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RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation [sRNA-seq]

ABSTRACT: RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation [sRNA-seq]

PROVIDER: PRJNA1031111 | ENA |

REPOSITORIES: ENA

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RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation [sRNA-seq]

Project description:Background: Plant-unique RNA polymerase IV (Pol IV) governs the establishment of small RNA-directed DNA methylation (RdDM) and contributes to the maintenance of transposable element (TE) silencing. Pol IV-dependent RdDM is highly active during embryonic development, and its absence occasionally reduces seed sets in species with high TE content. However, the mechanism underlying embryonic development failure due to the loss of Pol IV-RdDM remains largely unclear. Results: Here, we report that the loss-of-function of SlNRPD1, encoding the largest subunit of the Pol IV complex leads to aberrant embryogenesis in tomato (Solanum lycopersicum). The slnrpd1 mutants show non-CG hypomethylation and a burst of 21/22-nt sRNA from the distal chromatin region. We found that non-CG hypomethylation at the gene body region is generally associated with the activation of transcription, and knocking out DEMETER-like DNA demethylases cannot reverse slnrpd1 embryo lethality. mCHH hypomethylation in slnrpd1 disrupts gene expression related to auxin and WUSCHEL-related homeobox (WOX) signaling. TE reactivation in slnrpd1 mainly affects the expression of a limited number of nearby genes rather than contributing to excessive sRNA. Conclusion: We conclude that Pol IV-mediated RdDM is essential for tomato embryogenesis via non-CG methylation. mCHH hypomethylation in the slnrpd1 embryo leads to abnormal auxin/WOX signaling and TE reactivation which probably disrupts the tissue and organ initiation. This study provides new insights into the epigenetic regulation of gene and TE expression during embryogenesis. Keywords: DNA methylation, RdDM, NRPD1, Embryogenesis, Tomato

2024-10-01 | GSE246017 | GEO

RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation [Bisulfite_seq]

2024-10-01 | GSE246015 | GEO

RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation [RNA-Seq]

2024-10-01 | GSE246016 | GEO

RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation

Project description:RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation

| PRJNA1031104 | ENA

RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation [Bisulfite_seq]

Project description:RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation [Bisulfite_seq]

| PRJNA1031108 | ENA

RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation [RNA-Seq]

Project description:RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation [RNA-Seq]

| PRJNA1031110 | ENA

RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-10-01 | GSE246018 | GEO

RNA Polymerase IV sensitises the chromatin via histone modifications modulating protein coding genes [sRNA-Seq]

Project description:Knock down of RNA polymerase IV in rice caused pleiotropic reproductive defects. We investigated the molecular effects of loss of pol IV in different rice tissues by profiling sRNA and mRNA transcriptomes, DNA methylomes, histone modifications and degradome sequencing. These analyses revealed the multifaceted roles of RNA polymerase IV in bringing about regulation of protein coding genes.

2023-02-28 | GSE180456 | GEO