scholarly journals A H3K9me2-Binding Protein AGDP3 Limits DNA Methylation and Transcriptional Gene Silencing in Arabidopsis

2021 ◽  
Author(s):  
Xuelin Zhou ◽  
Mengwei Wei ◽  
Wenfeng Nie ◽  
Yue Xi ◽  
Xuan Du ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Silencing ◽  
Histone Acetylation ◽  
Binding Capacity ◽  
Dna Demethylation ◽  
Transcriptional Gene Silencing ◽  
Dna Hypermethylation ◽  
Active Dna Demethylation ◽  
Aromatic Cage ◽  
Deleterious Gene

AbstractDNA methylation is critical for tuning gene expression to prevent potentially deleterious gene-silencing. The Arabidopsis DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1) initiates active DNA demethylation and is required for the prevention of DNA hypermethylation at thousands of genomic loci. However, the mechanism recruiting ROS1 to specific loci is not well understood. Here, we report the discovery of Arabidopsis AGENET Domain Containing Protein 3 (AGDP3) as a cellular factor required for ROS1-mediated DNA demethylation, and targets ROS1 to specific loci. We found that AGDP3 could bind to the H3K9me2 mark by its AGD12 cassette. The crystal structure of the AGDP3 AGD12 in complex with an H3K9me2 peptide reveals the molecular basis for the specific recognition, that the dimethylated H3K9 and unmodified H3K4 are specifically anchored into two different surface pockets. Interestingly, a histidine residue located in the methylysine binding aromatic cage enables AGDP3 pH-dependent H3K9me2 binding capacity. Considering the intracellular pH correlates with the histone acetylation status, our results provide the molecular mechanism for the regulation of ROS1 DNA demethylase by the gene silencing H3K9me2 mark and the potential crosstalk with active histone acetylation mark.

scholarly journals Histone acetylation recruits the SWR1 complex to regulate active DNA demethylation in Arabidopsis

2019 ◽  
Vol 116 (33) ◽  
pp. 16641-16650 ◽  
Author(s):  
Wen-Feng Nie ◽  
Mingguang Lei ◽  
Mingxuan Zhang ◽  
Kai Tang ◽  
Huan Huang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Conceptual Framework ◽  
Histone Acetylation ◽  
Chromatin Remodeling ◽  
Nuclear Protein ◽  
Dna Demethylation ◽  
Specific Target ◽  
Active Dna Demethylation ◽  
Chromatin Remodeling Complex ◽  
Genomic Regions

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.

scholarly journals The Methyl-CpG-Binding Protein MBD7 Facilitates Active DNA Demethylation to Limit DNA Hyper-Methylation and Transcriptional Gene Silencing

2015 ◽  
Vol 57 (6) ◽  
pp. 971-983 ◽  
Author(s):  
Zhaobo Lang ◽  
Mingguang Lei ◽  
Xingang Wang ◽  
Kai Tang ◽  
Daisuke Miki ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Binding Protein ◽  
Dna Demethylation ◽  
Transcriptional Gene Silencing ◽  
Active Dna Demethylation

scholarly journals SIZ1-mediated SUMOylation of ROS1 Enhances Its Stability and Positively Regulates Active DNA Demethylation in Arabidopsis

2020 ◽  
Author(s):  
Xiangfeng Kong ◽  
Yechun Hong ◽  
Yi-Feng Hsu ◽  
Huan Huang ◽  
Xue Liu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Demethylation ◽  
Dna Glycosylase ◽  
Wild Type ◽  
Dna Hypermethylation ◽  
Post Translational Modifications ◽  
Active Dna Demethylation ◽  
Short Summary ◽  
The Stability ◽  
Genomic Regions

AbstractThe 5-methylcytosine DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1)-mediated active DNA demethylation is critical for shaping the genomic DNA methylation landscape in Arabidopsis. Whether and how the stability of ROS1 may be regulated by post-translational modifications is unknown. Using a methylation-sensitive PCR (CHOP-PCR)-based forward genetic screen for Arabidopsis DNA hypermethylation mutants, we identified the SUMO E3 ligase SIZ1 as a critical regulator of active DNA demethylation. Dysfunction of SIZ1 leads to hyper-methylation at approximately one thousand genomic regions. SIZ1 physically interacts with ROS1 and mediates the SUMOylation of ROS1. The SUMOylation of ROS1 is reduced in siz1 mutant plants. Compared to that in wild type plants, the protein level of ROS1 is significantly decreased, even though there is an increased level of ROS1 transcripts in siz1 mutant plants. Our results suggest that SIZ1 positively regulates active DNA demethylation by promoting the stability of ROS1 protein through SUMOylation.Short SummaryThe 5-methylcytosine DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1) is indispensable for proper DNA methylation landscape in Arabidopsis. Whether and how the stability of ROS1 may be regulated by post-translational modifications is unknown. Here, we show that SIZ1-mediated SUMOylation of ROS1 enhances its stability and positively regulates active DNA demethylation.

scholarly journals A novel protein complex that regulates active DNA demethylation in Arabidopsis

2020 ◽  
Author(s):  
Pan Liu ◽  
Wen-Feng Nie ◽  
Xiansong Xiong ◽  
Yuhua Wang ◽  
Yuwei Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Protein Complex ◽  
Excision Repair ◽  
Dna Demethylation ◽  
Loss Of Function ◽  
Dna Hypermethylation ◽  
Active Dna Demethylation ◽  
Domain Protein ◽  
Genomic Regions

SUMMARYActive DNA demethylation is critical for altering DNA methylation patterns and regulating gene expression. The 5-methylcytosine DNA glycosylase/lyase ROS1 initiates a base excision repair pathway for active DNA demethylation and is required for the prevention of DNA hypermethylation at thousands of genomic regions in Arabidopsis. How ROS1 is regulated and targeted to specific genomic regions is not well understood. Here, we report the discovery of an Arabidopsis protein complex that contains ROS1, regulates ROS1 gene expression, and likely targets the ROS1 protein to specific genomic regions. ROS1 physically interacts with a WD40 domain protein (RWD40), which in turn interacts with a methyl-DNA binding protein (RMB1) as well as with a zinc finger and homeobox domain protein (RHD1). RMB1 binds to DNA that is methylated in any sequence context, and this binding is necessary for its function in vivo.Loss-of-function mutations in RWD40, RMB1, or RHD1 cause DNA hypermethylation at several tested genomic regions independently of the known ROS1 regulator IDM1. Because the hypermethylated genomic regions include the DNA methylation monitoring sequence in the ROS1 promoter, plants mutated in RWD40, RMB1, or RHD1 show increased ROS1 expression. Importantly, ROS1 binding to the ROS1 promoter requires RWD40, RMB1, and RHD1, suggesting that this complex dictates ROS1 targeting to this locus. Our results demonstrate that ROS1 forms a protein complex with RWD40, RMB1, and RHD1, and that this novel complex regulates active DNA demethylation at several endogenous loci in Arabidopsis.

scholarly journals Preventing transcriptional gene silencing by active DNA demethylation

FEBS Letters ◽  
2005 ◽  
Vol 579 (26) ◽  
pp. 5889-5898 ◽  
Author(s):  
Avnish Kapoor ◽  
Fernanda Agius ◽  
Jian-Kang Zhu
Keyword(s):  
Gene Silencing ◽  
Dna Demethylation ◽  
Transcriptional Gene Silencing ◽  
Active Dna Demethylation

scholarly journals Regulatory link between DNA methylation and active demethylation in Arabidopsis

2015 ◽  
Vol 112 (11) ◽  
pp. 3553-3557 ◽  
Author(s):  
Mingguang Lei ◽  
Huiming Zhang ◽  
Russell Julian ◽  
Kai Tang ◽  
Shaojun Xie ◽  
...  
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Gene Promoter ◽  
Dna Demethylation ◽  
Target Sequence ◽  
Loss Of Function ◽  
Dna Hypermethylation ◽  
Active Demethylation ◽  
Active Dna Demethylation ◽  
Regulatory Link

De novo DNA methylation through the RNA-directed DNA methylation (RdDM) pathway and active DNA demethylation play important roles in controlling genome-wide DNA methylation patterns in plants. Little is known about how cells manage the balance between DNA methylation and active demethylation activities. Here, we report the identification of a unique RdDM target sequence, where DNA methylation is required for maintaining proper active DNA demethylation of the Arabidopsis genome. In a genetic screen for cellular antisilencing factors, we isolated several REPRESSOR OF SILENCING 1 (ros1) mutant alleles, as well as many RdDM mutants, which showed drastically reduced ROS1 gene expression and, consequently, transcriptional silencing of two reporter genes. A helitron transposon element (TE) in the ROS1 gene promoter negatively controls ROS1 expression, whereas DNA methylation of an RdDM target sequence between ROS1 5′ UTR and the promoter TE region antagonizes this helitron TE in regulating ROS1 expression. This RdDM target sequence is also targeted by ROS1, and defective DNA demethylation in loss-of-function ros1 mutant alleles causes DNA hypermethylation of this sequence and concomitantly causes increased ROS1 expression. Our results suggest that this sequence in the ROS1 promoter region serves as a DNA methylation monitoring sequence (MEMS) that senses DNA methylation and active DNA demethylation activities. Therefore, the ROS1 promoter functions like a thermostat (i.e., methylstat) to sense DNA methylation levels and regulates DNA methylation by controlling ROS1 expression.

scholarly journals Global increase in DNA methylation during orange fruit development and ripening

2019 ◽  
Vol 116 (4) ◽  
pp. 1430-1436 ◽  
Author(s):  
Huan Huang ◽  
Ruie Liu ◽  
Qingfeng Niu ◽  
Kai Tang ◽  
Bo Zhang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Fruit Ripening ◽  
Tomato Fruit ◽  
Dna Demethylation ◽  
Epigenetic Mark ◽  
Dna Hypermethylation ◽  
Active Dna Demethylation ◽  
Orange Fruit ◽  
Global Increase ◽  
Genomic Regions

DNA methylation is an important epigenetic mark involved in many biological processes. The genome of the climacteric tomato fruit undergoes a global loss of DNA methylation due to active DNA demethylation during the ripening process. It is unclear whether the ripening of other fruits is also associated with global DNA demethylation. We characterized the single-base resolution DNA methylomes of sweet orange fruits. Compared with immature orange fruits, ripe orange fruits gained DNA methylation at over 30,000 genomic regions and lost DNA methylation at about 1,000 genomic regions, suggesting a global increase in DNA methylation during orange fruit ripening. This increase in DNA methylation was correlated with decreased expression of DNA demethylase genes. The application of a DNA methylation inhibitor interfered with ripening, indicating that the DNA hypermethylation is critical for the proper ripening of orange fruits. We found that ripening-associated DNA hypermethylation was associated with the repression of several hundred genes, such as photosynthesis genes, and with the activation of hundreds of genes, including genes involved in abscisic acid responses. Our results suggest important roles of DNA methylation in orange fruit ripening.

scholarly journals Epigenetic Regulation of Genomic Stability by Vitamin C

2021 ◽  
Vol 12 ◽  
Author(s):  
John P. Brabson ◽  
Tiffany Leesang ◽  
Sofia Mohammad ◽  
Luisa Cimmino
Keyword(s):  
Dna Methylation ◽  
Vitamin C ◽  
Excision Repair ◽  
Antioxidant Properties ◽  
Genomic Stability ◽  
Dna Demethylation ◽  
Dna Hypermethylation ◽  
Active Dna Demethylation ◽  
Base Excision ◽  
Tet Enzymes

DNA methylation plays an important role in the maintenance of genomic stability. Ten-eleven translocation proteins (TETs) are a family of iron (Fe2+) and α-KG -dependent dioxygenases that regulate DNA methylation levels by oxidizing 5-methylcystosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). These oxidized methylcytosines promote passive demethylation upon DNA replication, or active DNA demethylation, by triggering base excision repair and replacement of 5fC and 5caC with an unmethylated cytosine. Several studies over the last decade have shown that loss of TET function leads to DNA hypermethylation and increased genomic instability. Vitamin C, a cofactor of TET enzymes, increases 5hmC formation and promotes DNA demethylation, suggesting that this essential vitamin, in addition to its antioxidant properties, can also directly influence genomic stability. This review will highlight the functional role of DNA methylation, TET activity and vitamin C, in the crosstalk between DNA methylation and DNA repair.

scholarly journals Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1187
Author(s):  
Michael Wassenegger ◽  
Athanasios Dalakouras
Keyword(s):  
Dna Methylation ◽  
Rna Interference ◽  
Gene Silencing ◽  
Plant Cells ◽  
Transcriptional Gene Silencing ◽  
Rnai Machinery ◽  
Double Stranded Rna ◽  
Post Transcriptional Gene Silencing ◽  
Cumulative Amount

Viroids are plant pathogenic, circular, non-coding, single-stranded RNAs (ssRNAs). Members of the Pospiviroidae family replicate in the nucleus of plant cells through double-stranded RNA (dsRNA) intermediates, thus triggering the host’s RNA interference (RNAi) machinery. In plants, the two RNAi pillars are Post-Transcriptional Gene Silencing (PTGS) and RNA-directed DNA Methylation (RdDM), and the latter has the potential to trigger Transcriptional Gene Silencing (TGS). Over the last three decades, the employment of viroid-based systems has immensely contributed to our understanding of both of these RNAi facets. In this review, we highlight the role of Pospiviroidae in the discovery of RdDM, expound the gradual elucidation through the years of the diverse array of RdDM’s mechanistic details and propose a revised RdDM model based on the cumulative amount of evidence from viroid and non-viroid systems.

scholarly journals Post-transcriptional gene silencing triggers dispensable DNA methylation in gene body in Arabidopsis

2019 ◽  
Vol 47 (17) ◽  
pp. 9104-9114 ◽  
Author(s):  
Christelle Taochy ◽  
Agnès Yu ◽  
Nicolas Bouché ◽  
Nathalie Bouteiller ◽  
Taline Elmayan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Silencing ◽  
De Novo ◽  
Transcriptional Silencing ◽  
Transcriptional Gene Silencing ◽  
Gene Body ◽  
Coding Sequence ◽  
Post Transcriptional Gene Silencing ◽  
Methylation Signal ◽  
Rule Out

Abstract Spontaneous post-transcriptional silencing of sense transgenes (S-PTGS) is established in each generation and is accompanied by DNA methylation, but the pathway of PTGS-dependent DNA methylation is unknown and so is its role. Here we show that CHH and CHG methylation coincides spatially and temporally with RDR6-dependent products derived from the central and 3′ regions of the coding sequence, and requires the components of the RNA-directed DNA methylation (RdDM) pathway NRPE1, DRD1 and DRM2, but not CLSY1, NRPD1, RDR2 or DCL3, suggesting that RDR6-dependent products, namely long dsRNAs and/or siRNAs, trigger PTGS-dependent DNA methylation. Nevertheless, none of these RdDM components are required to establish S-PTGS or produce a systemic silencing signal. Moreover, preventing de novo DNA methylation in non-silenced transgenic tissues grafted onto homologous silenced tissues does not inhibit the triggering of PTGS. Overall, these data indicate that gene body DNA methylation is a consequence, not a cause, of PTGS, and rule out the hypothesis that a PTGS-associated DNA methylation signal is transmitted independent of a PTGS signal.

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