Project description:H3K27me3 profiles using Cleavage under targets and Release using nuclease (Cut&Run) in control and KD Drosophila melanogaster ovaries. We examined the impact on chromatin profiles in Drosophila melanogaster ovaries in which the lid, the Sin3a, the Snr1 or the mod(mdg4) gene have been selectively knocked down by tissue-specific shRNA expression. We additionally explored H3K27me3 and H3K9me3 in control and dhd mutant ovaries either carrying or not a transgene.

2021-12-10 | GSE174250 | GEO

upSET, the Drosophila homologue of SET3, is required for viability and the proper balance of active and repressive chromatin marks

Project description:Chromatin plays a critical role in faithful implementation of gene expression programs. Different post-translational modifications of histone proteins reflect the underlying state of gene activity, and many chromatin proteins write, erase, bind, or are repelled by these histone marks. One such protein is UpSET, the Drosophila homolog of yeast Set3 and mammalian KMT2E (MLL5). Here we show that UpSET is necessary for the proper balance between active and repressed states. Using CRISPR/Cas-9 editing, we generated S2 cells which are mutant for upSET. We found that loss of UpSET is tolerated in S2 cells, but that heterochromatin is misregulated, as evidenced by a strong decrease in H3K9me2 levels assessed by bulk histone post-translational modification quantification. To test whether this finding was consistent in the whole organism, we deleted the upSET coding sequence using CRISPR/Cas-9, which we found to be lethal in both sexes in flies. We were able to rescue this lethality using a tagged upSET transgene, and found that UpSET protein localizes to transcriptional start sites of active genes throughout the genome. Misregulated heterochromatin is apparent by suppressed position effect variegation of the wm4 allele in heterozygous upSET-deleted flies. We show that this result applies to heterochromatin genes generally using nascent-RNA sequencing in the upSET-mutant S2 lines. Our findings support a critical role for UpSET in maintaining heterochromatin, perhaps by delimiting the active chromatin environment.

2017-03-07 | GSE90703 | GEO

Drosophila melanogaster

Project description:Expression analyses in Drosophila ovaries

| PRJNA193414 | ENA

Drosophila melanogaster

Project description:DamID-based chromatin profiling of UpSET in Kc cells and chromatic accesibility evaluation in UpSET knock down Kc cells

| PRJNA156225 | ENA

Expression analysis of wildtype (OregonG) and upSET mutant ovaries.

Project description:Developmental gene expression results from the orchestrated interplay between genetic and epigenetic mechanisms. Here, we describe upSET, a transcriptional regulator encoding a SET domaincontaining protein recruited to active and inducible genes in Drosophila. However, unlike other Drosophila SET proteins associated with gene transcription, UpSET is part of an Rpd3/Sin3-containing complex that restricts chromatin accessibility and histone acetylation to promoter regions. In the absence of UpSET, active chromatin marks and chromatin accessibility increase and spread to genic and flanking regions due to destabilization of the histone deacetylase complex. Consistent with this, transcriptional noise increases, as manifest by activation of repetitive elements and off-target genes. Interestingly, upSET mutant flies are female sterile due to upregulation of key components of Notch signaling during oogenesis. Thus UpSET defines a class of metazoan transcriptional regulators required to fine tune transcription by preventing the spread of active chromatin. A six chip study using total RNA recovered from three separate dissections wild-type ovaries and three separate dissections of epic mutant ovaries. Each chip measures the expression level of 15,473 genes from Drosophila melanogaster with four 60-mer probes per target gene. Investigation of whole genome gene expression level changes in epic(e00365) mutants, compared to the wild-type strain (OregonG). The mutation was generated by the insertion of the PBac{WH}CG9007e000365 transposon. The mutants analyzed in this study are further described in Rincon-Arano H., et al 2012. in Press.

2012-12-07 | E-GEOD-34717 | biostudies-arrayexpress

Drosophila melanogaster

Project description:AGO1 immunoprecipitated small RNAs from D. melanogaster wildtype and mutant ovaries

| PRJNA268781 | ENA