecular Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Kenji Sugase
- Department
of Molecular Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Masahiro Shirakawa
- Department
of Molecular Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
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9
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Wu Z, Chen S, Zhou M, Jia L, Li Z, Zhang X, Min J, Liu K. Family-wide Characterization of Methylated DNA Binding Ability of Arabidopsis MBDs. J Mol Biol 2021; 434:167404. [PMID: 34919920 DOI: 10.1016/j.jmb.2021.167404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/15/2021] [Accepted: 12/07/2021] [Indexed: 01/28/2023]
Abstract
13 MBD-containing genes (AtMBD1-13) have been identified in Arabidopsis thaliana so far, however, their DNA binding ability is still controversial. Here, we systematically measured the DNA binding affinities of these MBDs by ITC and EMSA binding assays, except for those of pseudogenes AtMBD3 and AtMBD13, and found that only AtMBD6 and AtMBD7 function as methylated DNA readers. We also found that the MBD of AtMBD5 exhibits very weak binding to methylated DNA compared to that of AtMBD6. To further investigate the structural basis of AtMBDs in binding to methylated DNA, we determined the complex structure of the AtMBD6 MBD with a 12mer mCG DNA and the apo structure of the AtMBD5 MBD. Structural analysis coupled with mutagenesis studies indicated that, in addition to the conserved arginine fingers contributing to the DNA binding specificity, the residues located in the loop1 and α1 are also essential for the methylated DNA binding of these MBDs in Arabidopsis thaliana, which explains why AtMBD5 MBD and the other AtMBDs display very weak or no binding to methylated DNA. Thus, our study here systematically demonstrates the DNA binding ability of the MBDs in Arabidopsis thaliana, which also provides a general guideline in understanding the DNA binding ability of the MBDs in other plants as a whole.
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Affiliation(s)
- Zhibin Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Sizhuo Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Mengqi Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Lingbo Jia
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Zhenhua Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Xiyou Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
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10
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Talbert PB, Henikoff S. Remodeller-variant tag team slams transposons. Nat Cell Biol 2021; 23:297-8. [PMID: 33833427 DOI: 10.1038/s41556-021-00661-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Ichino L, Boone BA, Strauskulage L, Harris CJ, Kaur G, Gladstone MA, Tan M, Feng S, Jami-Alahmadi Y, Duttke SH, Wohlschlegel JA, Cheng X, Redding S, Jacobsen SE. MBD5 and MBD6 couple DNA methylation to gene silencing through the J-domain protein SILENZIO. Science 2021; 372:eabg6130. [PMID: 34083448 PMCID: PMC8639832 DOI: 10.1126/science.abg6130] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/20/2021] [Indexed: 01/02/2023]
Abstract
DNA methylation is associated with transcriptional repression of eukaryotic genes and transposons, but the downstream mechanism of gene silencing is largely unknown. Here we describe two Arabidopsis methyl-CpG binding domain proteins, MBD5 and MBD6, that are recruited to chromatin by recognition of CG methylation, and redundantly repress a subset of genes and transposons without affecting DNA methylation levels. These methyl-readers recruit a J-domain protein, SILENZIO, that acts as a transcriptional repressor in loss-of-function and gain-of-function experiments. J-domain proteins often serve as co-chaperones with HSP70s. Indeed, we found that SILENZIO's conserved J-domain motif was required for its interaction with HSP70s and for its silencing function. These results uncover an unprecedented role of a molecular chaperone J-domain protein in gene silencing downstream of DNA methylation.
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Affiliation(s)
- Lucia Ichino
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Brandon A Boone
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Luke Strauskulage
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - C Jake Harris
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Gundeep Kaur
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew A Gladstone
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Maverick Tan
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sascha H Duttke
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Steven E Jacobsen
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA.
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute (HHMI), UCLA, Los Angeles, CA 90095, USA
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12
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Osakabe A, Jamge B, Axelsson E, Montgomery SA, Akimcheva S, Kuehn AL, Pisupati R, Lorković ZJ, Yelagandula R, Kakutani T, Berger F. The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W. Nat Cell Biol 2021; 23:391-400. [PMID: 33833428 DOI: 10.1038/s41556-021-00658-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 03/01/2021] [Indexed: 12/16/2022]
Abstract
Mobile transposable elements (TEs) not only participate in genome evolution but also threaten genome integrity. In healthy cells, TEs that encode all of the components that are necessary for their mobility are specifically silenced, yet the precise mechanism remains unknown. Here, we characterize the mechanism used by a conserved class of chromatin remodelers that prevent TE mobility. In the Arabidopsis chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1), we identify two conserved binding domains for the histone variant H2A.W, which marks plant heterochromatin. DDM1 is necessary and sufficient for the deposition of H2A.W onto potentially mobile TEs, yet does not act on TE fragments or host protein-coding genes. DDM1-mediated H2A.W deposition changes the properties of chromatin, resulting in the silencing of TEs and, therefore, prevents their mobility. This distinct mechanism provides insights into the interplay between TEs and their host in the contexts of evolution and disease, and potentiates innovative strategies for targeted gene silencing.
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Affiliation(s)
- Akihisa Osakabe
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Bhagyshree Jamge
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Elin Axelsson
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Svetlana Akimcheva
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Annika Luisa Kuehn
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Rahul Pisupati
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Zdravko J Lorković
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Ramesh Yelagandula
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Tetsuji Kakutani
- National Institute of Genetics, Mishima, Japan
- Department of Genetics, School of Life science, The Graduate University of Advanced Studies (SOKENDAI), Mishima, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
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13
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Khadka J, Pesok A, Grafi G. Plant Histone HTB (H2B) Variants in Regulating Chromatin Structure and Function. Plants (Basel) 2020; 9:E1435. [PMID: 33113795 PMCID: PMC7694166 DOI: 10.3390/plants9111435] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/09/2020] [Accepted: 10/23/2020] [Indexed: 02/07/2023]
Abstract
Besides chemical modification of histone proteins, chromatin dynamics can be modulated by histone variants. Most organisms possess multiple genes encoding for core histone proteins, which are highly similar in amino acid sequence. The Arabidopsis thaliana genome contains 11 genes encoding for histone H2B (HTBs), 13 for H2A (HTAs), 15 for H3 (HTRs), and 8 genes encoding for histone H4 (HFOs). The finding that histone variants may be expressed in specific tissues and/or during specific developmental stages, often displaying specific nuclear localization and involvement in specific nuclear processes suggests that histone variants have evolved to carry out specific functions in regulating chromatin structure and function and might be important for better understanding of growth and development and particularly the response to stress. In this review, we will elaborate on a group of core histone proteins in Arabidopsis, namely histone H2B, summarize existing data, and illuminate the potential function of H2B variants in regulating chromatin structure and function in Arabidopsis thaliana.
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Affiliation(s)
| | | | - Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel; (J.K.); (A.P.)
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14
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Abstract
In plants, DNA methylation occurs in distinct sequence contexts, including CG, CHG, and CHH. Thus, plants have developed a surprisingly diverse set of DNA methylation readers to cope with an extended repertoire of methylated sites. The Arabidopsis genome contains twelve Methyl-Binding Domain proteins (MBD), and nine SET and RING finger-associated (SRA) domain containing proteins belonging to the SUVH clade, in addition to three homologs of UHRF1, namely VIM1-3, all containing SRA domains. In this review, we will highlight several research questions that remain unresolved with respect to the function of plant DNA methylation readers, which can have both de novo demethylase and maintenance activity. We argue that maintenance of CG methylation in plants likely involved actors not found in their mammalian counterparts, and that new evidence suggests significant reprogramming of DNA methylation during plant reproduction as an important new development in the field.
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Affiliation(s)
- Daniel Grimanelli
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, 911 Avenue Agropolis, 34394, Montpellier, France.
| | - Mathieu Ingouff
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, 911 Avenue Agropolis, 34394, Montpellier, France.
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15
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Nie WF, Lei M, Zhang M, Tang K, Huang H, Zhang C, Miki D, Liu P, Yang Y, Wang X, Zhang H, Lang Z, Liu N, Xu X, Yelagandula R, Zhang H, Wang Z, Chai X, Andreucci A, Yu JQ, Berger F, Lozano-Duran R, Zhu JK. Histone acetylation recruits the SWR1 complex to regulate active DNA demethylation in Arabidopsis. Proc Natl Acad Sci U S A 2019; 116:16641-50. [PMID: 31363048 DOI: 10.1073/pnas.1906023116] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Active DNA demethylation is critical for controlling the DNA methylomes in plants and mammals. However, little is known about how DNA demethylases are recruited to target loci, and the involvement of chromatin marks in this process. Here, we identify 2 components of the SWR1 chromatin-remodeling complex, PIE1 and ARP6, as required for ROS1-mediated DNA demethylation, and discover 2 SWR1-associated bromodomain-containing proteins, AtMBD9 and nuclear protein X1 (NPX1). AtMBD9 and NPX1 recognize histone acetylation marks established by increased DNA methylation 1 (IDM1), a known regulator of DNA demethylation, redundantly facilitating H2A.Z deposition at IDM1 target loci. We show that at some genomic regions, H2A.Z and DNA methylation marks coexist, and H2A.Z physically interacts with ROS1 to regulate DNA demethylation and antisilencing. Our results unveil a mechanism through which DNA demethylases can be recruited to specific target loci exhibiting particular histone marks, providing a conceptual framework to understand how chromatin marks regulate DNA demethylation.
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16
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Iwakawa N, Mahana Y, Ono A, Ohki I, Walinda E, Morimoto D, Sugase K, Shirakawa M. Backbone and side-chain resonance assignments of the methyl-CpG-binding domain of MBD6 from Arabidopsis thaliana. Biomol NMR Assign 2019; 13:59-62. [PMID: 30242623 DOI: 10.1007/s12104-018-9851-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 04/23/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
Epigenetic regulation is essential to various biological phenomena such as cell differentiation and cancer. DNA methylation is one of the most important epigenetic signals, as it is directly involved in gene silencing of transposable elements, genomic imprinting, and chromosome X inactivation. To mediate these processes, methyl-CpG-binding domain (MBD) proteins recognize specific signals encoded in the form of DNA methylation patterns. AtMBD6, one of the 12 MBD proteins in Arabidopsis thaliana, shares a high sequential homology in the MBD domain with mammalian MBD proteins, but a detailed characterization of its structural and functional properties remains elusive. Here, we report the 1H, 13C, and 15N resonance assignments of the isolated MBD domain of AtMBD6. Analysis of the chemical shift data implied that the MBD domain of AtMBD6 has a secondary structure similar to that of mammalian MeCP2, while the β-strands β1 and β3 of AtMBD6 were found to be longer than those of MeCP2. The structural differences provide insight into the different recognition mechanisms of methylated DNA by plant and mammalian MBDs. The assignments reported here will aid further analyses such as titration experiments and three-dimensional structure determination using NMR to yield a detailed characterization of the interaction between AtMBD6 and methylated DNAs.
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Affiliation(s)
- Naoto Iwakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Yutaka Mahana
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Arina Ono
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Izuru Ohki
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-Cho, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan.
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17
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Parida AP, Sharma A, Sharma AK. AtMBD4: A methylated DNA binding protein negatively regulates a subset of phosphate starvation genes. J Biosci 2019; 44:14. [PMID: 30837365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA methylation is an important epigenetic modification that governs transcriptional regulation. The methylation mark is read by a special class of proteins called methyl-CpG-binding domain proteins. The role of DNA methylation has been found in X-chromosome inactivation, genomic imprinting, transposon silencing, and self-incompatibility. Recently, remodeling of global DNA methylation was demonstrated in Arabidopsis during low phosphate availability. The present study reports that AtMBD4 gene of Arabidopsis negatively regulates phosphate starvation. The T-DNA insertion mutation at the AtMBD4 locus exhibited altered root architecture as compared to wild-type plants. Using microarray hybridization and analysis, an increased transcript accumulation of 242 genes was observed in the mutant. Many of these genes were related to phosphate transporters and transcription factors, involved in phosphate starvation response. Comparison of data of atmbd4 mutant with publicly available microarray data of phosphate starvation response indicated the role of AtMBD4 protein in phosphate starvation response. Further, promoter analysis of up-regulated genes suggested that cis-regulatory elements like MBS, W-box, and B1BS are more prominent in the promoters of up-regulated genes. Upon performing a methylation-specific PCR, a decreased DNA methylation in the promoter regions of up-regulated genes was observed. The accumulation of anthocyanin and inorganic phosphate in the atmbd4 mutant was found to be higher than the wild-type plant. Altered root morphology, up-regulation of phosphate starvation-induced genes in atmbd4 mutant suggests that AtMBD4 negatively regulates the phosphate starvation response.
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18
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Parida AP, Sharma A, Sharma AK. AtMBD4: A methylated DNA binding protein negatively regulates a subset of phosphate starvation genes. J Biosci 2019; 44. [DOI: 10.1007/s12038-018-9843-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Parida AP, Raghuvanshi U, Pareek A, Singh V, Kumar R, Sharma AK. Genome-wide analysis of genes encoding MBD domain-containing proteins from tomato suggest their role in fruit development and abiotic stress responses. Mol Biol Rep 2018; 45:2653-2669. [PMID: 30350236 DOI: 10.1007/s11033-018-4435-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/10/2018] [Indexed: 01/25/2023]
Abstract
In tomato, DNA methylation has an inhibitory effect on fruit ripening. The inhibition of DNA methyltransferase by 5-azacytidine results in premature fruit ripening. Methyl CpG binding domain (MBD) proteins are the readers of DNA methylation marks and help in the recruitment of chromatin-modifying enzymes which affect gene expression. Therefore, we investigate their contribution during fruit development. In this study, we identified and analyzed 18 putative genes of Solanum lycopersicum and Solanum pimpinellifolium encoding MBD proteins. We also identified tomato MBD syntelogs in Capsicum annum and Solanum tuberosum. Sixty-three MBD genes identified from four different species of solanaceae were classified into three groups. An analysis of the conserved domains in these proteins identified additional domains along with MBD motif. The transcript profiling of tomato MBDs in wild-type and two non-ripening mutants, rin and Nr, indicated constructive information regarding their involvement during fruit development. When we performed a stage-specific expression analysis during fruit ripening, a gradual decrease in transcript accumulation in the wild-type fruit was detected. However, a very low expression was observed in the ripening mutants. Furthermore, many ethylene-responsive cis-elements were found in SlMBD gene promoters, and some of them were induced in the presence of exogenous ethylene. Further, we detected the possible role of these MBDs in abiotic stresses. We found that few genes were differentially expressed under various abiotic stress conditions. Our results provide an evidence of the involvement of the tomato MBDs in fruit ripening and abiotic stress responses, which would be helpful in further studies on these genes in tomato fruit ripening.
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Affiliation(s)
- Adwaita Prasad Parida
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Utkarsh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Amit Pareek
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Vijendra Singh
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Rahul Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
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20
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Abstract
In situ nucleus and chromatin analyses rely on microscopy imaging that benefits from versatile, efficient fluorescent probes and proteins for static or live imaging. Yet the broad choice in imaging instruments offered to the user poses orientation problems. Which imaging instrument should be used for which purpose? What are the main caveats and what are the considerations to best exploit each instrument's ability to obtain informative and high-quality images? How to infer quantitative information on chromatin or nuclear organization from microscopy images? In this review, we present an overview of common, fluorescence-based microscopy systems and discuss recently developed super-resolution microscopy systems, which are able to bridge the resolution gap between common fluorescence microscopy and electron microscopy. We briefly present their basic principles and discuss their possible applications in the field, while providing experience-based recommendations to guide the user toward best-possible imaging. In addition to raw data acquisition methods, we discuss commercial and noncommercial processing tools required for optimal image presentation and signal evaluation in two and three dimensions.
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Affiliation(s)
- Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
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21
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Saroha M, Singroha G, Sharma M, Mehta G, Gupta OP, Sharma P. sRNA and epigenetic mediated abiotic stress tolerance in plants. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40502-017-0330-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ghan R, Petereit J, Tillett RL, Schlauch KA, Toubiana D, Fait A, Cramer GR. The common transcriptional subnetworks of the grape berry skin in the late stages of ripening. BMC Plant Biol 2017; 17:94. [PMID: 28558655 PMCID: PMC5450095 DOI: 10.1186/s12870-017-1043-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 09/20/2016] [Accepted: 05/22/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND Wine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage. RESULTS To better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed. RNA-seq analysis identified approximately 2000 common differentially expressed genes for all seven cultivars across four different berry sugar levels (20 to 26 °Brix). Network analyses, both a posteriori (standard) and a priori (gene co-expression network analysis), were used to elucidate transcriptional subnetworks and hub genes associated with traits in the berry skins of the late stages of berry ripening. These independent approaches revealed genes involved in photosynthesis, catabolism, and nucleotide metabolism. The transcript abundance of most photosynthetic genes declined with increasing sugar levels in the berries. The transcript abundance of other processes increased such as nucleic acid metabolism, chromosome organization and lipid catabolism. Weighted gene co-expression network analysis (WGCNA) identified 64 gene modules that were organized into 12 subnetworks of three modules or more and six higher order gene subnetworks. Some gene subnetworks were highly correlated with sugar levels and some subnetworks were highly enriched in the chloroplast and nucleus. The petal R package was utilized independently to construct a true small-world and scale-free complex gene co-expression network model. A subnetwork of 216 genes with the highest connectivity was elucidated, consistent with the module results from WGCNA. Hub genes in these subnetworks were identified including numerous members of the core circadian clock, RNA splicing, proteolysis and chromosome organization. An integrated model was constructed linking light sensing with alternative splicing, chromosome remodeling and the circadian clock. CONCLUSIONS A common set of differentially expressed genes and gene subnetworks from seven different cultivars were examined in the skin of the late stages of grapevine berry ripening. A densely connected gene subnetwork was elucidated involving a complex interaction of berry senescent processes (autophagy), catabolism, the circadian clock, RNA splicing, proteolysis and epigenetic regulation. Hypotheses were induced from these data sets involving sugar accumulation, light, autophagy, epigenetic regulation, and fruit development. This work provides a better understanding of berry development and the transcriptional processes involved in the late stages of ripening.
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Affiliation(s)
- Ryan Ghan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
| | - Juli Petereit
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - Richard L. Tillett
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - Karen A. Schlauch
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - David Toubiana
- Telekom Innovation, Laboratories and Cyber Security Research Center, Department of Information, Systems Engineering, Ben Gurion University, Beer Sheva, Israel
| | - Aaron Fait
- Ben-Gurion University of the Negev, Jacob Blaustein Institutes for Desert Research, 84990 Midreshet Ben-Gurion, Israel
| | - Grant R. Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
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23
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Li D, Palanca AMS, Won SY, Gao L, Feng Y, Vashisht AA, Liu L, Zhao Y, Liu X, Wu X, Li S, Le B, Kim YJ, Yang G, Li S, Liu J, Wohlschlegel JA, Guo H, Mo B, Chen X, Law JA. The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status. eLife 2017; 6. [PMID: 28452714 PMCID: PMC5462541 DOI: 10.7554/elife.19893] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 07/25/2016] [Accepted: 04/24/2017] [Indexed: 12/23/2022] Open
Abstract
DNA methylation is associated with gene silencing in eukaryotic organisms. Although pathways controlling the establishment, maintenance and removal of DNA methylation are known, relatively little is understood about how DNA methylation influences gene expression. Here we identified a METHYL-CpG-BINDING DOMAIN 7 (MBD7) complex in Arabidopsis thaliana that suppresses the transcriptional silencing of two LUCIFERASE (LUC) reporters via a mechanism that is largely downstream of DNA methylation. Although mutations in components of the MBD7 complex resulted in modest increases in DNA methylation concomitant with decreased LUC expression, we found that these hyper-methylation and gene expression phenotypes can be genetically uncoupled. This finding, along with genome-wide profiling experiments showing minimal changes in DNA methylation upon disruption of the MBD7 complex, places the MBD7 complex amongst a small number of factors acting downstream of DNA methylation. This complex, however, is unique as it functions to suppress, rather than enforce, DNA methylation-mediated gene silencing. DOI:http://dx.doi.org/10.7554/eLife.19893.001
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Affiliation(s)
- Dongming Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,School of Life Sciences, Lanzhou University, Lanzhou, China.,State Key Laboratory of Plant Cell and Chromosome Engineering, Hebei Collaboration Innovation Center for Cell Signaling, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Ana Marie S Palanca
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - So Youn Won
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Lei Gao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, Shenzhen, China
| | - Ying Feng
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,State Key Laboratory of Protein and Plant Gene research, College of Life Sciences, Peking University, Beijing, China
| | - Ajay A Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, United States
| | - Li Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Yuanyuan Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Xigang Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,State Key Laboratory of Plant Cell and Chromosome Engineering, Hebei Collaboration Innovation Center for Cell Signaling, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Xiuyun Wu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,Laboratory of Molecular Biology and Protein Science, Laboratory of the Ministry of Education, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, China
| | - Shaofang Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Brandon Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Yun Ju Kim
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Guodong Yang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Shengben Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Jinyuan Liu
- Laboratory of Molecular Biology and Protein Science, Laboratory of the Ministry of Education, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, China
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, United States
| | - Hongwei Guo
- State Key Laboratory of Protein and Plant Gene research, College of Life Sciences, Peking University, Beijing, China
| | - Beixin Mo
- College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, Shenzhen, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,Howard Hughes Medical Institute, University of California, Riverside, United States
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
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Parida AP, Sharma A, Sharma AK. AtMBD6, a methyl CpG binding domain protein, maintains gene silencing in Arabidopsis by interacting with RNA binding proteins. J Biosci 2017; 42:57-68. [PMID: 28229965 DOI: 10.1007/s12038-016-9658-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
DNA methylation, mediated by double-stranded RNA, is a conserved epigenetic phenomenon that protects a genome from transposons, silences unwanted genes and has a paramount function in plant or animal development. Methyl CpG binding domain proteins are members of a class of proteins that bind to methylated DNA. The Arabidopsis thaliana genome encodes 13 methyl CpG binding domain (MBD) proteins, but the molecular/biological functions of most of these proteins are still not clear. In the present study, we identified four proteins that interact with AtMBD6. Interestingly, three of them contain RNA binding domains and are co-localized with AtMBD6 in the nucleus. The interacting partners includes AtRPS2C (a 40S ribosomal protein), AtNTF2 (nuclear transport factor 2) and AtAGO4 (Argonoute 4). The fourth protein that physically interacts with AtMBD6 is a histone-modifying enzyme, histone deacetylase 6 (AtHDA6), which is a known component of the RNA-mediated gene silencing system. Analysis of genomic DNA methylation in the atmbd6, atrps2c and atntf2 mutants, using methylation-sensitive PCR detected decreased DNA methylation at miRNA/siRNA producing loci, pseudogenes and other targets of RNA-directed DNA methylation. Our results indicate that AtMBD6 is involved in RNA-mediated gene silencing and it binds to RNA binding proteins like AtRPS2C, AtAGO4 and AtNTF2. AtMBD6 also interacts with histone deacetylase AtHDA6 that might have a role in chromatin condensation at the targets of RdDM.
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25
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Givaty-Rapp Y, Yadav NS, Khan A, Grafi G. S1-Type Endonuclease 2 in Dedifferentiating Arabidopsis Protoplasts: Translocation to the Nucleus in Senescing Protoplasts Is Associated with De-Glycosylation. PLoS One 2017; 12:e0170067. [PMID: 28068427 PMCID: PMC5222596 DOI: 10.1371/journal.pone.0170067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/28/2016] [Indexed: 11/18/2022] Open
Abstract
Cell dedifferentiation characterizes the transition of leaf cells to protoplasts and is accompanied by global chromatin decondensation. Here we show that in Arabidopsis, chromocentric chromatin undergoes prompt and gradual decondensation upon protoplasting. We hypothesized that prompt chromatin decondensation is unlikely to be driven solely by epigenetic means and other factors might be involved. We investigated the possibility that S1-type endonucleases are involved in prompt chromatin decondensation via their capability to target and cleave unpaired regions within superhelical DNA, leading to chromatin relaxation. We showed that the expression and activity of the S1-type endonuclease 2 (ENDO2) is upregulated in dedifferentiating protoplasts concomitantly with chromatin decondensation. Mutation of the ENDO2 gene did not block or delay chromocentric chromatin decondensation upon protoplasting. Further study showed that ENDO2 subcellular localization is essentially cytoplasmic (endoplasmic reticulum-associated) in healthy cells, but often localized to the nucleus and in senescing/dying cells it was associated with fragmented nuclei. Using in gel nuclease assays we identified two ENDO2 variants, designated N1 (cytoplasmic variant) and N2 (cytoplasmic and nuclear variant), and based on their capability to bind concanavalin A (ConA), they appear to be glycosylated and de-glycosylated (or decorated with ConA non-binding sugars), respectively. Our data showed that the genome is responding promptly to acute stress (protoplasting) by acquiring decondensation state, which is not dependent on ENDO2 activity. ENDO2 undergoes de-glycosylation and translocation to the nucleus where it is involved in early stages of cell death probably by introducing double strand DNA breaks into superhelical DNA leading to local chromatin relaxation and fragmentation of nuclei.
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Affiliation(s)
- Yemima Givaty-Rapp
- French Associates Institute of Agriculture and Biotechnology of Drylands, The Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Narendra Singh Yadav
- French Associates Institute of Agriculture and Biotechnology of Drylands, The Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Asif Khan
- French Associates Institute of Agriculture and Biotechnology of Drylands, The Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Gideon Grafi
- French Associates Institute of Agriculture and Biotechnology of Drylands, The Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- * E-mail:
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26
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Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ. Widespread natural variation of DNA methylation within angiosperms. Genome Biol 2016; 17:194. [PMID: 27671052 DOI: 10.1101/045880] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. RESULTS By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. CONCLUSIONS These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.
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Affiliation(s)
- Chad E Niederhuth
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Adam J Bewick
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Magdy S Alabady
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Nicholas A Rohr
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Aditi Rambani
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Joshua A Udall
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Km 8 Ikot Ekpene Road, PMB 7006, Umuahia, 440001, Nigeria
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Nathan M Springer
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA.
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27
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Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ. Widespread natural variation of DNA methylation within angiosperms. Genome Biol 2016; 17:194. [PMID: 27671052 PMCID: PMC5037628 DOI: 10.1186/s13059-016-1059-0] [Citation(s) in RCA: 313] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. RESULTS By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. CONCLUSIONS These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.
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Affiliation(s)
- Chad E Niederhuth
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Adam J Bewick
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Magdy S Alabady
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Nicholas A Rohr
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Aditi Rambani
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Joshua A Udall
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Km 8 Ikot Ekpene Road, PMB 7006, Umuahia, 440001, Nigeria
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Nathan M Springer
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA.
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28
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Khan A, Yadav NS, Morgenstern Y, Zemach A, Grafi G. Activation of Tag1 transposable elements in Arabidopsis dedifferentiating cells and their regulation by CHROMOMETHYLASE 3-mediated CHG methylation. Biochim Biophys Acta 2016; 1859:1289-98. [PMID: 27475038 DOI: 10.1016/j.bbagrm.2016.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 12/11/2022]
Abstract
Dedifferentiation, that is, the acquisition of stem cell-like state, commonly induced by stress (e.g., protoplasting), is characterized by open chromatin conformation, a chromatin state that could lead to activation of transposable elements (TEs). Here, we studied the activation of the Arabidopsis class II TE Tag1, in which two copies, situated close to each other (near genes) on chromosome 1 are found in Landsberg erecta (Ler) but not in Columbia (Col). We first transformed protoplasts with a construct in which a truncated Tag1 (ΔTag1 non-autonomous) blocks the expression of a reporter gene AtMBD5-GFP and found a relatively high ectopic excision of ΔTag1 accompanied by expression of AtMBD5-GFP in protoplasts derived from Ler compared to Col; further increase was observed in ddm1 (decrease in DNA methylation1) protoplasts (Ler background). Ectopic excision was associated with transcription of the endogenous Tag1 and changes in histone H3 methylation at the promoter region. Focusing on the endogenous Tag1 elements we found low level of excision in Ler protoplasts, which was slightly and strongly enhanced in ddm1 and cmt3 (chromomethylase3) protoplasts, respectively, concomitantly with reduction in Tag1 gene body (GB) CHG methylation and increased Tag1 transcription; strong activation of Tag1 was also observed in cmt3 leaves. Notably, in cmt3, but not in ddm1, Tag1 elements were excised out from their original sites and transposed elsewhere in the genome. Our results suggest that dedifferentiation is associated with Tag1 activation and that CMT3 rather than DDM1 plays a central role in restraining Tag1 activation via inducing GB CHG methylation.
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Affiliation(s)
- Asif Khan
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel
| | - Narendra Singh Yadav
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel
| | - Yaakov Morgenstern
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel
| | - Assaf Zemach
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, 69978 Tel Aviv, Israel
| | - Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel.
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29
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Li Y, Deng H, Miao M, Li H, Huang S, Wang S, Liu Y. Tomato MBD5, a methyl CpG binding domain protein, physically interacting with UV-damaged DNA binding protein-1, functions in multiple processes. New Phytol 2016; 210:208-26. [PMID: 26551231 DOI: 10.1111/nph.13745] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 08/19/2015] [Accepted: 10/02/2015] [Indexed: 05/22/2023]
Abstract
In tomato (Solanum lycopersicum), high pigment mutations (hp-1 and hp-2) were mapped to genes encoding UV-damaged DNA binding protein 1 (DDB1) and de-etiolated-1 (DET1), respectively. Here we characterized a tomato methyl-CpG-binding domain protein SlMBD5 identified by yeast two-hybrid screening using SlDDB1 as a bait. Yeast two-hybrid assay demonstrated that the physical interaction of SlMBD5 with SlDDB1 is mediated by the C-termini of SlMBD5 and the β-propeller-C (BPC) of SlDDB1. Co-immunoprecipitation analyses revealed that SlMBD5 associates with SlDDB1-interacting partners including SlDET1, SlCUL4, SlRBX1a and SlRBX1b in vivo. SlMBD5 was shown to target to nucleus and dimerizes via its MBD motif. Electrophoresis mobility shift analysis suggested that the MBD of SlMBD5 specifically binds to methylated CpG dinucleotides but not to methylated CpHpG or CpHpH dinucleotides. SlMBD5 expressed in protoplast is capable of activating transcription of CG islands, whereas CUL4/DDB1 antagonizes this effect. Overexpressing SlMBD5 resulted in diverse developmental alterations including darker green fruits with increased plastid level and elevated pigmentation, as well as enhanced expression of SlGLK2, a key regulator of plastid biogenesis. Taken together, we hypothesize that the physical interaction of SlMBD5 with the CUL4-DDB1-DET1 complex component may affect its binding activity to methylated DNA and subsequently attenuate its transcription activation of downstream genes.
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Affiliation(s)
- Yuxiang Li
- Ministry of education Key Laboratory for Bio-resource and Eco-environment, State key laboratory of Hydraulics and mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Heng Deng
- Ministry of education Key Laboratory for Bio-resource and Eco-environment, State key laboratory of Hydraulics and mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Min Miao
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Huirong Li
- Ministry of education Key Laboratory for Bio-resource and Eco-environment, State key laboratory of Hydraulics and mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Shengxiong Huang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Songhu Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yongsheng Liu
- Ministry of education Key Laboratory for Bio-resource and Eco-environment, State key laboratory of Hydraulics and mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610064, China
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
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30
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Questa JI, Rius SP, Casadevall R, Casati P. ZmMBD101 is a DNA-binding protein that maintains Mutator elements chromatin in a repressive state in maize. Plant Cell Environ 2016; 39:174-184. [PMID: 26147461 DOI: 10.1111/pce.12604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 01/27/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 06/04/2023]
Abstract
In maize (Zea mays), as well as in other crops, transposable elements (TEs) constitute a great proportion of the genome. Chromatin modifications play a vital role in establishing transposon silencing and perpetuating the acquired repressive state. Nucleosomes associated with TEs are enriched for dimethylation of histone H3 at lysine 9 and 27 (H3K9me2 and H3K27me2, respectively), signals of repressive chromatin. Here, we describe a chromatin protein, ZmMBD101, involved in the regulation of Mutator (Mu) genes in maize. ZmMBD101 is localized to the nucleus and contains a methyl-CpG-binding domain (MBD) and a zinc finger CW (CW) domain. Transgenic lines with reduced levels of ZmMBD101 transcript present enhanced induction of Mu genes when plants are irradiated with UV-B. Chromatin immunoprecipitation analysis with H3K9me2 and H3K27me2 antibodies indicated that ZmMBD101 is required to maintain the levels of these histone repressive marks at Mu terminal inverted repeats (TIRs) under UV-B conditions. Although Mutator inactivity is associated with DNA methylation, cytosine methylation at Mu TIRs is not affected in ZmMBD101 deficient plants. Several plant proteins are predicted to share the simple CW-MBD domain architecture present in ZmMBD101. We hypothesize that plant CW-MBD proteins may also function to protect plant genomes from deleterious transposition.
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Affiliation(s)
- Julia I Questa
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Sebastián P Rius
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Romina Casadevall
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
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31
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Li Q, Wang X, Sun H, Zeng J, Cao Z, Li Y, Qian W. Regulation of Active DNA Demethylation by a Methyl-CpG-Binding Domain Protein in Arabidopsis thaliana. PLoS Genet 2015; 11:e1005210. [PMID: 25933434 PMCID: PMC4416881 DOI: 10.1371/journal.pgen.1005210] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/13/2015] [Indexed: 12/21/2022] Open
Abstract
Active DNA demethylation plays crucial roles in the regulation of gene expression in both plants and animals. In Arabidopsis thaliana, active DNA demethylation is initiated by the ROS1 subfamily of 5-methylcytosine-specific DNA glycosylases via a base excision repair mechanism. Recently, IDM1 and IDM2 were shown to be required for the recruitment of ROS1 to some of its target loci. However, the mechanism(s) by which IDM1 is targeted to specific genomic loci remains to be determined. Affinity purification of IDM1- and IDM2- associating proteins demonstrated that IDM1 and IDM2 copurify together with two novel components, methyl-CpG-binding domain protein 7 (MBD7) and IDM2-like protein 1 (IDL1). IDL1 encodes an α-crystallin domain protein that shows high sequence similarity with IDM2. MBD7 interacts with IDM2 and IDL1 in vitro and in vivo and they form a protein complex associating with IDM1 in vivo. MBD7 directly binds to the target loci and is required for the H3K18 and H3K23 acetylation in planta. MBD7 dysfunction causes DNA hypermethylation and silencing of reporter genes and a subset of endogenous genes. Our results suggest that a histone acetyltransferase complex functions in active DNA demethylation and in suppression of gene silencing at some loci in Arabidopsis.
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Affiliation(s)
- Qi Li
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Xiaokang Wang
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Han Sun
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Jun Zeng
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Zhendong Cao
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Yan Li
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
- * E-mail:
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32
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Wang C, Dong X, Jin D, Zhao Y, Xie S, Li X, He X, Lang Z, Lai J, Zhu JK, Gong Z. Methyl-CpG-binding domain protein MBD7 is required for active DNA demethylation in Arabidopsis. Plant Physiol 2015; 167:905-14. [PMID: 25593350 PMCID: PMC4348759 DOI: 10.1104/pp.114.252106] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/14/2015] [Indexed: 05/20/2023]
Abstract
Although researchers have established that DNA methylation and active demethylation are dynamically regulated in plant cells, the molecular mechanism for the regulation of active DNA demethylation is not well understood. By using an Arabidopsis (Arabidopsis thaliana) line expressing the Promoter RESPONSIVE TO DEHYDRATION 29A:LUCIFERASE (ProRD29A:LUC) and Promoter cauliflower mosaic virus 35S:NEOMYCIN PHOSPHOTRANSFERASE II (Pro35S:NPTII) transgenes, we isolated an mbd7 (for methyl-CpG-binding domain protein7) mutant. The mbd7 mutation causes an inactivation of the Pro35S:NPTII transgene but does not affect the expression of the ProRD29A:LUC transgene. The silencing of the Pro35S:NPTII reporter gene is associated with DNA hypermethylation of the reporter gene. MBD7 interacts physically with REPRESSOR OF SILENCING5/INCREASED DNA METHYLATION2, a protein in the small heat shock protein family. MBD7 prefers to target the genomic loci with high densities of DNA methylation around chromocenters. The Gypsy-type long terminal repeat retrotransposons mainly distributed around chromocenters are most affected by mbd7 in all transposons. Our results suggest that MBD7 is required for active DNA demethylation and antisilencing of the genomic loci with high densities of DNA methylation in Arabidopsis.
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Affiliation(s)
- Chunlei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Xiaomei Dong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Dan Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Yusheng Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Shaojun Xie
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Xiaojie Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Xinjian He
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Zhaobo Lang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Jian-Kang Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
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Wang H, Qi X, Chen S, Fang W, Guan Z, Teng N, Liao Y, Jiang J, Chen F. Limited DNA methylation variation and the transcription of MET1 and DDM1 in the genus Chrysanthemum (Asteraceae): following the track of polyploidy. Front Plant Sci 2015; 6:668. [PMID: 26379692 PMCID: PMC4550781 DOI: 10.3389/fpls.2015.00668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 08/13/2015] [Indexed: 05/06/2023]
Abstract
Polyploidy has been recognized as a widespread and common phenomenon among flowering plants. DNA-5'-CCGG site cytosine methylation (C-methylation) is one of the major and immediate epigenetic responses of the plant genome. Elucidating the ways in which altered C-methylation patterns, either at the whole genomic level or at specific sites can affect genome stability in polyploidy will require substantial additional investigation. Methylation sensitive amplification polymorphism profiling was used to evaluate variation in C-methylation among a set of 20 Chrysanthemum species and their close relatives of varying ploidy levels from diploid to decaploid. The range in relative C-methylation level was within 10%, and there was no significant difference neither between different ploidy levels nor between different species in the same ploidy level (U-values < 1.96). The transcript abundances of MET1 and DDM1 genes, which both involved in the regulation of C-methylation at CpG sites, were enhanced with increased ploidy level, but only MET1 was positively correlated with the nuclear DNA content. Considering the key role and efficiency of MET1 in maintaining CpG methylation, the limited variation observed with respect to C-methylation may reflect a balance between the increased activity of MET1 in the higher ploidy genomes and the larger number of CpG dinucleotide sites available for methylation.
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Affiliation(s)
- Haibin Wang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology and EquipmentNanjing, China
| | - Xiangyu Qi
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Nianjun Teng
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yuan Liao
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- *Correspondence: Fadi Chen and Jiafu Jiang, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China, ;
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology and EquipmentNanjing, China
- *Correspondence: Fadi Chen and Jiafu Jiang, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China, ;
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Costa-Nunes P, Pontes O, Preuss SB, Pikaard CS. Extra views on RNA-dependent DNA methylation and MBD6-dependent heterochromatin formation in nucleolar dominance. Nucleus 2014. [DOI: 10.4161/nucl.11741] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Kumar S, Kumari R, Sharma V, Sharma V. Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants. J Genet 2013; 92:629-66. [PMID: 24371187 DOI: 10.1007/s12041-013-0273-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Heritable information in plants consists of genomic information in DNA sequence and epigenetic information superimposed on DNA sequence. The latter is in the form of cytosine methylation at CG, CHG and CHH elements (where H = A, T orC) and a variety of histone modifications in nucleosomes. The epialleles arising from cytosine methylation marks on the nuclear genomic loci have better heritability than the epiallelic variation due to chromatin marks. Phenotypic variation is increased manifold by epiallele comprised methylomes. Plants (angiosperms) have highly conserved genetic mechanisms to establish, maintain or erase cytosine methylation from epialleles. The methylation marks in plants fluctuate according to the cell/tissue/organ in the vegetative and reproductive phases of plant life cycle. They also change according to environment. Epialleles arise by gain or loss of cytosine methylation marks on genes. The changes occur due to the imperfection of the processes that establish and maintain the marks and on account of spontaneous and stress imposed removal of marks. Cytosine methylation pattern acquired in response to abiotic or biotic stress is often inherited over one to several subsequent generations.Cytosine methylation marks affect physiological functions of plants via their effect(s) on gene expression levels. They also repress transposable elements that are abundantly present in plant genomes. The density of their distribution along chromosome lengths affects meiotic recombination rate, while their removal increases mutation rate. Transposon activation due to loss of methylation causes rearrangements such that new gene regulatory networks arise and genes for microRNAs may originate. Cytosine methylation dynamics contribute to evolutionary changes. This review presents and discusses the available evidence on origin, removal and roles of cytosine methylation and on related processes, such as RNA directed DNA methylation, imprinting, paramutation and transgenerational memory in plants.
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Engelhorn J, Blanvillain R, Carles CC. Gene activation and cell fate control in plants: a chromatin perspective. Cell Mol Life Sci 2014; 71:3119-37. [PMID: 24714879 DOI: 10.1007/s00018-014-1609-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 01/02/2023]
Abstract
In plants, environment-adaptable organogenesis extends throughout the lifespan, and iterative development requires repetitive rounds of activation and repression of several sets of genes. Eukaryotic genome compaction into chromatin forms a physical barrier for transcription; therefore, induction of gene expression requires alteration in chromatin structure. One of the present great challenges in molecular and developmental biology is to understand how chromatin is brought from a repressive to permissive state on specific loci and in a very specific cluster of cells, as well as how this state is further maintained and propagated through time and cell division in a cell lineage. In this review, we report recent discoveries implementing our knowledge on chromatin dynamics that modulate developmental gene expression. We also discuss how new data sets highlight plant specificities, likely reflecting requirement for a highly dynamic chromatin.
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Affiliation(s)
- Julia Engelhorn
- Université Grenoble Alpes, UMR5168, 38041, Grenoble, France,
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Florentin A, Damri M, Grafi G. Stress induces plant somatic cells to acquire some features of stem cells accompanied by selective chromatin reorganization. Dev Dyn 2013; 242:1121-33. [DOI: 10.1002/dvdy.24003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 06/11/2013] [Accepted: 06/11/2013] [Indexed: 12/13/2022] Open
Affiliation(s)
- Assa Florentin
- French Associates Institute for Agriculture and Biotechnology of Drylands; Jacob Blaustein Institutes for Desert Research; Ben-Gurion University of the Negev; Midreshet Ben-Gurion Israel
| | - Meytal Damri
- French Associates Institute for Agriculture and Biotechnology of Drylands; Jacob Blaustein Institutes for Desert Research; Ben-Gurion University of the Negev; Midreshet Ben-Gurion Israel
- The Shraga Segal Department of Microbiology and Immunology; Faculty of Health Sciences; Center for Multidisciplinary Research on Aging; Ben-Gurion University of the Negev; Beer Sheva Israel
| | - Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands; Jacob Blaustein Institutes for Desert Research; Ben-Gurion University of the Negev; Midreshet Ben-Gurion Israel
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Zhu R, Shevchenko O, Ma C, Maury S, Freitag M, Strauss SH. Poplars with a PtDDM1-RNAi transgene have reduced DNA methylation and show aberrant post-dormancy morphology. Planta 2013; 237:1483-93. [PMID: 23455459 DOI: 10.1007/s00425-013-1858-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 02/07/2013] [Indexed: 05/22/2023]
Abstract
The Arabidopsis thaliana DDM1 (Decreased DNA Methylation) gene is necessary for the maintenance of DNA methylation and heterochromatin assembly. In Arabidopsis, ddm1 mutants exhibit strong but delayed morphological phenotypes. We used RNA interference (RNAi) to suppress transcripts of two orthologous DDM1 paralogs in Populus trichocarpa and examined effects on whole plant phenotypes during perennial growth and seasonal dormancy. The RNAi-PtDDM1 transgenic poplars showed a wide range of DDM1 transcript suppression; the most strongly suppressed line had 37.5 % of the expression of the non-transgenic control. Genomic cytosine methylation (mC %) was 11.1 % in the non-transgenic control, compared with 9.1 % for the transgenic event with lowest mC %, a reduction of 18.1 %. An evaluation of greenhouse growth directly after acclimation of in vitro grown plants showed no developmental or growth rate abnormalities associated with the decrease in PtDDM1 expression. However, after a dormancy cycle and growth outdoors, a mottled leaf phenotype appeared in some of the transgenic insertion events that had strongly reduced PtDDM1 expression and DNA methylation. The phenotypic consequences of reduced DDM1 activity and DNA methylation appears to increase with cumulative plant propagation and growth.
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Affiliation(s)
- Ruoqing Zhu
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
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Saze H, Tsugane K, Kanno T, Nishimura T. DNA methylation in plants: relationship to small RNAs and histone modifications, and functions in transposon inactivation. Plant Cell Physiol 2012; 53:766-84. [PMID: 22302712 DOI: 10.1093/pcp/pcs008] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
DNA methylation is a type of epigenetic marking that strongly influences chromatin structure and gene expression in plants and mammals. Over the past decade, DNA methylation has been intensively investigated in order to elucidate its control mechanisms. These studies have shown that small RNAs are involved in the induction of DNA methylation, that there is a relationship between DNA methylation and histone methylation, and that the base excision repair pathway has an important role in DNA demethylation. Some aspects of DNA methylation have also been shown to be shared with mammals, suggesting that the regulatory pathways are, in part at least, evolutionarily conserved. Considerable progress has been made in elucidating the mechanisms that control DNA methylation; however, many aspects of the mechanisms that read the information encoded by DNA methylation and mediate this into downstream regulation remain uncertain, although some candidate proteins have been identified. DNA methylation has a vital role in the inactivation of transposons, suggesting that DNA methylation is a key factor in the evolution and adaptation of plants.
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Affiliation(s)
- Hidetoshi Saze
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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Farage-Barhom S, Burd S, Sonego L, Mett A, Belausov E, Gidoni D, Lers A. Localization of the Arabidopsis senescence- and cell death-associated BFN1 nuclease: from the ER to fragmented nuclei. Mol Plant 2011; 4:1062-73. [PMID: 21665915 DOI: 10.1093/mp/ssr045] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant senescence- or PCD-associated nucleases share significant homology with nucleases from different organisms. However, knowledge of their function is limited. Intracellular localization of the Arabidopsis senescence- and PCD-associated nuclease BFN1 was investigated. Analysis of BFN1-GFP localization in transiently transformed tobacco protoplasts revealed initial localization in filamentous structures spread throughout the cytoplasm, which then clustered around the nuclei as the protoplasts senesced. These filamentous structures were identified as being of ER origin. In BFN1-GFP-transgenic Arabidopsis plants, similar localization of BFN1-GFP was observed in young leaves, that is, in filamentous structures that reorganized around the nuclei only in senescing cells. In late senescence, BFN1-GFP was localized with fragmented nuclei in membrane-wrapped vesicles. BFN1's postulated function as a nucleic acid-degrading enzyme in senescence and PCD is supported by its localization pattern. Our results suggest the existence of a dedicated compartment mediating nucleic acid degradation in senescence and PCD processes.
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Affiliation(s)
- Sarit Farage-Barhom
- Department of Postharvest Science of Fresh Produce, Volcani Center, Agricultural Research Organization, Bet Dagan, 50250, Israel
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Ma KW, Flores C, Ma W. Chromatin configuration as a battlefield in plant-bacteria interactions. Plant Physiol 2011; 157:535-43. [PMID: 21825106 PMCID: PMC3192555 DOI: 10.1104/pp.111.182295] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 08/04/2011] [Indexed: 05/18/2023]
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Zhang M, Kimatu JN, Xu K, Liu B. DNA cytosine methylation in plant development. J Genet Genomics 2010; 37:1-12. [PMID: 20171573 DOI: 10.1016/s1673-8527(09)60020-5] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2009] [Revised: 11/15/2009] [Accepted: 11/30/2009] [Indexed: 10/19/2022]
Abstract
Cytosine bases of the nuclear genome in higher plants are often extensively methylated. Cytosine methylation has been implicated in the silencing of both transposable elements (TEs) and endogenous genes, and loss of methylation may have severe functional consequences. The recent methylation profiling of the entire Arabidopsis genome has provided novel insights into the extent and pattern of cytosine methylation and its relationships with gene activity. In addition, the fresh studies also revealed the more dynamic nature of this epigenetic modification across plant development than previously believed. Cytosine methylation of gene promoter regions usually inhibits transcription, but methylation in coding regions (gene-body methylation) does not generally affect gene expression. Active demethylation (though probably act synergistically with passive loss of methylation) of promoters by the 5-methyl cytosine DNA glycosylase or DEMETER (DME) is required for the uni-parental expression of imprinting genes in endosperm, which is essential for seed viability. The opinion that cytosine methylation is indispensible for normal plant development has been reinforced by using single or combinations of diverse loss-of-function mutants for DNA methyltransferases, DNA glycosylases, components involved in siRNA biogenesis and chromatin remodeling factors. Patterns of cytosine methylation in plants are usually faithfully maintained across organismal generations by the concerted action of epigenetic inheritance and progressive correction of strayed patterns. However, some variant methylation patterns may escape from being corrected and hence produce novel epialleles in the affected somatic cells. This, coupled with the unique property of plants to produce germline cells late during development, may enable the newly acquired epialleles to be inherited to future generations, which if visible to selection may contribute to adaptation and evolution.
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Affiliation(s)
- Meishan Zhang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
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Abstract
In eukaryotic genomes, gene expression and DNA recombination are affected by structural chromatin traits. Chromatin structure is shaped by the activity of enzymes that either introduce covalent modifications in DNA and histone proteins or use energy from ATP to disrupt histone-DNA interactions. The genomic 'marks' that are generated by covalent modifications of histones and DNA, or by the deposition of histone variants, are susceptible to being altered in response to stress. Recent evidence has suggested that proteins generating these epigenetic marks play crucial roles in the defence against pathogens. Histone deacetylases are involved in the activation of jasmonic acid- and ethylene-sensitive defence mechanisms. ATP-dependent chromatin remodellers mediate the constitutive repression of the salicylic acid-dependent pathway, whereas histone methylation at the WRKY70 gene promoter affects the activation of this pathway. Interestingly, bacterial-infected tissues show a net reduction in DNA methylation, which may affect the disease resistance genes responsible for the surveillance against pathogens. As some epigenetic marks can be erased or maintained and transmitted to offspring, epigenetic mechanisms may provide plasticity for the dynamic control of emerging pathogens without the generation of genomic lesions.
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Affiliation(s)
- María E Alvarez
- CIQUIBIC-CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, 5000 Córdoba, Argentina.
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Costa-Nunes P, Pontes O, Preuss SB, Pikaard CS. Extra views on RNA-dependent DNA methylation and MBD6-dependent heterochromatin formation in nucleolar dominance. Nucleus 2010; 1:254-9. [PMID: 21327072 DOI: 10.4161/nucl.1.3.11741] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 03/02/2010] [Indexed: 11/19/2022]
Abstract
Nucleolar dominance is a widespread epigenetic phenomenon, describing the preferential silencing of ribosomal RNA (rRNA) genes inherited from one progenitor of an interspecific hybrid, independent of maternal or paternal effects. In the allotetraploid hybrid plant species Arabidopsis suecica, A. thaliana-derived rRNA genes are silenced whereas the A. arenosa-derived rRNA genes are transcribed. We reported previously on an RNAi-based screen of DNA methyltransferases, methylcytosine binding proteins and RNA-dependent DNA methylation pathway proteins that identified specific activities required for the establishment or enforcement of nucleolar dominance. Here we present additional molecular and cell biological evidence that siRNA-directed cytosine methylation and the methylcytosine binding protein MBD6 bring about large-scale chromosomal effects on rRNA gene loci subjected to nucleolar dominance in A. suecica.
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Abstract
Histone methylation plays a fundamental role in regulating diverse developmental processes and is also involved in silencing repetitive sequences in order to maintain genome stability. The methylation marks are written on lysine or arginine by distinct enzymes, namely, histone lysine methyltransferases (HKMTs) or protein arginine methyltransferases (PRMTs). Once established, the methylation marks are specifically recognized by the proteins that act as readers and are interpreted into specific biological outcomes. Histone methylation status is dynamic; methylation marks can be removed by eraser enzymes, the histone demethylases (HDMs). The proteins responsible for writing, reading, and erasing the methylation marks are known mostly in animals. During the past several years, a growing body of literature has demonstrated the impact of histone methylation on genome management, transcriptional regulation, and development in plants. The aim of this review is to summarize the biochemical, genetic, and molecular action of histone methylation in two plants, the dicot Arabidopsis and the monocot rice.
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Affiliation(s)
- Chunyan Liu
- National Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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Zemach A, Paul LK, Stambolsky P, Efroni I, Rotter V, Grafi G. The C-terminal domain of the Arabidopsis AtMBD7 protein confers strong chromatin binding activity. Exp Cell Res 2009; 315:3554-62. [PMID: 19647732 DOI: 10.1016/j.yexcr.2009.07.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/26/2009] [Accepted: 07/27/2009] [Indexed: 12/01/2022]
Abstract
The Arabidopsis MBD7 (AtMBD7) - a naturally occurring poly MBD protein - was previously found to be functional in binding methylated-CpG dinucleotides in vitro and localized to highly methylated chromocenters in vivo. Furthermore, AtMBD7 has significantly lower mobility within the nucleus conferred by cooperative activity of its three MBD motifs. Here we show that besides the MBD motifs, AtMBD7 possesses a strong chromatin binding domain located at its C-terminus designated sticky-C (StkC). Mutational analysis showed that a glutamic acid residue near the C-terminus is essential though not sufficient for the StkC function. Further analysis demonstrated that this motif can render nuclear proteins highly immobile both in plant and animal cells, without affecting their native subnuclear localization. Thus, the C-terminal, StkC motif plays an important role in fastening AtMBD7 to its chromosomal, CpG-methylated sites. It may be possible to utilize this motif for fastening nuclear proteins to their chromosomal sites both in plant and animal cells for research and gene therapy applications.
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Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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Yaish MWF, Peng M, Rothstein SJ. AtMBD9 modulates Arabidopsis development through the dual epigenetic pathways of DNA methylation and histone acetylation. Plant J 2009; 59:123-135. [PMID: 19419532 DOI: 10.1111/j.1365-313x.2009.03860.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Mutations within the Arabidopsis METHYL-CpG BINDING DOMAIN 9 gene (AtMBD9) cause pleotropic phenotypes including early flowering and multiple lateral branches. Early flowering was previously attributed to the repression of flowering locus C (FLC) due to a reduction in histone acetylation. However, the reasons for other phenotypic variations remained obscure. Recent studies suggest an important functional correlation between DNA methylation and histone modifications. By investigating this relationship, we found that the global genomic DNA of atmbd9 was over-methylated, including the FLC gene region. Recombinant AtMBD9 does not have detectable DNA demethylation activity in vitro, but instead has histone acetylation activity. Ectopic over-expression of AtMBD9 and transient DNA demethylation promotes flowering and causes partial recovery of the normal branching phenotype. Co-immunoprecipitation assays suggest that AtMBD9 interacts in vivo with some regions of the FLC gene and binds to histone 4 (H4). Gene expression profile analysis revealed earlier up-regulation of some flower-specific transcriptional factors and alteration of potential hormonal and signal transducer axillary branching regulatory genes. In accordance with this result, AtMBD9 itself was found to be localized in the nucleus and expressed in the flower and axillary buds. Together, these results suggest that AtMBD9 controls flowering time and axillary branching by modulating gene expression through DNA methylation and histone acetylation, and reveal another component of the epigenetic mechanism controlling gene expression.
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Affiliation(s)
- Mahmoud W F Yaish
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
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Abstract
Development of ChIP-chip and ChIP-seq technologies has allowed genome-wide high-resolution profiling of chromatin-associated marks and binding sites for epigenetic regulators. However, signals for directing epigenetic modifiers to their target sites are not understood. In this paper, we tested the hypothesis that genome location can affect the involvement of epigenetic regulators using Chromatin Charting (CC) Lines, which have an identical transgene construct inserted at different locations in the Arabidopsis genome. Four CC lines that showed evidence for epigenetic silencing of the luciferase reporter gene were transformed with RNAi vectors individually targeting epigenetic regulators LHP1, MOM1, CMT3, DRD1, DRM2, SUVH2, CLF, and HD1. Involvement of a particular epigenetic regulator in silencing the transgene locus in a CC line was determined by significant alterations in luciferase expression after suppression of the regulator's expression. Our results suggest that the targeting of epigenetic regulators can be influenced by genome location as well as sequence context. In addition, the relative importance of an epigenetic regulator can be influenced by tissue identity. We also report a novel approach to predict interactions between epigenetic regulators through clustering analysis of the regulators using alterations in gene expression of putative downstream targets, including endogenous loci and transgenes, in epigenetic mutants or RNAi lines. Our data support the existence of a complex and dynamic network of epigenetic regulators that serves to coordinate and control global gene expression in higher plants.
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Affiliation(s)
- Chongyuan Luo
- Biotechnology Center for Agriculture and the Environment, Rutgers The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA; Department of Plant Biology and Pathology, Rutgers The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA
| | - Brittany G Durgin
- Biotechnology Center for Agriculture and the Environment, Rutgers The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA
| | - Naohide Watanabe
- Biotechnology Center for Agriculture and the Environment, Rutgers The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA
| | - Eric Lam
- Biotechnology Center for Agriculture and the Environment, Rutgers The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA; Department of Plant Biology and Pathology, Rutgers The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA.
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Stangeland B, Rosenhave EM, Winge P, Berg A, Amundsen SS, Karabeg M, Mandal A, Bones AM, Grini PE, Aalen RB. AtMBD8 is involved in control of flowering time in the C24 ecotype of Arabidopsis thaliana. Physiol Plant 2009; 136:110-26. [PMID: 19374717 DOI: 10.1111/j.1399-3054.2009.01218.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Arabidopsis thaliana accession C24 is a vernalization-responsive, moderately late flowering ecotype. We report that a mutation in AtMBD8, which encodes a protein with a putative Methyl-CpG-Binding Domain (MBD), in C24 background, results in a delay in flowering time during both long and short days. The atmbd8-1 mutant responded to vernalization as wild type (wt) plants. Consistent with a role in modulation of flowering time, an AtMBD8::GUS-reporter construct was expressed in the shoot meristem region and developing leaves. Full-genome transcriptional profiling revealed very few changes in gene expression between atmbd8-1 and wt plants. The expression level of FLC, the major repressor of transition to flowering, was unchanged in atmbd8-1, and in accordance with that, genes upstream of FLC were unaffected by the mutation. The expression level of CONSTANS, involved in photoperiodic control of flowering, was very similar in atmbd8-1 and wt plants. In contrast, the major promoters of flowering, FT and SOC1, were both downregulated. As FT is a regulator of SOC1, we conclude that AtMBD8 is a novel promoter of flowering that acts upstream of FT in the C24 accession. In contrast to atmbd8-1, the Colombia (Col) SALK T-DNA insertion line, atmbd8-2, did not display a delayed transition to flowering. Transcriptional profiling revealed that a substantial number of genes were differentially expressed between C24 and Col wt seedlings. Several of these genes are also differentially expressed in late flowering mutants. We suggest that these differences contribute to the contrasting effect of a mutation in AtMBD8 in the two ecotypes.
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Affiliation(s)
- Biljana Stangeland
- Department of Molecular Biosciences, University of Oslo, Blindern, N-0316 Oslo, Norway
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Abstract
In the December 5th issue of Molecular Cell, Preuss et al. (2008) demonstrated a link between small interfering RNA (siRNA)-directed de novo DNA methylation and rDNA silencing in nucleolar dominance.
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Affiliation(s)
- Patrick Finigan
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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