Drosophila
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR061000_1.fastq.gz | Fastqsanger.gz | |||
| DRR061000_2.fastq.gz | Fastqsanger.gz | |||
| DRR061001_1.fastq.gz | Fastqsanger.gz | |||
| DRR061001_2.fastq.gz | Fastqsanger.gz |
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Project description:We report the evolutionary behaviour of Polycomb group proteins, their recruitment factors and their underlying sequences by performing ChIP-seq analysis in 4-5 different Drosophila species. We demonstrate an extremely high conservation of Polycomb repressive domains across Drosophila species We validate few cases of PRE divergence that shows that cis-driven PRE evolution is a rare event. We further show that PHO recruitment to Polycomb domains is evolutionarily robust to motif changes and that PRC1 stabilizes binding of its key recruiter ChIP-seq analysis of histone marks and chromatin associated factors across 4-5 Drosophila species
2014-10-20 | E-GEOD-60428 | biostudies-arrayexpress
Project description:We report the evolutionary behaviour of Polycomb group proteins, their recruitment factors and their underlying sequences by performing ChIP-seq analysis in 4-5 different Drosophila species. We demonstrate an extremely high conservation of Polycomb repressive domains across Drosophila species We validate few cases of PRE divergence that shows that cis-driven PRE evolution is a rare event. We further show that PHO recruitment to Polycomb domains is evolutionarily robust to motif changes and that PRC1 stabilizes binding of its key recruiter
2014-10-20 | GSE60428 | GEO
Project description:Phenotypic differences between closely related species are thought to arise primarily from changes in gene expression due to mutations in cis-regulatory sequences (enhancers). However, it has remained unclear how frequently mutations alter enhancer activity or create functional enhancers de novo. Here we use STARR-seq, a recently developed quantitative enhancer assay, to determine genome-wide enhancer activity profiles for five Drosophila species in the constant trans-regulatory environment of Drosophila melanogaster S2 cells. We find that the functions of a large fraction of D. melanogaster enhancers are conserved for their orthologous sequences owing to selection and stabilizing turnover of transcription factor motifs. Moreover, hundreds of enhancers have been gained since the D. melanogaster-Drosophila yakuba split about 11 million years ago without apparent adaptive selection and can contribute to changes in gene expression in vivo. Our finding that enhancer activity is often deeply conserved and frequently gained provides functional insights into regulatory evolution.
2014-04-28 | GSE48251 | GEO
Project description:Genome sequences and assemblies of Drosophila simulans, Drosophila sechellia and Drosophila mauritiana.
| PRJNA383250 | ENA
Project description:Cytosine methylation in the genome of Drosophila melanogaster has been elusive and controversial: methylcytosine has been detected at very low levels in early embryos, but the genomic location and function of methylation has not been established. We have mapped cytosine methylation genomewide in Stage 5 Drosophila embryo DNA by combining immuno-enrichment for 5-methylcytosine, bisulfite conversion, and deep sequencing. Unlike methylation patterns observed in other eukaryotic species, methylation in Drosophila is punctate and highly strand-asymmetrical; we confirmed this by direct PCR amplification and sequencing of bisulfite-converted DNA. Despite the locally asymmetric nature of methylation, large-scale patterns of methylation are symmetric. Methylated regions make up ~1% of the genome, and within these regions methylation of individual cytosines averages 2-10%. Methylation is concentrated in specific 5-base sequence motifs that are CA- and CT-rich but depleted of guanine. It is depleted from promoters, coding sequences, and most retrotransposons, and enriched in introns and in certain simple sequence repeats containing the commonly methylated motifs. Comparison with available gene expression data indicates that methylation in a gene is associated with lower expression; the X chromosome, which is subject to gene dosage compensation, is more densely methylated than the autosomes. This study firmly establishes the presence of cytosine methylation in Drosophila; the temporal overlap of methylation with the maternal-zygotic transition raises the possibility that methylation participates in the transition to zygotic gene expression. To enrich for rare cytosine methylation in Drosophila at embryonic Stage 5 (2-3 hours post-fertilization), we enriched sonicated Stage 5 genomic DNA for methylcytosine by immunoprecipitation with antibody to 5-methylcytosine. The immunoprecipitated DNA was then bisulfite converted and Illumina sequenced to obtain direct evidence for the presence of methylation. The presence and extent of DNA methylation was confirmed by Illumina sequencing of bisulfite-converted PCR amplicons.
2014-02-18 | E-GEOD-34425 | biostudies-arrayexpress
Project description:Co-expression of genes that physically cluster together is a common characteristic of eukaryotic transcriptomes. Identifying these groups of co-expressed genes is important to the functional annotation of genomes and understanding the evolutionary fates of the clustered genes. We used microarrays to measure gene expression in seven closely related Drosophila species, to identify domains clusters within a species of Drosophila (D. simulans) and that are evolving among species in the D. melanogater subgroup. Experiment Overall Design: Assays were carried out on three independent (biological) replicates per species for a single line of the following five species: D.yakuba (Tuscon Stock Center Number: 14021-0261.00), D.santomea (TSCN: 14021-0271.00), D.teissieri (TSCN: 14021-0257.00), D.mauritiana (David 105, TSCN: 14021-0241.01), D.sechellia (Roberstson, TSCN: 14021-0248.21). Three biological replicates for D.melanogaster. The samples assayed for D.melanogaster reflect an even genotypic contribution of 10 isogenic lines developed from a wild population (Winters, CA) and crossed in a round-robin design.For D. simulans, three replicate arrays were used to assay each of 10 round-robin crosses between 10 isogenic lines developed from the same population. the entire data set therefore included a total of 48 independent transcript assays covering seven Drosophila species in the D.melanogaster subgroup
2008-06-16 | E-GEOD-7873 | biostudies-arrayexpress
Project description:Cytosine methylation in the genome of Drosophila melanogaster has been elusive and controversial: methylcytosine has been detected at very low levels in early embryos, but the genomic location and function of methylation has not been established. We have mapped cytosine methylation genomewide in Stage 5 Drosophila embryo DNA by combining immuno-enrichment for 5-methylcytosine, bisulfite conversion, and deep sequencing. Unlike methylation patterns observed in other eukaryotic species, methylation in Drosophila is punctate and highly strand-asymmetrical; we confirmed this by direct PCR amplification and sequencing of bisulfite-converted DNA. Despite the locally asymmetric nature of methylation, large-scale patterns of methylation are symmetric. Methylated regions make up ~1% of the genome, and within these regions methylation of individual cytosines averages 2-10%. Methylation is concentrated in specific 5-base sequence motifs that are CA- and CT-rich but depleted of guanine. It is depleted from promoters, coding sequences, and most retrotransposons, and enriched in introns and in certain simple sequence repeats containing the commonly methylated motifs. Comparison with available gene expression data indicates that methylation in a gene is associated with lower expression; the X chromosome, which is subject to gene dosage compensation, is more densely methylated than the autosomes. This study firmly establishes the presence of cytosine methylation in Drosophila; the temporal overlap of methylation with the maternal-zygotic transition raises the possibility that methylation participates in the transition to zygotic gene expression.
2014-02-18 | GSE34425 | GEO
Project description:We report the evolutionary behaviour of Polycomb group proteins, their recruitment factors and their underlying sequences by performing ChIP-seq analysis in 4-5 different Drosophila species (GSE60428) and HiC analysis in Drosophila melanogaster. We demonstrate an extremely high conservation of Polycomb repressive domains across Drosophila species We validate few cases of PRE divergence that shows that cis-driven PRE evolution is a rare event. We further show that PHO recruitment to Polycomb domains is evolutionarily robust to motif changes and that PRC1 stabilizes binding of its key recruiter
2014-10-20 | GSE61471 | GEO
Project description:Centromeres are the chromosomal sites of assembly for kinetochores, the protein complexes that attach to spindle fibers and mediate separation of chromosomes to daughter cells in mitosis and meiosis. In most multicellular organisms, centromeres comprise a single specific family of tandem repeats, often 100-400 bp in length, found on every chromosome, typically in one location within heterochromatin. Drosophila melanogaster is unusual in that the heterochromatin contains many families of mostly short (5-12 bp) tandem repeats, none of which appears to be present at all centromeres, and none of which is found only at centromeres. Although centromere sequences from a minichromosome have been identified and candidate centromere sequences have been proposed, the DNA sequences at native Drosophila centromeres remain unknown. Here we use native chromatin immunoprecipitation to identify the centromeric sequences bound by the foundational kinetochore protein cenH3, known in vertebrates as CENP-A. In D. melanogaster, these sequences include a few families of 5-bp and 10-bp repeats, but in closely related D. simulans, a partially overlapping set of short repeats and more complex repeats comprise the centromeres. The results suggest that a recent expansion of short repeats is replacing more complex centromeric repeats in the melanogaster subgroup of Drosophila.
2018-01-08 | GSE105100 | GEO
Project description:We identified 6,975 insertion/deletion events of between 10 and 100 bp in length from the Drosophila simulans and Drosophila sechellia Mercator/MAVID genomic sequence alignment. Replicate pure samples of Drosophila simulans and Drosophila sechellia gDNA were competitively hybridized to measure the expected relative hybridization intensity of alleles from each species. We used these measured intensities to assess the likelihood that the hybridization signal at each probe in an experimental animal reflected homozygosity or heterozygosity at that locus.
2013-02-26 | GSE44443 | GEO