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.
Reviewing Editor
- Steven Henikoff, Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, United States
Version 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.
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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
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Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remain controversial, with opposing models suggesting splicing occurs either during or after transcription. We used single-molecule RNA FISH, expansion microscopy, and live-cell imaging to reveal the spatiotemporal distribution of nascent transcripts in mammalian cells. At super-resolution levels, we found that pre-mRNA formed clouds around the transcription site. These clouds indicate the existence of a transcription-site-proximal zone through which RNA move more slowly than in the nucleoplasm. Full-length pre-mRNA undergo continuous splicing as they move through this zone following transcription, suggesting a model in which splicing can occur post-transcriptionally but still within the proximity of the transcription site, thus seeming co-transcriptional by most assays. These results may unify conflicting reports of co-transcriptional versus post-transcriptional splicing.
