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.
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
-
- 2,880
- views
-
- 761
- downloads
-
- 19
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
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
-
- Chromosomes and Gene Expression
- Developmental Biology
Transcription often occurs in bursts as gene promoters switch stochastically between active and inactive states. Enhancers can dictate transcriptional activity in animal development through the modulation of burst frequency, duration, or amplitude. Previous studies observed that different enhancers can achieve a wide range of transcriptional outputs through the same strategies of bursting control. For example, in Berrocal et al., 2020, we showed that despite responding to different transcription factors, all even-skipped enhancers increase transcription by upregulating burst frequency and amplitude while burst duration remains largely constant. These shared bursting strategies suggest that a unified molecular mechanism constraints how enhancers modulate transcriptional output. Alternatively, different enhancers could have converged on the same bursting control strategy because of natural selection favoring one of these particular strategies. To distinguish between these two scenarios, we compared transcriptional bursting between endogenous and ectopic gene expression patterns. Because enhancers act under different regulatory inputs in ectopic patterns, dissimilar bursting control strategies between endogenous and ectopic patterns would suggest that enhancers adapted their bursting strategies to their trans-regulatory environment. Here, we generated ectopic even-skipped transcription patterns in fruit fly embryos and discovered that bursting strategies remain consistent in endogenous and ectopic even-skipped expression. These results provide evidence for a unified molecular mechanism shaping even-skipped bursting strategies and serve as a starting point to uncover the realm of strategies employed by other enhancers.
-
- Chromosomes and Gene Expression
- Developmental Biology
About 70% of human cleavage stage embryos show chromosomal mosaicism, falling to 20% in blastocysts. Chromosomally mosaic human blastocysts can implant and lead to healthy new-borns with normal karyotypes. Studies in mouse embryos and human gastruloids showed that aneuploid cells are eliminated from the epiblast by p53-mediated apoptosis while being tolerated in the trophectoderm. These observations suggest a selective loss of aneuploid cells from human embryos, but the underlying mechanisms are not yet fully understood. Here, we investigated the cellular consequences of aneuploidy in a total of 125 human blastocysts. RNA-sequencing of trophectoderm cells showed activated p53 pathway and apoptosis proportionate to the level of chromosomal imbalance. Immunostaining corroborated that aneuploidy triggers proteotoxic stress, autophagy, p53-signaling, and apoptosis independent from DNA damage. Total cell numbers were lower in aneuploid embryos, due to a decline both in trophectoderm and in epiblast/primitive endoderm cell numbers. While lower cell numbers in trophectoderm may be attributed to apoptosis, aneuploidy impaired the second lineage segregation, particularly primitive endoderm formation. This might be reinforced by retention of NANOG. Our findings might explain why fully aneuploid embryos fail to further develop and we hypothesize that the same mechanisms lead to the removal of aneuploid cells from mosaic embryos.
