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PNET-seq in Arabidopsis after flavopiridol (FLA) treatment

ABSTRACT: pNET-seq in Arabidopsis after flavopiridol (FLA) treatment

PROVIDER: PRJNA1183353 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31277584_1.fastq.gz	Fastqsanger.gz
	SRR31277584_2.fastq.gz	Fastqsanger.gz
	SRR31277585_1.fastq.gz	Fastqsanger.gz
	SRR31277585_2.fastq.gz	Fastqsanger.gz
	SRR31277586_1.fastq.gz	Fastqsanger.gz

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Project description:Eukaryotic euchromatin is the less compact chromatin and modified by many histone modifications such as H3 Lysine 36 methylation (H3K36me). Here we report a new chromatin state, Transcription Resistive, which is differentiated from activation and silencing. Transcription resistive is stamped by H3K36me with almost undetectable transcription activity but open chromatin state, and occupies most documented plant essential genes. Mutating SDG8, previously known as the major H3K36 methyltransferase in Arabidopsis, surprisingly elevates 78.7% H3K36me3 marked resistive loci, which count for 39.4% of the coding genome. Genetically, SDG8 prevents H3K36me activity of SDG4 at short and intron-less genes to secure plant fertility, while SDG8 collaborates with other H3K36me methyltransferases on long and intron-rich genes. Together, our results reveal SDG8 is the primary sensor to suppress excessive H3K36me, and uncovered the resistive is the conserved H3K36me-stamped novel transcription state in plants, highlighting the regulatory diversities and biological significances of H3K36 methylation in eukaryotes.

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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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