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SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE155581 | GEO | 2020/08/04

REPOSITORIES: GEO

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SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster [RNA-seq]

Project description:Three distinct enzymes are known to be capable of methylating lysine 9 residue of the histone H3 in Drosophila melanogaster: Su(var)3-9, SetDB1, and G9a. Here, we explored functional specialization of the two of them: SetDB1 and Su(var)3-9. Using DamID approach, we generated the binding profile for SetDB1 in salivary gland chromosomes, and matched it to the previously published profile of Su(var)3-9. Unlike Su(var)3-9, SetDB1 is an euchromatic protein that is absent from repeated DNA compartment, and is largely restricted to TSSes and 5'UTRs of moderately active ubiquitously expressed genes. Significant SetDB1 association is also observed at or near insulator protein CP190 binding sites. Extensive, yet not exact colocalization SetDB1 with Su(var)3-9 occurs only along the chromosome 4. Importantly, SetDB1 and H3K9me2/3-enriched sites tend to display poor overlap. At the same time, SetDB1 has clear connection with the distribution of H3K27me3 mark. SetDB1 binds outside the domains possessing this modification, and about half of the borders of H3K27me3 domains are decorated by SetDB1 binding sites together with actively transcribed genes. Given that SetDB1 displays low correlation with H3K9 methylation and binds to the TSSes of active genes, that are usually nucleosome-poor, we speculate that in somatic cells, SetDB1 may contribute to the methylation of a broader set of chromosomal proteins than just H3K9. In addition, via association with insulator proteins and transcription machinery, SetDB1 can be expected to play a role in the establishment of chromatin functional domains.

2020-08-04 | GSE155580 | GEO

SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster [DamID-seq]

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Binding of SU(VAR)3-9 Partially Depends on SETDB1 in the Chromosomes of Drosophila melanogaster.

Project description: Not available

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SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster

Project description:SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster

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Binding of SU(VAR)3-9 partially depends on SETDB1 in the chromosomes of Drosophila melanogaster

Project description:Histone modifications are a class of epigenetic marks with prominent roles in gene regulation in eukaryotes. One such mark, predominantly inactivation-related, is methylation of histone H3 lysine 9 (H3K9). In the present study, we decipher the interplay between two evolutionary conserved Drosophila H3K9-specific histone methyltransferases, SU(VAR)3-9 and SETDB1. We asked whether SETDB1 is required for targeting of SU(VAR)3-9. Using DamID-seq, we obtained SU(VAR)3-9 binding profiles for the chromosomes from larval salivary glands and germline cells from adult females, and compared profiles between the wild type and SETDB1-mutant backgrounds. Our analyses indicate that the vast majority of single-copy genes in euchromatin are targeted by SU(VAR)3-9 only in the presence of SETDB1, whereas repeated sequences in heterochromatin is largely SETDB1-independent. Interestingly, piRNA clusters 42AB and 38C behave differently in terms of SU(VAR)3-9 binding in somatic and germline cells. Namely, SU(VAR)3-9 binding to these piRNA clusters is independent of SETDB1 in somatic cells, whereas it is SETDB1-dependent in the germline. In addition, we compared SU(VAR)3-9 profiles in female germline cells at different developmental stages (whole juvenile ovaries and mature nurse cells). It turned out that SU(VAR)3-9 binding is influenced both by the presence of SETDB1, as well as by the differentiation stage.

2019-07-16 | GSE134250 | GEO

SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster [DamID-seq]

Project description:SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster [DamID-seq]

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SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster [RNA-seq]

Project description:SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster [RNA-seq]

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Mutations in Su(var)205 and Su(var)3-7 suppress P-element-dependent silencing in Drosophila melanogaster.

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Genome-wide analysis of Su(var)3-9 distribution in chromosomes of Drosophila melanogaster

Project description:Histone modifications represent one of the key factors contributing to proper genome regulation. One of the histone modifications involved in gene silencing is H3K9 methylation, which is found in the chromosomes across different eukaryotes and controlled by SU(VAR)3-9 and its orthologs. Although SU(VAR)3-9 was discovered over two decades ago, little is known about the details of its chromosomal distribution pattern. To fill in this gap, we used DamID-seq approach and obtained high-resolution genome-wide profiles for SU(VAR)3-9 in two somatic and two germline tissues of fruitfly.

2017-04-04 | GSE97351 | GEO

HP1a, Su(var)3-9, SETDB1 and POF stimulate or repress gene expression depending on genomic position, gene length and expression pattern in Drosophila melanogaster.

Project description: Not available

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