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Loss of H3K9me3 heterochromatin at protein coding genes enables developmental lineage specification (RNA-Seq)

ABSTRACT: Loss of H3K9me3 heterochromatin at protein coding genes enables developmental lineage specification (RNA-Seq)

PROVIDER: PRJNA470536 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7135020.fastq.gz	Fastqsanger.gz
	SRR7135030.fastq.gz	Fastqsanger.gz
	SRR7135021.fastq.gz	Fastqsanger.gz
	SRR7135022.fastq.gz	Fastqsanger.gz
	SRR7135023.fastq.gz	Fastqsanger.gz

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Loss of H3K9me3 heterochromatin at protein coding genes enables developmental lineage specification

Project description:Loss of H3K9me3 heterochromatin at protein coding genes enables developmental lineage specification

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Loss of H3K9me3 heterochromatin at protein coding genes enables developmental lineage specification (ChIP-Seq)

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Loss of H3K9me3 heterochromatin at protein coding genes enables developmental lineage specification (srHC-seq)

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Loss of H3K9me3 heterochromatin at protein coding genes enables developmental lineage specification (ChIP-Seq)

Project description:Domains of transcriptionally repressed heterochromatin, decorated by histone 3 lysine 9 trimethylation (H3K9me3), are reduced in embryonic stem cells compared to fully differentiated cells. However, the establishment and dynamics of closed regions of chromatin at protein coding genes, in natural embryologic development, has not been described. We developed a novel, antibody-independent method to isolate and map compacted heterochromatin from low cell number samples. Unexpectedly, we uncovered extensive high levels of H3K9me3-decorated, compacted heterochromatin at protein coding genes in early, uncommitted cells in the three germ layers, undergoing profound rearrangements and reduction upon differentiation, concomitant with cell type-specific gene expression. Perturbation of the three H3K9me3-related methyltransferases revealed that H3K9me3 heterochromatin is required to maintain cell lineage fidelity. We propose a key role for chromatin-based restriction of gene activity via H3K9me3 during embryologic development

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Loss of H3K9me3 heterochromatin at protein coding genes enables developmental lineage specification (srHC-seq)

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Loss of H3K9me3 heterochromatin at protein coding genes enables developmental lineage specification (RNA-Seq)

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H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification.

Project description:Gene silencing by chromatin compaction is integral to establishing and maintaining cell fates. Trimethylated histone 3 lysine 9 (H3K9me3)-marked heterochromatin is reduced in embryonic stem cells compared to differentiated cells. However, the establishment and dynamics of closed regions of chromatin at protein-coding genes, in embryologic development, remain elusive. We developed an antibody-independent method to isolate and map compacted heterochromatin from low-cell number samples. We discovered high levels of compacted heterochromatin, H3K9me3-decorated, at protein-coding genes in early, uncommitted cells at the germ-layer stage, undergoing profound rearrangements and reduction upon differentiation, concomitant with cell type-specific gene expression. Perturbation of the three H3K9me3-related methyltransferases revealed a pivotal role for H3K9me3 heterochromatin during lineage commitment at the onset of organogenesis and for lineage fidelity maintenance.

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The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [TT-Seq]

Project description:H3K9me3-heterochromatin, compacted by HP1 proteins, restricts transcription factor binding and functions as a barrier to cell fate changes in development and reprogramming1,2. To investigate principles underlying H3K9me3-heterochromatin maintenance in mammalian cells, we applied degron engineering3,4 on mouse ESCs to conditionally deplete all three H3K9me3-methyltransferases within one hour and found an unexpectedly dynamic nature of heterochromatin maintenance. Following H3K9me3 methyltransferases degradation, HP1β dissociates from heterochromatin within three hours, and transcription factors quickly access the de-compacted heterochromatin, activating transcription of their targets, which then promotes H3K9me3 decay. Both passive dilution and active removal contribute to the H3K9me3 decay. Mathematical modeling reveals distinct H3K9me3 heterochromatin states with diverse chromatin features which influence initial H3K9me3 levels and the stability of H3K9me3 domains, thereby expanding our understanding of distinct heterochromatin domains. Rampant transposable element de-repression interferes with transcription of poised early developmental and signaling genes outside H3K9me3-domains, highlighting the intricate roles of dynamic H3K9me3-heterochromatin maintenance in safeguarding developmental programs. Our findings deconvolve the hierarchical relationships between H3K9me3 marks, methyltransferases, HP1 and transcription factors to reveal principles of H3K9me3-heterochromatin maintenance and how its remodeling enables transcription and cell fate change.

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