Contributors: unknown

Date: 2013-08-17

Drosophila species: Drosophila melanogaster, Drosophila simulans, Drosophila...ChIP-seq data can be found in GSE25663, GSE25668...ChIP-seq data of H3K27me3 and RNA-seq data in Drosophila white prepupa...Drosophila pseudoobscura. The processed RPKM values are calculated following...Drosophila species and its correlation with gene expression levels in ... This data consists of RNA-seq data of whole animal white pre pupa of four Drosophila species: Drosophila melanogaster, Drosophila simulans, Drosophila yakuba, and Drosophila pseudoobscura. The processed RPKM values are calculated following the method in Garber et al 2011 Nature Methods paper. Examination of H3K27me3 in 4 Drosophila species and its correlation with gene expression levels in the same development stage relevant ChIP-seq data can be found in GSE25663, GSE25668

Contributors: Gan Q, Schones DE, Ho Eun S, Wei G, Cui K, Zhao K, Chen X

Date: 2010-04-16

ChIP-seq. We integrate the ChIP-seq data with RNA-seq data that measures...Drosophila testis...Drosophila S2 cells to perform ChIP-seq and RNA-seq and compare the results...ChIP-seq: Profiling chromatin modifications using antibodies against 3...Drosophila strain that allows us to obtain enough cells at their primitive ... We use male gonads isolated from a Drosophila strain that allows us to obtain enough cells at their primitive status as the starting material to study the endogenous chromatin structure of undifferentiated cells using ChIP-seq. We integrate the ChIP-seq data with RNA-seq data that measures the transcriptome in a digital manner. Our genome-wide analyses indicate that the majority of differentiation genes in undifferentiated cells lack an active chromatin mark and paused Pol II; instead, they are associated with either the repressive H3K27me3 mark or no detectable mark. In order to address the possibility that distinct techniques are responsible for such a difference, we also use the Drosophila S2 cells to perform ChIP-seq and RNA-seq and compare the results directly with published work using ChIP-chip and microarray on S2 cells. For the S2 cell ChIP-chip data, we used data from the following paper: Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, Zeitlinger J, Adelman K: RNA polymerase is poised for activation across the genome. /Nat Genet /2007, 39(12):1507-1511. The accession number for this data is: GSE6714. ChIP-seq: Profiling chromatin modifications using antibodies against 3 histone modifications and RNA Pol II in S2 cells Profiling chromatin structure in bam testis using antibodies against 3 histone modifications and RNA Pol II RNA-seq: Profiling transcriptome of S2 cells using RNA-seq

Contributors: Alekseyenko AA, Gorchakov AA, Zee BM, Fuchs SM, Kharchenko PV, Kuroda MI

Date: 2014-07-03

Drosophila S2 cells and from whole organisms across embryonic, larval ...Drosophila HP1 with dADD1, HIPP1, and repetitive RNAs...ChIP-seq-like pulldown/input samples were generated using BioTAP-XL to ... We report chromatin-associated protein and RNA interactions of HP1a, indentified by BioTAP-XL mass spectrometry and sequencing. We identify an extensive list of both known and novel HP1a-interacting proteins from Drosophila S2 cells and from whole organisms across embryonic, larval and adult stages. BioTAP-XL protocol was used to identify HP1a interacting proteins through mass-spectrometry analysis. ChIP-seq-like pulldown/input samples were generated using BioTAP-XL to validate genomic distribution of the HP1a-BioTAP contructs, and the newly identified interacting proteins (CG8290 and CG3680); To examine the RNAs associated with the HP1a complexes, the RNA fraction of the BioTAP-XL pulldowns was analyzed using Illumina-based RNA-seq protocols, as well as Helicos direct RNA sequencing.

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

Date: 2019-05-16

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.

Contributors: unknown

Date: 2014-03-01

ChIP-seq validation in order to identify a common downstream gene expression...Drosophila melanogaster by RNA Seq...Drosophila and mammals. Based on heterologous functional analysis of evolutionarily...Drosophila. Intriguingly, a subset of the newly-identified Yorkie target ... Throughout Metazoa, developmental processes are controlled by a surprisingly limited number of conserved signaling pathways. Precisely how these signaling cassettes were assembled in early animal evolution remains poorly understood, as do the molecular transitions that potentiated the acquisition of their myriad developmental functions. Here we analyze the molecular evolution of the proto-oncogene YAP/Yorkie, a key effector of the Hippo signaling pathway that controls organ size in both Drosophila and mammals. Based on heterologous functional analysis of evolutionarily distant Yap/Yorkie orthologs, we demonstrate that a structurally distinct interaction interface between Yap/Yorkie and its partner TEAD/Scalloped became fixed in the eumetazoan common ancestor. We then combine transcriptional profiling of tissues expressing phylogenetically diverse forms of Yap/Yorkie with ChIP-seq validation in order to identify a common downstream gene expression program underlying the control of tissue growth in Drosophila. Intriguingly, a subset of the newly-identified Yorkie target genes are also induced by Yap in mammalian tissues, thus revealing a conserved Yap-dependent gene expression signature likely to mediate organ size control throughout bilaterian animals. Combined, these experiments provide new mechanistic insights while revealing the ancient evolutionary history of Hippo signaling. We sought to define the downstream target genes of selected Yap variants by performing RNA sequencing analysis (RNA-seq) on total RNA isolated from GMR-Gal4>Yap eye discs. Transcriptional profiles were generated in triplicate from eye imaginal disks with either endogenous Yki, or GMR-Gal4 over-expressed Yki, Trichoplax Yap, Monosiga Yap, or Monisiga Yap+TEAD domain, using deep sequencing via Illumina Hi Seq.

Contributors: unknown

Date: 2014-03-27

ChIP-seq, but appears to rely on motifs for other factors, including Eip74...ChIP-seq (with and without ecdysone) was performed single-end sequencing...Drosophila cell types to derive the first genome-wide hormone-dependent ... Steroid hormones act as important developmental switches and their nuclear receptors regulate many genes. However, few hormone-dependent enhancers have been characterized and important aspects of their sequence architecture, cell type-specific activating and repressing functions, or the regulatory roles of their chromatin structure have remained unclear. We used STARR-seq, a recently developed enhancer-screening assay, and ecdysone signaling in two different Drosophila cell types to derive the first genome-wide hormone-dependent enhancer activity maps. We demonstrate that enhancer activation depends on cis-regulatory motif combinations that differ between cell types and can predict cell type-specific ecdysone targeting. Activated enhancers are often not accessible prior to induction. Enhancer repression following hormone treatment is independent of receptor motifs and receptor binding to the enhancer as we show using ChIP-seq, but appears to rely on motifs for other factors, including Eip74. Our strategy is applicable to study signal-dependent enhancers for different pathways and across organisms. STARR-seq was performed in S2 and OSC cells treated with ecdysone in two replicates. DHS-seq before and after treatment was done with single-end sequencing in two replicates. RNA-seq (with and without ecdysone) was performed with a strand-specific protocol using single-end sequencing in two replicates in S2. ChIP-seq (with and without ecdysone) was performed single-end sequencing in two replicates in S2 cells.

Contributors: Enderle D, Beisel C, Stadler MB, Gerstung M, Athri P, Paro R

Date: 2010-12-21

Drosophila S2 cell line. In addition to finding a preference for stalled...Drosophila genome for yet non-annotated transcription start sites (TSSs...ChIP-seq, RNA-seq, and genome-wide detection of transcription start sites ... The Polycomb group (PcG) and Trithorax group (TrxG) of proteins are required for stable and heritable maintenance of repressed and active gene expression states. Their antagonistic function on gene control, repression for PcG and activity for TrxG, is mediated by binding to chromatin and subsequent epigenetic modification of target loci. Despite our broad knowledge about composition and enzymatic activities of the protein complexes involved, our understanding still lacks important mechanistic detail and a comprehensive view on target genes. In this study, we use an extensive data set of ChIP-seq, RNA-seq, and genome-wide detection of transcription start sites (TSSs) to identify and analyze thousands of binding sites for the PcG proteins and Trithorax from a Drosophila S2 cell line. In addition to finding a preference for stalled promoter regions of annotated genes, we uncover many intergenic PcG-binding sites coinciding with non-annotated transcription start sites. Interestingly, this set includes previously unknown promoters for primary transcripts of microRNA genes, thereby expanding the scope of Polycomb control to non-coding RNAs essential for development, apoptosis and growth. Chromatin from S2 cells was immunoprecipitated using antibodies against Pc, Ph, Psc, Trx-C or H3K4me3. In parallel, we isolated RNA from S2 cells and generated global gene expression profiles by RNA-seq. We also surveyed the Drosophila genome for yet non-annotated transcription start sites (TSSs) using a newly adapted protocol for Illumina sequencing (termed 5’-MACE) with RNA isolated from S2 cells and embryos.

Contributors: unknown

Date: 2014-04-03

ChIP-seq and transcriptomics analysis in wt or/and mutant mice ... A 640kb non-coding interval at 8q24 has been associated with an increased risk of non-syndromic cleft lip and palate (CLP) in humans, but the genes and pathways involved in this genetic susceptibility have remained elusive. With a large series of rearrangements engineered over the syntenic mouse region, we showed that this interval contains very remote cis-acting enhancers that control c-myc expression in the developing face. Deletion of this interval led to mild alteration of facial morphologies in mice and, sporadically, to CLP. At a molecular level, we identified mis-expression of several downstream genes, highlighting a combined impact on cranio-facial developmental network and general metabolic capacity. This dual molecular etiology may account for the prominent role to the 8q24 region in human facial dysmorphologies. ChIP-seq and transcriptomics analysis in wt or/and mutant mice

Contributors: Zemach A, McDaniel IE, Silva P, Zilberman D

Date: 2010-04-15

... Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite sequencing, we have quantified DNA methylation in five plant, seven animal, and five fungal genomes. We find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons has evolved independently in the vertebrate lineage. We show that methylation of plant transposons in the CHG context extends to green algae, and present evidence for RNA-directed DNA methylation of fungal genes. We also show that antagonism between DNA methylation and histone H2A.Z is conserved between plants and animals. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes. Keywords: Epigenetics Examination of DNA methylation and transcription in plant, animal, and fungal genomes, and examination of how H2A.Z deposition relates to both methylation and transcription in puffer fish. Descriptions of the Samples' raw and processed data (provided as supplementary files) can be found in GSE19824_README.txt at the foot of this record.

Contributors: unknown

Date: 2011-03-23

Drosophila cell line by high throughput sequencing. We observe numerous ... modENCODE_submission_3201 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Analysis of copy number variation across modENCODE Drosophila cell line by high throughput sequencing. We observe numerous copy number variations for the different cell lines, with each cell line having a distinct ploidy signature. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: deep sequencing analysis. BIOLOGICAL SOURCE: Cell Line: CME-W1-Cl.8+; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Sex: Male; EXPERIMENTAL FACTORS: Cell Line CME-W1-Cl.8+ In this experiment, there is no ChIP step. Simply separate the polytene dna from the tissue (cell line) and seq them, if more reads (than other regions) then they are the CNV regions. Two independent samples were merged to generate the single wiggle file.