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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE217682 | GEO | 2023/08/21

REPOSITORIES: GEO

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