Methyl-CpG-Binding Domain Protein MBD7 Is Required for Active DNA Demethylation in Arabidopsis

Wang, Chunlei; Dong, Xiaomei; Jin, Dan; Zhao, Yusheng; Xie, Shaojun; Li, Xiaojie; He, Xin‐Jian; Lang, Zhaobo; Lai, Jinsheng; Zhu, Jian‐Kang; Gong, Zhizhong

doi:10.1104/pp.114.252106

Cited by 51 publications

(71 citation statements)

References 38 publications

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“…Since IDAP1 and IDAP2 physically interact, and when either IDAP1 or IDAP2 mutates, IDM1 targeting, active DNA demethylation, and transcriptional gene silencing at specific loci were affected (Figs 4 and 5), we concluded that IDAP1 and IDAP2 cooperate to promote IDM1 targeting and H3K18 and H3K23 acetylation at many endogenous loci. MBD7 was previously found to assist in IDM1 targeting by binding to methylated DNA via its MBD motifs Li et al, 2015a;Wang et al, 2015). To summarize our findings on IDM1 targeting regulated by these three proteins, we proposed a model in which domesticated IDAP1 and IDAP2 coordinate with MBD7 to regulate IDM1 targeting (Fig 8).…”

Section: Discussionmentioning

confidence: 94%

Retraction: ‘A pair of transposon‐derived proteins regulate active DNA demethylation in Arabidopsis’

Li¹,

Yuan²,

Wang³

et al. 2016

The EMBO Journal

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Fig 6D-E and Fig 7D, WT-LUC and idm1-14 were in an rdr6-11 background, while idap1-1 and idap2-1 were in wild type background. RDR6 has a demonstrated role in DNA methylation and transcriptional gene silencing, and the rdr6 mutation could therefore have a profound impact on gene silencing in these experiments. Thus, the observed reduced LUC luminescence in idap1-1 and idap2-1 mutants could have resulted from the combined effects of rdr6 and idap1 or idap2 mutations, which might change the main conclusion of this paper. Further experiments will be performed to confirm the phenotypes. All authors concur with this statement and wish to apologize for the inconvenience caused.'The EMBO Journal In Arabidopsis, IDM1 is a histone acetyltransferase that plays critical roles in preventing hypermethylation of DNA and transcriptional gene silencing, but the mechanism(s) by which IDM1 is targeted to specific genomic loci is still unclear. Here, we find two new components of the IDM1 complex, IDAP1 and IDAP2, which bear high similarities to the transposase and myb-like DNA-binding protein of PIF/Harbinger transposons, respectively. Dysfunction of IDAP1 or IDAP2 causes DNA hypermethylation and repression of reporter genes as well as endogenous genes. IDAP1 interacts with IDAP2, and they form a protein complex with IDM1. Furthermore, IDAP2 has DNA-binding activity, which facilitates the recruitment of IDM1 to its target loci. We propose that IDAP1 and IDAP2, co-opted from ancient PIF/ Harbinger-like transposon proteins, act together with IDM1 to regulate active DNA demethylation in higher plants.

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Section: Discussionmentioning

confidence: 94%

Retraction: ‘A pair of transposon‐derived proteins regulate active DNA demethylation in Arabidopsis’

Li¹,

Yuan²,

Wang³

et al. 2016

The EMBO Journal

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“…ROS1 can remove the 5mC base and nick the DNA backbone, leaving a single nucleotide gap that is filled with an unmethylated cytosine through a base excision repair pathway 9–13 . An anti-silencing protein complex containing methyl-DNA binding protein 7 (MBD7), increased DNA methylation 1 (IDM1), IDM2, and IDM3, was recently discovered to regulate ROS1 targeting, and in turn DNA demethylation 14–16 . In Arabidopsis, some TEs show lower expression levels in ros1 mutants due to increased DNA methylation 15,17 .…”

Section: Introductionmentioning

confidence: 99%

The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications

et al. 2016

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The Arabidopsis ROS1/DEMETER family of 5mC DNA glycosylases are the first genetically characterized DNA demethylases in eukaryotes. However, the features of ROS1 targeted genomic loci are not well-understood. In this study, we characterized ROS1 target loci in Arabidopsis Col-0 and C24 ecotypes. We found that ROS1 preferentially targets transposable elements (TEs) and intergenic regions. Compared to most TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting that ROS1 may prevent DNA methylation spreading from TEs to nearby genes. ROS1-targeted TEs are specifically enriched for H3K18Ac and H3K27me3, and depleted of H3K27me and H3K9me2. Importantly, we identified thousands of previously unknown RNA-directed DNA methylation (RdDM) targets upon depletion of ROS1, suggesting that ROS1 strongly antagonizes RdDM at these loci. In addition, we show that ROS1 also antagonizes RdDM-independent DNA methylation at some loci. Our results provide important insights into the genome-wide targets of ROS1 and the crosstalk between DNA methylation and ROS1-mediated active DNA demethylation.

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“…The raw sequence data were demultiplexed and converted to fastq files using bcl2fastq2 Conversion Software (version v2.16.0) under default parameters. The DNA methylation was analyzed according to Zhao et al (2014) and Wang et al (2015).…”

Section: Bs-seqmentioning

confidence: 99%

The second subunit of DNA-polymerase delta is required for genomic stability and epigenetic regulation

et al. 2016

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ORCID IDs: 0000-0002-1641-8650 (J.Z.); 0000-0002-6719-9814 (S.X.); 0000-0001-5134-731X (J.-K.Z.).DNA polymerase d plays crucial roles in DNA repair and replication as well as maintaining genomic stability. However, the function of POLD2, the second small subunit of DNA polymerase d, has not been characterized yet in Arabidopsis (Arabidopsis thaliana). During a genetic screen for release of transcriptional gene silencing, we identified a mutation in POLD2. Whole-genome bisulfite sequencing indicated that POLD2 is not involved in the regulation of DNA methylation. POLD2 genetically interacts with Ataxia Telangiectasia-mutated and Rad3-related and DNA polymerase a. The pold2-1 mutant exhibits genomic instability with a high frequency of homologous recombination. It also exhibits hypersensitivity to DNA-damaging reagents and short telomere length. Whole-genome chromatin immunoprecipitation sequencing and RNA sequencing analyses suggest that pold2-1 changes H3K27me3 and H3K4me3 modifications, and these changes are correlated with the gene expression levels. Our study suggests that POLD2 is required for maintaining genome integrity and properly establishing the epigenetic markers during DNA replication to modulate gene expression.

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Methyl-CpG-Binding Domain Protein MBD7 Is Required for Active DNA Demethylation in Arabidopsis

Cited by 51 publications

References 38 publications

Retraction: ‘A pair of transposon‐derived proteins regulate active DNA demethylation in Arabidopsis’

Retraction: ‘A pair of transposon‐derived proteins regulate active DNA demethylation in Arabidopsis’

The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications

The second subunit of DNA-polymerase delta is required for genomic stability and epigenetic regulation

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