The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status
- University of California, Riverside, United States
- Salk Institute for Biological Studies, United States
- Rural Development Administration, Republic of Korea
- David Geffen School of Medicine at UCLA, United States
- Tsinghua University, China
- Peking University, China
- Shenzhen University, China
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.
Data availability
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LIL, an α-crystallin/Heat Shock Protein 20 family protein, associates with the Methyl -CpG-Binding Domain protein MBD7 to suppress cytosine methylation and transcriptional gene silencing in Arabidopsis (mRNA-seq)Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE83557).
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LIL, an α-crystallin/Heat Shock Protein 20 family protein, associates with the Methyl -CpG-Binding Domain protein MBD7 to suppress cytosine methylation and transcriptional gene silencing in Arabidopsis (smallRNA-seq)Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE59639).
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LIL, an α-crystallin/Heat Shock Protein 20 family protein, associates with the Methyl -CpG-Binding Domain protein MBD7 to suppress cytosine methylation and transcriptional gene silencing in ArabidopsisPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE83355).
Article and author information
Author details
Funding
Gordon and Betty Moore Foundation (GBMF3046)
- Xuemei Chen
National Science Foundation of China (91440105)
- Xuemei Chen
National Science Foundation of China (30970265)
- Beixin Mo
National Science Foundation of China (31210103901)
- Beixin Mo
Guangdong Innovation Research Team Fund (2014ZT05S078)
- Xuemei Chen
National Institutes of Health (GM061146)
- Xuemei Chen
National Academy of Agricultural Science (PJ008725)
- So Youn Won
China Scholarship Council
- Dongming Li
Glenn Center for Aging Research at the Salk Institute
- Ana Marie S Palanca
Helmsley Charitable Trust
- Ana Marie S Palanca
- Julie A Law
National Institutes of Health (GM112966)
- Julie A Law
National Institutes of Health (GM089778)
- James A Wohlschlegel
National Institutes of Health (P30 014195)
- Ana Marie S Palanca
- Julie A Law
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2017, Li et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status
eLife 6:e19893.
https://doi.org/10.7554/eLife.19893
Further reading
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- Chromosomes and Gene Expression
Since double-stranded RNA (dsRNA) is effective for silencing a wide variety of genes, all genes are typically considered equivalent targets for such RNA interference (RNAi). Yet, loss of some regulators of RNAi in the nematode Caenorhabditis elegans can selectively impair the silencing of some genes. Here, we show that such selective requirements can be explained by an intersecting network of regulators acting on genes with differences in their RNA metabolism. In this network, the Maelstrom domain-containing protein RDE-10, the intrinsically disordered protein MUT-16, and the Argonaute protein NRDE-3 work together so that any two are required for silencing one somatic gene, but each is singly required for silencing another somatic gene, where only the requirement for NRDE-3 can be overcome by enhanced dsRNA processing. Quantitative models and their exploratory simulations led us to find that (1) changing cis-regulatory elements of the target gene can reduce the dependence on NRDE-3, (2) animals can recover from silencing in non-dividing cells, and (3) cleavage and tailing of mRNAs with UG dinucleotides, which makes them templates for amplifying small RNAs, are enriched within ‘pUG zones’ matching the dsRNA. Similar crosstalk between pathways and restricted amplification could result in apparently selective silencing by endogenous RNAs.
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- Chromosomes and Gene Expression
Although the role of G-quadruplex (G4) DNA structures has been suggested in chromosomal looping this was not tested directly. Here, to test causal function, an array of G4s, or control sequence that does not form G4s, were inserted within chromatin in cells. In vivo G4 formation of the inserted G4 sequence array, and not the control sequence, was confirmed using G4-selective antibody. Compared to the control insert, we observed a remarkable increase in the number of 3D chromatin looping interactions from the inserted G4 array. This was evident within the immediate topologically associated domain (TAD) and throughout the genome. Locally, recruitment of enhancer histone marks and the transcriptional coactivator p300/Acetylated-p300 increased in the G4-array, but not in the control insertion. Resulting promoter-enhancer interactions and gene activation were clear up to 5 Mb away from the insertion site. Together, these show the causal role of G4s in enhancer function and long-range chromatin interactions. Mechanisms of 3D topology are primarily based on DNA-bound architectural proteins that induce/stabilize long-range interactions. Involvement of the underlying intrinsic DNA sequence/structure in 3D looping shown here therefore throws new light on how long-range chromosomal interactions might be induced or maintained.
