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Histone H3K9 methylation promotes formation of genome compartments in C. elegans via chromosome compaction and perinuclear anchoring

ABSTRACT: Histone H3K9 methylation promotes formation of genome compartments in C. elegans via chromosome compaction and perinuclear anchoring

PROVIDER: PRJNA603164 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10964906.fastq.gz	Fastqsanger.gz
	SRR10964907.fastq.gz	Fastqsanger.gz
	SRR10964908.fastq.gz	Fastqsanger.gz
	SRR10964909.fastq.gz	Fastqsanger.gz
	SRR10964910.fastq.gz	Fastqsanger.gz

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Histone H3K9 methylation promotes formation of genome compartments in C. elegans via chromosome compaction and perinuclear anchoring (Hi-C)

Project description:Genomic regions preferentially associate with regions of similar transcriptional activity, partitioning genomes into active and inactive compartments within the nucleus. Here we explored mechanisms controlling genome compartment organization in C. elegans and investigated roles for compartments in regulating gene expression. The distal arms of C. elegans chromosomes, which are enriched for heterochromatic histone modifications including H3K9me, interact with each other both in cis and in trans, while interacting less frequently with central regions of chromosomes, leading to genome compartmentalization. Arms are anchored to the nuclear periphery via the nuclear envelope protein CEC-4, which binds to H3K9me. By performing genome-wide chromosome conformation capture experiments (Hi-C), we showed that eliminating H3K9me1/me2/me3 through mutations in the methyltransferase genes met-2 and set-25 significantly impaired formation of genome compartments. cec-4 mutations also impaired compartmentalization, but to a lesser extent. We found that H3K9me promotes compartmentalization through two distinct mechanisms: perinuclear anchoring of chromosome arms via CEC-4 to promote their cis association, and an anchoring-independent mechanism that compacts individual chromosome arms. In both met-2 set-25 and cec-4 mutants, no dramatic changes in gene expression were found for genes that switched compartments or for genes that remained in their original compartment, suggesting that compartment strength does not dictate gene expression levels. Furthermore, H3K9me, but not perinuclear anchoring, also contributes to formation of another prominent feature of chromosome organization, megabase-scale topologically associating domains on X that are established by the dosage-compensation condensin complex. Our results demonstrate that H3K9me plays crucial roles in regulating genome organization at multiple levels.

2020-04-21 | GSE144252 | GEO

Histone H3K9 methylation promotes formation of genome compartments in C. elegans via chromosome compaction and perinuclear anchoring (ChIP-seq)

2020-04-21 | GSE144251 | GEO

Histone H3K9 methylation promotes formation of genome compartments in C. elegans via chromosome compaction and perinuclear anchoring (ChIP-seq)

Project description:Histone H3K9 methylation promotes formation of genome compartments in C. elegans via chromosome compaction and perinuclear anchoring (ChIP-seq)

| PRJNA603166 | ENA

Histone H3K9 methylation promotes formation of genome compartments in C. elegans via chromosome compaction and perinuclear anchoring (Hi-C)

Project description:Histone H3K9 methylation promotes formation of genome compartments in C. elegans via chromosome compaction and perinuclear anchoring (Hi-C)

| PRJNA603165 | ENA

Histone H3K9 methylation promotes formation of genome compartments in Caenorhabditis elegans via chromosome compaction and perinuclear anchoring.

Project description:Genomic regions preferentially associate with regions of similar transcriptional activity, partitioning genomes into active and inactive compartments within the nucleus. Here we explore mechanisms controlling genome compartment organization in Caenorhabditis elegans and investigate roles for compartments in regulating gene expression. Distal arms of C. elegans chromosomes, which are enriched for heterochromatic histone modifications H3K9me1/me2/me3, interact with each other both in cis and in trans, while interacting less frequently with central regions, leading to genome compartmentalization. Arms are anchored to the nuclear periphery via the nuclear envelope protein CEC-4, which binds to H3K9me. By performing genome-wide chromosome conformation capture experiments (Hi-C), we showed that eliminating H3K9me1/me2/me3 through mutations in the methyltransferase genes met-2 and set-25 significantly impaired formation of inactive Arm and active Center compartments. cec-4 mutations also impaired compartmentalization, but to a lesser extent. We found that H3K9me promotes compartmentalization through two distinct mechanisms: Perinuclear anchoring of chromosome arms via CEC-4 to promote their cis association, and an anchoring-independent mechanism that compacts individual chromosome arms. In both met-2 set-25 and cec-4 mutants, no dramatic changes in gene expression were found for genes that switched compartments or for genes that remained in their original compartment, suggesting that compartment strength does not dictate gene-expression levels. Furthermore, H3K9me, but not perinuclear anchoring, also contributes to formation of another prominent feature of chromosome organization, megabase-scale topologically associating domains on X established by the dosage compensation condensin complex. Our results demonstrate that H3K9me plays crucial roles in regulating genome organization at multiple levels.

| S-EPMC7261013 | biostudies-literature

Histone H3K9 methylation promotes formation of genome compartments in C. elegans via chromosome compaction and perinuclear anchoring

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

2020-04-21 | GSE144253 | GEO

An unstructured MET-2/SETDB1 cofactor ensures H3K9me2, focus formation and perinuclear anchoring [RNA-seq]

Project description:The segregation of the genome into accessible euchromatin and histone H3 lysine 9 methylated (H3K9me) heterochromatin is essential for the repression of repetitive elements and tissue-specific genes. In C. elegans, the SETDB1 homolog MET-2 catalyzes H3K9me1 and me2. In worms as in vertebrates, the regulation of this crucial enzyme remains enigmatic. Contrary to the localization of overexpressed MET-2, we find endogenous MET-2 to be nuclear throughout development, enriched in perinuclear foci in a cell cycle-dependent manner. We show by mass spectrometry that MET-2 associates with a highly unstructured protein, LIN-65, and a conserved GTPase effector ARLE-14. All three colocalize at heterochromatic foci. Ablation of lin-65, but not arle-14, mislocalizes and destabilizes MET-2, resulting in decreased H3K9me2, derepression of MET-2 targets, and loss of fertility. Importantly, mutation of met-2 or lin-65 is sufficient to disrupt the perinuclear clustering of heterochromatin genome-wide. Thus, LIN-65 is an essential cofactor of MET-2 required for H3K9me2 deposition, heterochromatin clustering, perinuclear anchoring, and transcriptional repression.

2019-02-06 | GSE122339 | GEO

An unstructured MET-2/SETDB1 cofactor ensures H3K9me2, focus formation and perinuclear anchoring [ChIP-seq]

2019-02-06 | GSE122335 | GEO

An unstructured MET-2/SETDB1 cofactor ensures H3K9me2, focus formation and perinuclear anchoring

Project description:An unstructured MET-2/SETDB1 cofactor ensures H3K9me2, focus formation and perinuclear anchoring

| PRJNA504655 | ENA

An unstructured MET-2/SETDB1 cofactor ensures H3K9me2, focus formation and perinuclear anchoring [RNA-seq]

Project description:An unstructured MET-2/SETDB1 cofactor ensures H3K9me2, focus formation and perinuclear anchoring [RNA-seq]

| PRJNA504660 | ENA