Ontology highlight
ABSTRACT:
PROVIDER: PRJNA277528 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1853006.fastq.gz | Fastqsanger.gz | |||
| SRR1853007.fastq.gz | Fastqsanger.gz | |||
| SRR1853008.fastq.gz | Fastqsanger.gz | |||
| SRR1853009.fastq.gz | Fastqsanger.gz | |||
| SRR2089860.fastq.gz | Fastqsanger.gz |
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Project description:An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster [RNA-seq]
| PRJNA289205 | ENA
Project description:An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster [ChIP-Seq]
| PRJNA277529 | ENA
Project description:Heterochromatin protein 1a (HP1a) is a chromatin associated protein that has been well studied in many model organisms, such as Drosophila, where it is a determining factor for classical heterochromatin. HP1a is associated with the two histone methyltransferases SETDB1 and Su(var)3-9, which mediate H3K9 methylation marks and participate in the establishment and spreading of HP1a enriched chromatin. While HP1a is generally regarded as a factor that represses gene transcription, several reports have linked HP1a binding to active genes, and in some cases, it has been shown to stimulate transcriptional activity. To clarify the function of HP1a in transcription regulation and its association with Su(var)3-9, SETDB1 and the chromosome 4 specific protein POF, we conducted genome-wide expression studies and combined the results with available binding data in Drosophila melanogaster. The results suggested that HP1a has a repressing function on chromosome 4, where it preferentially targets non-ubiquitously expressed genes (NUEGs), and a stimulating function in pericentromeric regions. Further, we showed that the effects of SETDB1 and Su(var)3-9 are similar to HP1a, and on chromosome 4, Su(var)3-9, SETDB1 and HP1a target the same genes. In contrast, transposons are repressed by HP1a and Su(var)3-9 but are un-affected by SETDB1 and POF. In addition, we found that the binding level and expression effects of HP1a are affected by gene length. Our results indicate that genes have adapted to be properly expressed in their local chromatin environment. We prepared total RNA from 1st instar larvae trans-heterozygous for HP1a04/HP1a05, trans-heterozygous Su(var)3-9evo/Su(var)3-906, homozygous Setdb110.1/ Setdb110.1 mutants and trans-heterozygous HP1a04 PofD119/HP1a05 PofD119 double mutants three biological replicates, as well as from six biological replicates of wildtype control 1st instar larvae.
2013-04-05 | E-GEOD-43478 | biostudies-arrayexpress
Project description:Heterochromatin protein 1a (HP1a) is a chromatin associated protein that has been well studied in many model organisms, such as Drosophila, where it is a determining factor for classical heterochromatin. HP1a is associated with the two histone methyltransferases SETDB1 and Su(var)3-9, which mediate H3K9 methylation marks and participate in the establishment and spreading of HP1a enriched chromatin. While HP1a is generally regarded as a factor that represses gene transcription, several reports have linked HP1a binding to active genes, and in some cases, it has been shown to stimulate transcriptional activity. To clarify the function of HP1a in transcription regulation and its association with Su(var)3-9, SETDB1 and the chromosome 4 specific protein POF, we conducted genome-wide expression studies and combined the results with available binding data in Drosophila melanogaster. The results suggested that HP1a has a repressing function on chromosome 4, where it preferentially targets non-ubiquitously expressed genes (NUEGs), and a stimulating function in pericentromeric regions. Further, we showed that the effects of SETDB1 and Su(var)3-9 are similar to HP1a, and on chromosome 4, Su(var)3-9, SETDB1 and HP1a target the same genes. In contrast, transposons are repressed by HP1a and Su(var)3-9 but are un-affected by SETDB1 and POF. In addition, we found that the binding level and expression effects of HP1a are affected by gene length. Our results indicate that genes have adapted to be properly expressed in their local chromatin environment.
2013-04-05 | GSE43478 | GEO
Project description:We have investigated the effect of RRP6 depletion on the transcriptome of S2 cells using Illumina deep RNA sequencing. We have also carried out Illumina ChIP-seq analysis of RRP6 genome occupancy in control S2 cells (GFP-KD) and in cells depleted of SU(VAR)3-9.
2015-08-20 | GSE70625 | GEO
Project description:We have investigated the effect of RRP6 depletion on the transcriptome of S2 cells using Affymetrix whole-genome tiling arrays. We have also carried out Illumina ChIP-seq analysis of RRP6 genome occupancy in control S2 cells (GFP-KD) and in cells depleted of SU(VAR)3-9.
2015-08-20 | GSE66639 | GEO
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
Project description:Drosophila imaginal disc cells exhibit a remarkable ability to switch cell fates under various perturbations, a phenomenon known as transdetermination (TD). The winged eye (wge) gene induces eye-to-wing TD by its overexpression in eye imaginal discs using eye specific Gal4 driver (eyeless-Gal4). Gene network controlling this process, however, is largely unclear. Additionally, we identified that heterochromatin-related histone methyltransferase Su(var)3-9 is essential for wge-mediated TD. We used microarray to detail the global gene network underlying wge-mediated eye-to-wing TD, and the involvement of Su(var)3-9 in the gene network.
2017-12-31 | GSE87622 | GEO
Project description:In Drosophila, Piwi-induced transcriptional repression is associated with the establishment of repressive chromatin marks by the histone methyltrasferase SetDB1, however how the Piwi/piRNA complex recruits this effector to chromatin targets is poorly understood. We identified a new player in piRNA-guided transcriptional silencing encoded by the Su(var)2-10 gene. Su(var)2-10 is required for transcriptional silencing and deposition of repressive chromatin marks on transposons and it physically associates with the Piwi/piRNA target recognition complex. Recruitment of Su(var)2-10 to a target locus in a piRNA-independent fashion induces transcriptional repression and deposition of the H3K9 trimethyl mark by the histone methyltransferase dSetDB1/Eggless. Su(var)2-10 belongs to a conserved family of proteins that function as SUMO E3 ligases and we found that the SUMO pathway is essential for the repressive function of Su(var)2-10 and for transcriptional repression of transposons. Together, our data identifies Su(var)2-10 as an essential component of the piRNA-induced transcriptional silencing pathway that links the target recognition complex to the silencing effector and reveals a novel role of SUMO modification in the piRNA-induced repression.
2019-12-18 | GSE115277 | GEO
Project description:Methylation of H3K9 histone residue is a marker of gene silencing in eukaryotes. Three enzymes responsible for adding this modification – G9a, SetDB1/Egg, and Su(var)3-9 – are known in Drosophila. To understand how simultaneous mutations of SetDB1 and Su(var)3-9, or all three proteins may affect the fly development, appropriate combinations were obtained. Double mutants egg; Su(var)3-9 displayed pronounced embryonic lethality, slower larval growth and died before or during metamorphosis. Analysis of transcription in larval salivary glands and wing imaginal disks indicated that the effect of double mutation is tissue-specific. In salivary gland chromosomes, affected genes display low H3K9me2 enrichment and are rarely bound by SetDB1 or Su(var)3-9. We suppose that each of these enzymes directly or indirectly controls its own set of gene targets in different organs, and double mutation results in an imbalanced developmental program. This also indicates that SetDB1 and Su(var)3-9 may affect transcription via H3K9-independent mechanisms. Unexpectedly, in double and triple mutants, amount of di-and tri-methylated H3K9 is drastically reduced, but not completely absent. We hypothesize that this residual methylation implies the existence of additional H3K9-specific methyltransferase in Drosophila.
2023-12-25 | GSE223579 | GEO