Ontology highlight
ABSTRACT:
PROVIDER: PRJNA751209 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15323435_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR15323436_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR15323437_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR15312079_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR15312080.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 20 |
Similar Datasets
Project description:Interference exists ubiquitously in many biological processes. Crossover interference patterns meiotic crossovers, which are required for faithful chromosome segregation and evolutionary adaption. However, what the interference signal is and how it is generated and regulated are unknown. We show that yeast top2 alleles cannot bind or cleave DNA accumulate a higher level of negative supercoils and show weaker interference. However, top2 alleles cannot religate the cleaved DNA or release the religated DNA accumulate less negative supercoils and show stronger interference. Moreover, the level of negative supercoils is negatively correlated with crossover interference strength in various strains. Furthermore, negative supercoils preferentially enrich at crossover-associated Zip3 regions before the formation of meiotic DNA double-strand breaks, and regions with more negative supercoils tend to have more Zip3. Additionally, the strength of crossover interference and homeostasis change coordinately in mutants. These findings suggest that the accumulation and relief of negative supercoils pattern meiotic crossovers.
2022-08-24 | GSE201366 | GEO
Project description:We used DamID-seq to analyze the genome-wide binding patterns of the group B Sox proteins Dichaete and SoxNeuro in four species of Drosophila: D. melanogaster, D. simulans, D. yakuba and D. pseudoobscura. Both binding site turnover between species and a comparison of the binding properties of the two partially-redundant transcription factors were analyzed. We found that, despite widespread turnover, genomic intervals that are commonly bound by both Dichaete and SoxNeuro are highly conserved in Drosophila.
2014-11-18 | GSE63333 | GEO
Project description:We used DamID-seq to analyze the genome-wide binding patterns of the group B Sox proteins Dichaete and SoxNeuro in four species of Drosophila: D. melanogaster, D. simulans, D. yakuba and D. pseudoobscura. Both binding site turnover between species and a comparison of the binding properties of the two partially-redundant transcription factors were analyzed. We found that, despite widespread turnover, genomic intervals that are commonly bound by both Dichaete and SoxNeuro are highly conserved in Drosophila. DamID for Dichaete (Dichaete-Dam) was performed in D. melanogaster, D. simulans, D. yakuba and D. pseudoobscura, while DamID for SoxNeuro (SoxN-Dam) was performed in D. melanogaster and D. simulans. The control experiment, Dam-only, was performed in all species. Three biological replicates were sequenced for each condition in each species.
2014-11-18 | E-GEOD-63333 | biostudies-arrayexpress
Project description:Every chromosome requires at least one crossover to be faithfully segregated during meiosis. At least two levels of regulation govern crossover distribution; where the initiating DNA double-strand breaks (DSBs) occur and whether those DSBs are repaired as crossovers. We mapped meiotic DSBs in budding yeast by identifying sites of DSB-associated single-stranded DNA (ssDNA) accumulation. These analyses revealed substantial DSB activity in regions close to centromeres, where crossover formation is largely absent. Our data suggest that centromeric suppression of recombination occurs at the level of break repair rather than DSB formation. Additionally, we found an enrichment of DSBs within a ~100-kb region near the ends of all chromosomes. Introduction of new telomeres was sufficient to induce large ectopic regions of increased DSB formation, revealing a remarkable long-range effect of telomeres on DSB formation. The concentration of DSBs close to chromosome ends increases the relative DSB density on small chromosomes, providing an interference-independent mechanism to ensure that all chromosomes receive at least one crossover per homolog pair. Together, our results indicate that selective DSB repair accounts for crossover suppression near centromeres, and suggest a simple telomere-guided mechanism to ensure sufficient DSB activity on all chromosomes. Keywords: ssDNA analysis, comparative genomic hybridization, ChIP-chip
2007-11-15 | GSE9503 | GEO
Project description:How evolutionary changes in genes and neurons encode species variation in complex motor behaviors are largely unknown. Here, we develop genetic tools that permit a neural circuit comparison between the model species Drosophila melanogaster and the closely-related species D. yakuba, who has undergone a lineage-specific loss of sine song, one of the two major types of male courtship song in Drosophila. Neuroanatomical comparison of song patterning neurons called TN1 across the phylogeny demonstrates a link between the loss of sine song and a reduction both in the number of TN1 neurons and the neurites serving the sine circuit connectivity. Optogenetic activation confirms that TN1 neurons in D. yakuba have lost the ability to drive sine song, while maintaining the ability to drive the singing wing posture. Single-cell transcriptomic comparison shows that D. yakuba specifically lacks a cell type corresponding to TN1A neurons, the TN1 subtype that is essential for sine song. Genetic and developmental manipulation reveals a functional divergence of the sex determination gene doublesex in D. yakuba to reduce TN1 number by promoting apoptosis. Our work illustrates the contribution of motor patterning circuits and cell type changes in behavioral evolution, and uncovers the evolutionary lability of sex determination genes to reconfigure the cellular makeup of neural circuits.
2024-04-03 | GSE262732 | GEO
Project description:Meiotic crossover formation is critical for generating viable gametes and enhancing genetic diversity. The helicase Mer3 (HFM1 in humans) is a highly conserved factor essential for promoting crossovers and ensuring their proper distribution. Here, we identify replication protein A (RPA) as a direct interactor of budding yeast Mer3. We demonstrate that this interaction is conserved between human HFM1 and RPA. Cross-linking mass spectrometry and structural modelling with AlphaFold2 reveal a conserved and specific Mer3-RPA interface. Single-molecule magnetic tweezers assays demonstrate that direct RPA interaction is required for Mer3 helicase processivity under conditions of low DNA tension. Consistently, mer3 mutant deficient in RPA binding exhibit reduced crossover frequencies and accumulate unresolved recombination intermediates during budding yeast meiosis. Via genome-wide localisation experiments, we link this effect to a weakened recruitment to double-strand break sites of the mer3 mutant. Our findings provide mechanistic insights into coordination of meiotic recombination by the Mer3 helicase through interactions with the canonical DNA repair machinery, highlighting a conserved mechanism underlying crossover control during sexual reproduction.
2025-11-02 | GSE305755 | GEO
Project description:Recent studies have revealed key roles of non-coding RNAs in sex-related pathways, but little is known about the evolutionary forces acting on these non-coding RNAs. We used whole-genome tiling arrays to profile the transcriptome of Drosophila melanogaster tissues and found that 15% of male-biased transcribed fragments (transfrags) are intergenic non-coding RNAs (incRNAs), suggesting a potentially important role for incRNAs in sex-related biological processes. Statistical analysis revealed a paucity of male-biased incRNAs and coding genes on the X chromosome, suggesting that similar evolutionary forces could be affecting the genomic organization of both coding and non-coding genes. Expression profiling across germline and somatic tissues further suggests that both male meiotic sex chromosome inactivation (MSCI) and sexual antagonism contribute to the chromosomal distribution of male-biased incRNAs. Comparative sequence analysis shows that the evolutionary age of male-biased incRNAs is a significant predictor of their chromosomal locations. In addition to identifying abundant sex-biased incRNAs in fly genome, our work unveils a global picture of the complex interplay between non-coding RNAs and sexual chromosome evolution.
2013-12-18 | GSE53421 | GEO
Project description:Curration of small RNAs from four melanogaster-subgroup species (Drosophila simulans, Drosophila sechellia, Drosophila erecta, and Drosophila yakuba) for the purpose of non-coding RNA annotation and comparative genomics assessment.
2014-07-22 | GSE56244 | GEO
Project description:The predominant form of RNA editing in animals is the enzymatic conversion of adenosine to inosine that is sequenced in cDNA as guanine. While RNA editing should be identifiable from RNA-seq data alone, genomic SNPs as well as sequencing and mapping errors result in a high false-positive rate. We used Inosine Chemical Erasing (ICE) with deep sequencing (ICE-seq) in order to validate A-to-I RNA editing genome-wide without the need for the sequencing of the underlying genomic DNA. We called RNA editing events in the head transcriptome of the reference strain of Drosophila melanogaster and six resequenced strains of Drosophila yakuba using the Illumina HiSeq and NextSeq platforms. We compared RNA editing sites reported in other studies and measured the level of conservation between D. melanogaster and D. yakuba. We found that while some of the best-studied editing sites in D. melanogaster are also edited in D. yakuba, we also detect a significant amount of species-specific editing in genes with different Gene Ontology enrichments, which suggests that the biological function of RNA editing in the two Drosophila species is diverging.
2017-04-23 | GSE60851 | GEO
Project description:Mlh3 internally tagged with Flag was pulled down from synchronous meiotic cells at t = 4 h in meiosis, in order to identify its interacting partners involved in meiotic crossover formation
2020-11-06 | PXD014180 | Pride