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Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes

ABSTRACT: Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes

PROVIDER: PRJNA523829 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8610310_1.fastq.gz	Fastqsanger.gz
	SRR8610310_2.fastq.gz	Fastqsanger.gz
	SRR8610560_1.fastq.gz	Fastqsanger.gz
	SRR8610560_2.fastq.gz	Fastqsanger.gz
	SRR8610561_1.fastq.gz	Fastqsanger.gz

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Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes [5C]

Project description:Transcription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code. Regulatory mechanisms of Drosophila melanogaster heterochromatic gene transcription remain largely unknown. We investigated the contribution of pericentromeric genome organization and heterochromatic factors in orchestrating heterochromatic gene expression. Using 5C-seq, we characterized the pericentromeric TADs in Drosophila melanogaster. Het TAD borders are enriched in nuclear matrix attachment regions while the intra-TAD interactions are mediated by various insulator binding proteins. Heterochromatic genes of similar expression levels cluster into Het TADs, indicating transcriptional co-regulation. HP1a or Su(var)3-9 RNAi results in perturbation of global pericentromeric TAD organization but the expression of the heterochromatic genes is minimally affected. A subset of active heterochromatic genes has been shown to have combination of HP1a/H3K9me3 with H3K36me3 at their exons. Consequently, knock-down of dMES-4 (H3K36 methyl transferase) downregulates expression of the heterochromatic genes. Furthermore, dADD1, present near the TSS of the active heterochromatic genes, is likely to regulate the heterochromatic gene expression in the presence of HP1a or H3K9me3 marks. Therefore, our findings provide mechanistic insights into the interplay of chromatin interactions and the combination of heterochromatic factors (HP1a, H3K9me3, dMES-4 and dADD1) in regulating heterochromatic gene expression.

2020-10-08 | GSE126951 | GEO

Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes [RNA-seq]

2020-10-08 | GSE126950 | GEO

Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes [5C]

Project description:Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes [5C]

| PRJNA523833 | ENA

Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes [RNA-seq]

Project description:Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes [RNA-seq]

| PRJNA523832 | ENA

Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes.

Project description:BackgroundTranscription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code. The regulatory mechanisms of Drosophila melanogaster heterochromatic gene transcription remain largely unknown. Emerging evidence suggests that genome organization and transcriptional regulation are inter-linked. However, the pericentromeric genome organization is relatively less studied. Therefore, we sought to characterize the pericentromeric genome organization and understand how this organization along with the pericentromeric factors influences heterochromatic gene expression.ResultsHere, we characterized the pericentromeric genome organization in Drosophila melanogaster using 5C sequencing. Heterochromatic topologically associating domains (Het TADs) correlate with distinct epigenomic domains of active and repressed heterochromatic genes at the pericentromeres. These genes are known to depend on the heterochromatic landscape for their expression. However, HP1a or Su(var)3-9 RNAi has minimal effects on heterochromatic gene expression, despite causing significant changes in the global Het TAD organization. Probing further into this observation, we report the role of two other chromatin proteins enriched at the pericentromeres-dMES-4 and dADD1 in regulating the expression of a subset of heterochromatic genes.ConclusionsDistinct pericentromeric genome organization and chromatin landscapes maintained by the interplay of heterochromatic factors (HP1a, H3K9me3, dMES-4 and dADD1) are sufficient to support heterochromatic gene expression despite the loss of global Het TAD structure. These findings open new avenues for future investigations into the mechanisms of heterochromatic gene expression.

| S-EPMC7541242 | biostudies-literature

Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms[CUT&RUN]

Project description:Whether and how histone post-translational modifications and the proteins that bind them drive 3D genome organization remains unanswered. Here, we evaluate the contribution of H3K9-methylated constitutive heterochromatin to 3D genome organization in Drosophila tissues. We find that the predominant organizational feature of wildtype tissues is segregation of euchromatic chromosome arms from heterochromatic pericentromeres. Reciprocal perturbation of HP1a•H3K9me binding, using a point mutation in the HP1a chromodomain or replacement of the replication-dependent histone H3 with H3K9R mutant histones, revealed that HP1a binding to methylated H3K9 in constitutive heterochromatin is required to limit contact frequency between pericentromeres and chromosome arms and regulate the distance between arm and pericentromeric regions. Surprisingly, self-association of pericentromeric regions is largely preserved despite loss of H3K9 methylation and HP1a occupancy. Thus, the HP1a•H3K9 interaction contributes to, but does not solely drive, segregation of euchromatin and heterochromatin inside the nucleus.

2024-05-24 | GSE236964 | GEO

Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms[FAIRE-seq]

Project description:Histone post-translational modifications and the proteins that bind them are proposed to be drivers of 3D genome organization, but whether and how they do so remain unanswered. Here, we evaluate the contribution of H3K9-methylated constitutive heterochromatin to 3D genome organization in Drosophila tissues. We find that the predominant organizational feature of wildtype tissues is segregation of euchromatic chromosome arms from heterochromatic pericentromeres. Reciprocal perturbation of HP1a•H3K9 binding, using a point mutation in the HP1a chromodomain or replacement of the replication-dependent H3 with H3K9R mutant histones, revealed that HP1a binding to methylated H3K9 in constitutive heterochromatin is required to restrict long-range interactions between pericentromeres and chromosome arms. Surprisingly, self-association of pericentromeric heterochromatin is largely preserved upon disruption of HP1a•H3K9 binding despite loss of pericentromeric H3K9 methylation and HP1a occupancy. Thus, the HP1a•H3K9 interaction contributes to, but does not solely drive, segregation of euchromatin and heterochromatin inside the nucleus.

2024-05-24 | GSE236965 | GEO

Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms [RNA-seq]

2024-05-24 | GSE234276 | GEO

Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms [Hi-C]

2024-05-24 | GSE233384 | GEO

Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes

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

2020-10-08 | GSE126952 | GEO