The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status

Li, Dongming; Palanca, Ana Marie S.; Won, So Youn; Gao, Lei; Feng, Ying; Vashisht, Ajay A.; Liu, Li; Zhao, Yuanyuan; Liu, Xigang; Wu, Xiuyun; Li, Shaofang; Le, Brandon H.; Kim, Yun Ju; Yang, Guodong; Li, Shengben; Liu, Jinyuan; Wohlschlegel, James A.; Guo, Hongwei; Mo, Beixin; Law, Julie A.

doi:10.7554/elife.19893

Cited by 19 publications

(18 citation statements)

References 80 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2.0μg of purified genomic DNA was then used to generate MethylC-seq libraries as described in Li et al . 73 . The resulting libraries were pooled and sequenced (single end 50bp, SE50) on a HiSeq 2500 machine (Illumina).…”

Section: Methodsmentioning

confidence: 99%

Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family

2018

Self Cite

View full text Add to dashboard Cite

DNA methylation is essential for gene regulation, transposon silencing and imprinting. Although the generation of specific DNA methylation patterns is critical for these processes, how methylation is regulated at individual loci remains unclear. Here we show that a family of four putative chromatin remodeling factors, CLASSY (CLSY) 1-4, are required for both locus-specific and global regulation of DNA methylation in Arabidopsis thaliana. Mechanistically, these factors act in connection with RNA polymerase-IV (Pol-IV) to control the production of 24-nucleotide small interfering RNAs (24nt-siRNAs), which guide DNA methylation. Individually, the CLSYs regulate Pol-IV-chromatin association and 24nt-siRNA production at thousands of distinct loci, and together, they regulate essentially all 24nt-siRNAs. Depending on the CLSYs involved, this regulation relies on different repressive chromatin modifications to facilitate locus-specific control of DNA methylation. Given the conservation between methylation systems in plants and mammals, analogous pathways may operate in a broad range of organisms.

show abstract

Section: Methodsmentioning

confidence: 99%

Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family

2018

Self Cite

View full text Add to dashboard Cite

show abstract

“…DNA isolation, methyl-seq library construction, and sequencing: ~0.1 g of tissue from 15 day old rosettes, 25 day old leaves, or >5,000 unfertilized ovules were collected for genomic DNA isolation using the DNeasy Plant Mini Kit (Qiagen, Cat# 69104). MethylC-seq libraries were generated using 2.0 μg of DNA from rosettes and leaves, and 0.5-1.0 μg of DNA from ovules as described in Li et al 62 . The libraries were then pooled and sequenced (single end 50 bp, SE50) on a HiSeq 2500 machine (Illumina).…”

Section: Methylc-seq Library Preparation Mapping and Differentially Methylated Region (Dmr) Callingmentioning

confidence: 99%

The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis

Zhou

Çoruh

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

DNA methylation shapes the epigenetic landscape of the genome, plays critical roles in regulating gene expression, and ensures transposon silencing. As evidenced by the numerous defects associated with aberrant DNA methylation landscapes, establishing proper tissue-specific methylation patterns is critical. Yet, how such differences arise remains a largely open question in both plants and animals. Here we demonstrate that CLASSY1-4 (CLSY1-4), four locus-specific regulators of DNA methylation that are differentially expressed during plant development, play major roles in controlling tissue-specific DNA methylation patterns. Depending on the tissue, the genetic requirements for specific CLSYs differ significantly and, on a global scale, certain clsy mutants are sufficient to largely shift the epigenetic landscape between tissues. Together, these findings not only reveal substantial epigenetic diversity between tissues, but assign these changes to specific CLSY proteins, revealing how locus-specific targeting combined with tissue-specific expression enables the CLSYs to generate epigenetic diversity during plant development.

show abstract

“…While the anti‐silencing protein complex IDM was reported to target ROS1 for active DNA demethylation and thereby suppress gene silencing, an independent study showed that the same complex functions to suppress gene silencing primarily at a downstream step of DNA methylation (Li et al ). Thus, the IDM complex is most likely to possess both DNA demethylation‐dependent and independent roles in suppression of gene silencing even though the DNA demethylation‐independent mechanism is elusive.…”

Section: Introductionmentioning

confidence: 99%

A methylated‐DNA‐binding complex required for plant development mediates transcriptional activation of promoter methylated genes

Zhao

Lin

et al. 2019

JIPB

View full text Add to dashboard Cite

Although the mechanism of DNA methylation‐mediated gene silencing is extensively studied, relatively little is known about how promoter methylated genes are protected from transcriptional silencing. SUVH1, an Arabidopsis Su(var)3‐9 homolog, was previously shown to be required for the expression of a few promoter methylated genes. By chromatin immunoprecipitation combined with sequencing, we demonstrate that SUVH1 binds to methylated genomic loci targeted by RNA‐directed DNA methylation. SUVH1 and its homolog SUVH3 function partially redundantly and interact with three DNAJ domain‐containing homologs, SDJ1, SDJ2, and SDJ3, thus forming a complex which we named SUVH‐SDJ. The SUVH‐SDJ complex components are co‐localized in a large number of methylated promoters and are required for the expression of a subset of promoter methylated genes. We demonstrate that the SUVH‐SDJ complex components have transcriptional activation activity. SUVH1 and SUVH3 function synergistically with SDJ1, SDJ2, and SDJ3 and are required for plant viability. This study reveals how the SUVH‐SDJ complex protects promoter methylated genes from transcriptional silencing and suggests that the transcriptional activation of promoter methylated genes mediated by the SUVH‐SDJ complex may play a critical role in plant growth and development.

show abstract

The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status

Cited by 19 publications

References 80 publications

Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family

Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family

The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis

A methylated‐DNA‐binding complex required for plant development mediates transcriptional activation of promoter methylated genes

Contact Info

Product

Resources

About