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Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [BS-PCR-seq]

ABSTRACT: Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [BS-PCR-seq]

PROVIDER: PRJNA513322 | ENA |

REPOSITORIES: ENA

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Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis

Project description:Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis

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Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [WGBS]

Project description:Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [WGBS]

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Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [BS-PCR-seq]

Project description:The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). We studied their order of action within the RdDM pathway by testing their ability to target methylation in different mutants. We also evaluated ectopic siRNA biogenesis, RNA Polymerase V (Pol V) recruitment, targeted DNA methylation, and gene expression changes at thousands of ZF-RdDM targets. We found that co-targeting both arms of the RdDM pathway, siRNA biogenesis and Pol V recruitment, dramatically enhanced targeted methylation. This work defines how RdDM components establish DNA methylation, and enables new strategies for epigenetic gene regulation via targeted DNA methylation.

2019-02-07 | GSE124744 | GEO

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CUT&Tag-BS: an efficient and low-cost method for simultaneous profiling of histone modification and DNA methylation

Project description:It remains a challenge to decipher the complex relationship between DNA methylation, histone modification, and the underlying DNA sequence with limited input material. Here, we developed an efficient, low-input, and low-cost method for simultaneous profiling of genomic binding sites of histone modification and methylation status of the underlying DNA at single-base resolution from the same cells in a single experiment by integrating CUT&Tag with tagmentation-based bisulfite sequencing (CUT&Tag-BS). We demonstrated the validity of our method for both active and repressive histone modifications using 250,000 mouse ESCs. CUT&Tag-BS showed similar enrichment patterns of histone modification to those observed in non-bisulfite-treated control; it further revealed that H3K4me1-marked regions are mostly CpG-poor, lack of methylation concordance, and exhibit prevalent DNA methylation heterogeneity among the cells. We anticipate that CUT&Tag-BS will be widely applied to directly address the genomic relationship between DNA methylation and histone modification, especially in low-input scenario with precious biological samples.

2021-10-20 | GSE179266 | GEO

Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis

2019-02-07 | GSE124546 | GEO

Co-targeting RNA Polymerases IV and V Promotes Efficient De Novo DNA Methylation in Arabidopsis.

Project description:The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). We studied their order of action within the RdDM pathway by testing their ability to target methylation in different mutants. We also evaluated ectopic siRNA biogenesis, RNA polymerase V (Pol V) recruitment, targeted DNA methylation, and gene-expression changes at thousands of ZF-RdDM targets. We found that co-targeting both arms of the RdDM pathway, siRNA biogenesis and Pol V recruitment, dramatically enhanced targeted methylation. This work defines how RdDM components establish DNA methylation and enables new strategies for epigenetic gene regulation via targeted DNA methylation.

| S-EPMC6386582 | biostudies-literature

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