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
-
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).
-
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).
-
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.
Reviewing Editor
- Steven Henikoff, Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, United States
Publication history
- Received: July 25, 2016
- Accepted: April 24, 2017
- Accepted Manuscript published: April 28, 2017 (version 1)
- Version of Record published: June 7, 2017 (version 2)
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.
Metrics
-
- 2,676
- Page views
-
- 732
- Downloads
-
- 13
- Citations
Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
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
-
- Cell Biology
- Chromosomes and Gene Expression
The shape and size of the human cell nucleus is highly variable amongst cell types and tissues. Changes in nuclear morphology are associated with disease, including cancer, as well as with premature and normal aging. Despite the very fundamental nature of nuclear morphology, the cellular factors that determine nuclear shape and size are not well understood. To identify regulators of nuclear architecture in a systematic and unbiased fashion, we performed a high-throughput imaging-based siRNA screen targeting 867 nuclear proteins including chromatin-associated proteins, epigenetic regulators, and nuclear envelope components. Using multiple morphometric parameters and eliminating cell cycle effectors, we identified a set of novel determinants of nuclear size and shape. Interestingly, most identified factors altered nuclear morphology without affecting the levels of lamin proteins, which are known prominent regulators of nuclear shape. In contrast, a major group of nuclear shape regulators were modifiers of repressive heterochromatin. Biochemical and molecular analysis uncovered a direct physical interaction of histone H3 with lamin A mediated via combinatorial histone modifications. Furthermore, disease-causing lamin A mutations that result in disruption of nuclear shape inhibited lamin A-histone H3 interactions. Finally, oncogenic histone H3.3 mutants defective for H3K27 methylation resulted in nuclear morphology abnormalities. Altogether, our results represent a systematic exploration of cellular factors involved in determining nuclear morphology and they identify the interaction of lamin A with histone H3 as an important contributor to nuclear morphology in human cells.
-
- Biochemistry and Chemical Biology
- Chromosomes and Gene Expression
Cells have evolved the DNA damage response (DDR) pathways in response to DNA replication stress or DNA damage. In the ATR-Chk1 DDR pathway, it has been proposed that ATR is recruited to RPA-coated single-stranded DNA (ssDNA) by direct ATRIP-RPA interaction. However, it remains elusive how ATRIP is recruited to ssDNA in an RPA-independent manner. Here, we provide evidence that APE1 directly associates ssDNA to recruit ATRIP onto ssDNA in an RPA-independent fashion. The N-terminal motif within APE1 is required and sufficient for the APE1-ATRIP interaction in vitro and the distinct APE1-ATRIP interaction is required for ATRIP recruitment to ssDNA and the ATR-Chk1 DDR pathway activation in Xenopus egg extracts. In addition, APE1 directly associates with RPA70 and RPA32 via two distinct motifs. Taken together, our evidence suggests that APE1 recruits ATRIP onto ssDNA in an RPA-dependent and -independent manner in the ATR DDR pathway.
