Regulation of Active DNA Demethylation by a Methyl-CpG-Binding Domain Protein in Arabidopsis thaliana

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.

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

“…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).…”

“…To elucidate the mechanism(s) underlying IDM1 targeting in active DNA demethylation, we purified the IDM1 complex by affinity purification in a previous study and identified two proteins, MBD7 and IDL1, in this complex (Li et al, 2015a). In addition to MBD7 and IDL1, we also identified IDM1-associated protein 1 (IDAP1) and IDM1-associated protein 2 (IDAP2) from the mass spectrometric analysis of IDM1 co-purified proteins (Appendix Table S1).…”

“…Previous reports showed that IDM1 and other IDM1 complex components (IDM2, IDL1/IDM3, and MBD7) are required to prevent transcriptional silencing of specific transgenes and endogenous genes Lang et al, 2015;Li et al, 2015a). To determine whether IDAP1 and IDAP2 ▸ Figure 3.…”

“…Homozygous complemented lines were used for phenotypic analysis and ChIP assays. The IDM1-3HA-YFP/idm1-3 transgenic plants used for ChIP assays were previously described (Li et al, 2015a). The IDM1-3HA-YFP/idap2-1 transgenic plants were generated by crossing the IDM1-3HA-YFP/idm1-3 with the idap2-1 mutant plants.…”

Emerging links between iron-sulfur clusters and 5-methylcytosine base excision repair in plants

“…DEMETERs are bifunctional glycosylases (Choi et al, 2002;Gong et al, 2002), and are expected to cooperate with DNA polymerase δ/ε in long-patch BER, especially because plant genomes lack sequences encoding DNA polymerase β homologs (Uchiyama et al, 2008), which are characteristic for short-patch BER. Nevertheless, some homologous plant proteins involved in short-patch BER steps (such as X-ray repair cross-complementing protein 1 (XRCC1), AP endonuclease 1 (APE1), 3'-phosphatase zinc finger DNA 3'-phosphoesterase (ZDP) and DNA ligase 1 (AtLIG1) have been identified as the components affected in DNA demethylation (Andreuzza et al, 2010;Li et al, 2015a;Li et al, 2015b). The identity of all BER enzymes downstream of DEMETERs still needs to be revealed.…”