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DDM1-facilitated R-loop resolution and H2A.Z exclusion primes heterochromatin formation in Arabidopsis

ABSTRACT: DDM1-facilitated R-loop resolution and H2A.Z exclusion primes heterochromatin formation in Arabidopsis

PROVIDER: PRJNA902406 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22253200_1.fastq.gz	Fastqsanger.gz
	SRR22253200_2.fastq.gz	Fastqsanger.gz
	SRR22253201_1.fastq.gz	Fastqsanger.gz
	SRR22253201_2.fastq.gz	Fastqsanger.gz
	SRR22253202_1.fastq.gz	Fastqsanger.gz

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DDM1-facilitated R-loop resolution and H2A.Z exclusion primes heterochromatin formation in Arabidopsis [ssDRIP-seq, WGBS-seq, ChIP-seq]

Project description:DDM1-facilitated R-loop resolution and H2A.Z exclusion primes heterochromatin formation in Arabidopsis [ssDRIP-seq, WGBS-seq, ChIP-seq]

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DDM1-facilitated R-loop resolution and H2A.Z exclusion primes heterochromatin formation in Arabidopsis [ssDRIP-seq, WGBS-seq, ChIP-seq]

Project description:Programmed constitutive heterochromatin silencing is essential for eukaryotic genome regulation, yet the initial step of this process is ambiguous. A large proportion of R-loops (RNA:DNA hybrids) had been unexpectedly identified within Arabidopsis pericentromeric heterochromatin with unknown functions. Through a genome-wide R-loop profiling screen, we find DDM1 (Decrease in DNA Methylation 1) is the primary restrictor of pericentromeric R-loops via its RNA:DNA helicase activity. Low levels of pericentromeric R-loops resolved by DDM1 co-transcriptionally can prime constitutive heterochromatin silencing. Furthermore, we demonstrate that DDM1 physically excludes histone H2A variant H2A.Z, and promotes H2A.W deposition for faithful heterochromatin initiation soon after R-loop clearance. The dual functions of DDM1 in R-loop resolution and H2A.Z eviction are essential for sperm nuclei structure maintenance in mature pollen. Our work unravels the co-transcriptional R-loop resolution coupled with accurate H2A variants deposition is the primary step of constitutive heterochromatin silencing in Arabidopsis, which might be conserved across eukaryotes.

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DDM1-facilitated R-loop resolution and H2A.Z exclusion primes heterochromatin formation in Arabidopsis [ssDRIP-seq, ChIP-seq, pNET-seq, ATAC-seq]

Project description:DDM1-facilitated R-loop resolution and H2A.Z exclusion primes heterochromatin formation in Arabidopsis [ssDRIP-seq, ChIP-seq, pNET-seq, ATAC-seq]

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DDM1-facilitated R-loop resolution and H2A.Z exclusion primes heterochromatin formation in Arabidopsis [ssDRIP-seq, ChIP-seq, pNET-seq, ATAC-seq]

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DDM1-facilitated R-loop resolution and H2A.Z exclusion primes heterochromatin formation in Arabidopsis

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

2023-08-21 | GSE218148 | GEO

DDM1-mediated R-loop resolution and H2A.Z exclusion facilitates heterochromatin formation in Arabidopsis.

Project description:Programmed constitutive heterochromatin silencing is essential for eukaryotic genome regulation, yet the initial step of this process is ambiguous. A large proportion of R-loops (RNA:DNA hybrids) had been unexpectedly identified within Arabidopsis pericentromeric heterochromatin with unknown functions. Through a genome-wide R-loop profiling screen, we find that DDM1 (decrease in DNA methylation 1) is the primary restrictor of pericentromeric R-loops via its RNA:DNA helicase activity. Low levels of pericentromeric R-loops resolved by DDM1 cotranscriptionally can facilitate constitutive heterochromatin silencing. Furthermore, we demonstrate that DDM1 physically excludes histone H2A variant H2A.Z and promotes H2A.W deposition for faithful heterochromatin initiation soon after R-loop clearance. The dual functions of DDM1 in R-loop resolution and H2A.Z eviction are essential for sperm nuclei structure maintenance in mature pollen. Our work unravels the cotranscriptional R-loop resolution coupled with accurate H2A variants deposition is the primary step of constitutive heterochromatin silencing in Arabidopsis, which might be conserved across eukaryotes.

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Deposition of histone variant H2A.Z within gene bodies regulates responsive genes

Project description:The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that a loss of H2A.Z in Arabidopsis does not affect the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is caused by the exclusion of H2A.Z from methylated DNA. RNA-seq and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. We find that a loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to both endogenous and exogenous stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes. Examination of DNA methylation and transcription in an h2a.z mutant

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Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

Project description:Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5' ends of genes where it promotes transcriptional competence. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation. Keywords: Affinity-purification on microarray All experiments were done using two channels per chip. DNA methylation experiments compared immunoprecipitated, methylated DNA to control genomic DNA. H2A.Z experiments compared whole micrococcal nuclease-treated affinity-purified chromatin to input chromatin used for affinity purification. Affinity purification was performed using either biotin-tagged H2A.Z, pulled down using streptavidin, or endogenous H2A.Z pulled down using an anti-H2A.Z antibody.

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