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Drosophila melanogaster

ABSTRACT: Small RNA sequencing of control and Su(var)3-7 mutant Drosophila ovary

PROVIDER: PRJNA230679 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1043607.fastq.gz	Fastqsanger.gz
	SRR1043608.fastq.gz	Fastqsanger.gz

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Small RNA sequencing of control and Su(var)3-7 mutant Drosophila ovary

Project description:Comparison of small RNA fractions derived from piRNA clusters and transposon sequences in control and Su(var)3-7 null mutant.

2014-05-12 | GSE53015 | GEO

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

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

Project description: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 and effect on gene regulation during germ cells development. To fill in this gap, we used RNA-Seq approach to investigate the effect of Su(var)3-9 mutation on gene expression during Drosophila spermatogenesis.

2017-03-30 | GSE97130 | GEO

Small RNA sequencing of control and Su(var)3-7 mutant Drosophila ovary

Project description:Comparison of small RNA fractions derived from piRNA clusters and transposon sequences in control and Su(var)3-7 null mutant. Small RNA profile of 3-day old control and Su(var)3-7 mutant ovaries were generated by high-throughput sequencing on Illumina HiSeq 2000

2014-05-12 | E-GEOD-53015 | biostudies-arrayexpress

RNA expression in Drosophila melanogaster mutants lacking HP1a

Project description:mRNA expression levels were determined by NGS for wildtype larvae as well as for larvae lacking HP1a [Su(var)205^04/Su(var)205^05 transheterozygotes]. RNA samples from wildtype (OR) and HP1a mutant third instar larvae were examined, using duplicate biological samples and Illumina NGS.

2012-09-01 | E-GEOD-39083 | biostudies-arrayexpress

RNA expression in Drosophila melanogaster mutants lacking HP1a

Project description:mRNA expression levels were determined by NGS for wildtype larvae as well as for larvae lacking HP1a [Su(var)205^04/Su(var)205^05 transheterozygotes].

2012-09-01 | GSE39083 | GEO

Drosophila melanogaster

Project description:Genome-wide analyses of Su(Hw) binding in Drosophila ovary

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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: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

Drosophila melanogaster

Project description:Genome wide analyses of Su(Hw)M393 binding in the Drosophila ovary

| PRJNA341070 | ENA

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

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