5 results for chip-seq drosophila
Data from: A global change in RNA polymerase II pausing during the Drosophila midblastula transition
Contributors: Chen, Kai, Johnston, Jeff, Shao, Wanqing, Meier, Samuel, Staber, Cynthia, Zeitlinger, Julia
ChIP-seq experiments on tightly staged Drosophila embryos and show that...ChIP-seq enrichment values at the transcription start site (TSS) and transcription...ChIP-seq...Drosophila melanogaster...Drosophila midblastula transition ... Massive zygotic transcription begins in many organisms during the midblastula transition when the cell cycle of the dividing egg slows down. A few genes are transcribed before this stage but how this differential activation is accomplished is still an open question. We have performed ChIP-seq experiments on tightly staged Drosophila embryos and show that massive recruitment of RNA polymerase II (Pol II) with widespread pausing occurs de novo during the midblastula transition. However, ∼100 genes are strongly occupied by Pol II before this timepoint and most of them do not show Pol II pausing, consistent with a requirement for rapid transcription during the fast nuclear cycles. This global change in Pol II pausing correlates with distinct core promoter elements and associates a TATA-enriched promoter with the rapid early transcription. This suggests that promoters are differentially used during the zygotic genome activation, presumably because they have distinct dynamic properties.
Contributors: Chang, Ching-Ho, Chanvan, Ankita, Palladino, Jason, Wei, Xiaolu, Martins, Nuno M. C., Santinello, Bryce, Chen, Chin-Chi, Erceg, Jelena, Beliveau, Brian J., Wu, Chao-Ting
Drosophila centromeres...Drosophila simulans, revealing an unexpected conservation despite the ...ChIP-seq to 100x coverage using BBnorm (v37.54) with the parameters "threads...R2 ChIP-seq to 100x coverage using BBnorm (v37.54) with the parameters...ChIP-seq...satellite DNAs from Drosophila melanogaster....Drosophila simulans...Drosophila melanogaster...created a custom Drosophila-specific consensus repeat library modified...Drosophila melanogaster by combining long-read sequencing, chromatin immunoprecipitation...Drosophila...Drosophila-specific consensus repeat library modified from RepBase v20150807...Drosophila melanogaster. ... Centromeres are essential chromosomal regions that mediate kinetochore assembly and spindle attachments during cell division. Despite their functional conservation, centromeres are amongst the most rapidly evolving genomic regions and can shape karyotype evolution and speciation across taxa. Although significant progress has been made in identifying centromere-associated proteins, the highly repetitive centromeres of metazoans have been refractory to DNA sequencing and assembly, leaving large gaps in our understanding of their functional organization and evolution. Here, we identify the sequence composition and organization of the centromeres of Drosophila melanogaster by combining long-read sequencing, chromatin immunoprecipitation for the centromeric histone CENP-A, and high-resolution chromatin fiber imaging. Contrary to previous models that heralded satellite repeats as the major functional components, we demonstrate that functional centromeres form on islands of complex DNA sequences enriched in retroelements that are flanked by large arrays of satellite repeats. Each centromere displays distinct size and arrangement of its DNA elements but is similar in composition overall. We discover that a specific retroelement, G2/Jockey-3, is the most highly enriched sequence in CENP-A chromatin and is the only element shared among all centromeres. G2/Jockey-3 is also associated with CENP-A in the sister species Drosophila simulans, revealing an unexpected conservation despite the reported turnover of centromeric satellite DNA. Our work reveals the DNA sequence identity of the active centromeres of a premier model organism and implicates retroelements as conserved features of centromeric DNA.
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Data from: The Drosophila HNF4 nuclear receptor promotes glucose-stimulated insulin secretion and mitochondrial function in adults
Contributors: Thummel, Carl S., Barry, William E.
Drosophila melanogaster dm3 genome assembly. Transcripts meeting a cutoff...Drosophila melanogaster...ChIP-seq (MACS2) run with a peak shift of 100 bp. Enrichment peaks were... ChIP-seq (MACS2) run with a peak shift of 100 bp. Enrichment peaks were...Drosophila HNF4 recapitulates hallmark symptoms of MODY1, including adult-onset...Drosophila HNF4 nuclear receptor promotes glucose-stimulated insulin secretion ... Although mutations in HNF4A were identified as the cause of Maturity Onset Diabetes of the Young 1 (MODY1) two decades ago, the mechanisms by which this nuclear receptor regulates glucose homeostasis remain unclear. Here we report that loss of Drosophila HNF4 recapitulates hallmark symptoms of MODY1, including adult-onset hyperglycemia, glucose intolerance and impaired glucose-stimulated insulin secretion (GSIS). These defects are linked to a role for dHNF4 in promoting mitochondrial function as well as the expression of Hex-C, a homolog of the MODY2 gene Glucokinase. dHNF4 is required in the fat body and insulin-producing cells to maintain glucose homeostasis by supporting a developmental switch toward oxidative phosphorylation and GSIS at the transition to adulthood. These findings establish an animal model for MODY1 and define a developmental reprogramming of metabolism to support the energetic needs of the mature animal.
Contributors: Kok, Kurtulus, Ay, Ahmet, Li, Li M., Arnosti, David N.
C...command....Drosophila melanogaster...ChIP-Seq experiments were visualized as custom tracks using Integrative...ChIP-Seq experiments were visualized as custom tracks using Integrative...Customized Drosophila Genome Oligo Microarrays (Agilent). Slide image ...Drosophila embryos. This long-range repressor mediates histone acetylation...Drosophila Genome Oligo Microarrays (Agilent). Slide image data was quantified ... Metazoan transcriptional repressors regulate chromatin through diverse histone modifications. Contributions of individual factors to the chromatin landscape in development is difficult to establish, as global surveys reflect multiple changes in regulators. Therefore, we studied the conserved Hairy/Enhancer of Split family repressor Hairy, analyzing histone marks and gene expression in Drosophila embryos. This long-range repressor mediates histone acetylation and methylation in large blocks, with highly context-specific effects on target genes. Most strikingly, Hairy exhibits biochemical activity on many loci that are uncoupled to changes in gene expression. Rather than representing inert binding sites, as suggested for many eukaryotic factors, many regions are targeted errantly by Hairy to modify the chromatin landscape. Our findings emphasize that identification of active cis-regulatory elements must extend beyond the survey of prototypical chromatin marks. We speculate that this errant activity may provide a path for creation of new regulatory elements, facilitating the evolution of novel transcriptional circuits.
Contributors: Piwowar, Heather A., Vision, Todd J.
... Background: Attribution to the original contributor upon reuse of published data is important both as a reward for data creators and to document the provenance of research findings. Previous studies have found that papers with publicly available datasets receive a higher number of citations than similar studies without available data. However, few previous analyses have had the statistical power to control for the many variables known to predict citation rate, which has led to uncertain estimates of the "citation benefit". Furthermore, little is known about patterns in data reuse over time and across datasets. Method and Results: Here, we look at citation rates while controlling for many known citation predictors, and investigate the variability of data reuse. In a multivariate regression on 10,555 studies that created gene expression microarray data, we found that studies that made data available in a public repository received 9% (95% confidence interval: 5% to 13%) more citations than similar studies for which the data was not made available. Date of publication, journal impact factor, open access status, number of authors, first and last author publication history, corresponding author country, institution citation history, and study topic were included as covariates. The citation benefit varied with date of dataset deposition: a citation benefit was most clear for papers published in 2004 and 2005, at about 30%. Authors published most papers using their own datasets within two years of their first publication on the dataset, whereas data reuse papers published by third-party investigators continued to accumulate for at least six years. To study patterns of data reuse directly, we compiled 9,724 instances of third party data reuse via mention of GEO or ArrayExpress accession numbers in the full text of papers. The level of third-party data use was high: for 100 datasets deposited in year 0, we estimated that 40 papers in PubMed reused a dataset by year 2, 100 by year 4, and more than 150 data reuse papers had been published by year 5. Data reuse was distributed across a broad base of datasets: a very conservative estimate found that 20% of the datasets deposited between 2003 and 2007 had been reused at least once by third parties. Conclusion: After accounting for other factors affecting citation rate, we find a robust citation benefit from open data, although a smaller one than previously reported. We conclude there is a direct effect of third-party data reuse that persists for years beyond the time when researchers have published most of the papers reusing their own data. Other factors that may also contribute to the citation benefit are considered.We further conclude that, at least for gene expression microarray data, a substantial fraction of archived datasets are reused, and that the intensity of dataset reuse has been steadily increasing since 2003.