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This dataset contains zebrafish (Danio rerio) raw RNA and ChIP sequencing data: RNA-seq: RNAseq_Wildtype_rep[12].fastq.gz: 2 biological replicates of single-end RNA-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates RNAseq_Wildtype_rep[3-6].fastq.gz 4 biological replicates of paired-end RNA-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates ChIP-seq: lane1_MPZezh2WT-24hpf-Ezh2__R[12].fastq.gz: 1 sample of paired-end Ezh2 ChIP-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates lane1_MPZezh2WT-24hpf-Rnf2__R[12].fastq.gz: 1 sample of paired-end Rnf2 ChIP-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates lane1_MPZezh2WT-24hpf-H3K27me3__R[12].fastq.gz: 1 sample of paired-end H3K27me3 ChIP-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates *MPZezh2WT-24hpf-H3K4me3*: 2 biological replicates of paired-end H3K4me3 ChIP-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates MPZezh2WT-24hpf-Ezh2-spikein-13277_R[12].fastq.gz: 1 sample of paired-end Ezh2 ChIP-seq data (with Drosophila H2Ay spike in) from 24hpf wild-type (TU/TL background) whole embryo lysates MPZezh2WT-24hpf-H3K27A[cC]*: 2 biological replicates of paired-end H3K27ac ChIP-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates MPZezh2WT-24hpf-H3K27me3-spikein-13275_R[12].fastq.gz: 1 sample of paired-end H3K27me3 ChIP-seq data (with Drosophila H2Ay spike in) from 24hpf wild-type (TU/TL background) whole embryo lysates
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LID is a histone demethylase acting on H3K4me3, a mark related to transcription and found near the transcription start sites (TSS) of the genes. We analyzed where LID is localized and the effects of LID downregulation in the distribution of H3K4me3. Analysis of LID-binding sites in wild type, and of H3K4me3-binding sites in wild type and LID RNAi wing imaginal discs.
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ChIP-Seq... Best hits of AP2A (top panel) and E2F1 (bottom panel) PWMs in ChIP-Seq peaks ranked by their heights. X-Axis shows the peak rank; Y-axis shows the highest PWM score for a given ChIP-Seq peak. Each point corresponds to a given peak. A linear trend is shown by the solid line. ... LOGO representations of GMLA for PWM and dinucleotide PWM TFBS models for STAT1 (top panel) and JUN (bottom panel) TFs produced from ENCODE ChIP-Seq data processed for HOCOMOCO. The existing JASPAR models are shown for comparison. ... Taking into account base coverage data allows stable detection of ETS-like pattern in the EWS-FLI1 ChIP-Seq data set (Guillon et al., 2009). From top to bottom: the results of motif discovery from ChIP-Seq peaks truncated to a certain percent of their lengths around the peak summits. LOGO representations of motifs discovered are shown in columns: (left) ChIPMunk, the greedy algorithm that takes into account ChIP-Seq base coverage profiles; (middle) MEME, an EM-based conventional tool; (right) SeSiMCMC, the Gibbs sampler-based conventional tool. Peaks with GGAA satellites are filtered out. ... Features of regulatory regions in the vicinity of giant gene in Drosophila melanogaster genome. Three series of tracks for three TFs are given with LOGO representations of the corresponding TFBS models: (top) Bicoid, (middle) Caudal, and (bottom) Hunchback. Tracks within each series: (top) predicted binding sites, the darker background displays the coding region; (middle) homotypic clusters of predicted binding sites, the darker background displays DNAse accessibility regions; (bottom) ChIP-Seq peaks, the darker background displays DNAse accessibility regions. X-Axis shows the genomic location; Y-axis shows the estimated significance (for homotypic clusters) and the peak height (for ChIP-Seq). Experimental data are shown for stage 5 of embryo development. For details, see text. ... Distance preferences for pairs of Spi-1 TFBS model occurrences in tandem (top) and reverse complement (bottom) orientations predicted for ChIP-Seq peaks located in different functional regions. The functional categories are shown with lines: (solid) putative enhancer; (dashed) CpG island promoter; (dotted) promoter without CpG island overlap. X-Axis: distance between two Spi-1 motif occurrences (base pairs). Y-Axis: a fraction of ChIP-Seq peaks with two Spi-1 motif hits separated by a given spacer.
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Supplementary material: Includes references for known DV enhancers, ChIP-seq and ATAC-seq replicate correlations, and an overview of how some known DV enhancers were assigned to potential target genes. (DOCX 3548 kb)
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Chromatin profiling of nuclei isolated from genetically defined neuronal subpopulations of the adult Drosophila brain. Cell type-specific histone modification maps were generated from nuclei isolated from all neurons (R57C10-GAL4), Kenyon cells (OK107-GAL4), and octopaminergic (Tdc2-GAL4) neurons using a method similar to INTACT (Deal and Henikoff, 2010; Steinner et al., 2012). Three histone modifications were profiled: H3K4me3, H3K27ac, and H3K27me3. Sequencing was performed with an Illumina HiSeq 2000.
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Genome-wide Colocalization of Piwi and Piwi-Associated piRNAs (A) Genome-wide localization of Piwi and Piwi-associated piRNAs are shown for X, 2L, 2R, 3L, 3R, 4, and unassembled Contig U. The horizontal line shows the length of each chromosome arm proportionally. The red peak above the chromosomal line represents Piwi ChIP scores [sum of ChIP-seq (U+M) scores per 10 kb window; both unique-mapping and multiple-mapping reads were considered], and the green peak below the chromosomal line represents the abundance of Piwi-associated piRNAs (numbers of piRNAs per 10 kb window). Gray ovals indicate centromeres. Asterisks denote enrichment of Piwi in telomere regions. Boxed regions labeled as B, C, and D are 260 kb region containing the 42AB piRNA cluster, a 150 kb region of sporadic transposons, and a 75 kb region containing a gene CG32377, respectively. See also Figure S2. (B–D) Zoomed-in views of localization of Piwi and Piwi-associated piRNAs at the 42AB piRNA cluster (B), a sporadic transposon region (C), and CG32377 (D). ... Distinct Colocalization Patterns of Piwi and Piwi-Associated piRNAs in Euchromatin and Heterochromatin Suggest Two Modes of Piwi-piRNA Guidance Mechanism (A and B) Relative positions of Piwi, Piwi-associated piRNA, and transposons within the euchromatic genome (X, 2L, 2R, 3L, 3R, 4) and the heterochromatic genome (XHet, 2LHet, 2RHet, 3LHet, 3RHet, YHet, U, and Uextra). Piwi-associated piRNAs were aligned at their 5′ ends in the same direction. Gray dash lines indicate positions of piRNAs. Piwi ChIP-seq scores within upstream and downstream regions surrounding piRNA-transcribing regions (±3 kb) were separately plotted for euchromatic genome (orange) and heterochromatic genome (blue), together with the transposon density (TE density; green). See also Figure S4. (C and D) Relative positions of Piwi with piRNAs derived from piRNA clusters (green) and other sporadic piRNAs (orange). (E) Heatmaps depict Piwi ChIP-seq scores over various types/classes of transposons within genome. Average Piwi ChIP-seq scores of all same types of transposons within genome (total) or only within piRNA clusters (cluster) were separately calculated. (F) Heatmaps depict levels of chromatin-associated RNA Pol II over various types/classes of transposons within wild-type flies (left) and piwi1/piwi2 mutants (right). Average RNA Pol II ChIP-seq scores were separately calculated for all same types of transposons on chromosomal arms (X, 2L, 2R, 3L, 3R, 4), on contigs (U, Uextra) as well as for all same types of transposon within genome (genome average) or within piRNA clusters (cluster average). ... Distribution of ChIP-Seq (U+M) Scores over Genomic Features Distribution of ChIP-seq (U+M) scores over CDS, 5′ UTR, 3′ UTR, introns, transposons, repetitive sequences, and intergenic regions within the whole genome (X, 2L, 2R, 3L, 3R, 4, XHet, 2LHet, 2RHet, 3LHet, 3RHet, YHet, U, Uextra). The top and bottom rows show the distributions in wild-type and piwi1/piwi2 flies, respectively. See also Figure S1 and Table S1. ... Chromosome-wide Changes of Chromatin States in Piwi Mutants (A) Distribution of various epigenetic regulators/marks over the entire chromosome arm 2L [ChIP-seq (U+M) scores; both unique-mapping and repetitive sequences were considered] in wild-type and piwi1/piwi2 mutants. cen, the centromeric end of 2L; tel, the telomeric end of 2L. ChIP-seq scores were binned and averaged for every 20 kb window on the plots. See also Figures S5 and S6 and Tables S2 and S3. (B) Distribution of various epigenetic regulators/marks over the entire contig Uextra (ChIP-seq [U+M] scores; both unique-mapping and repetitive sequences were considered) in wild-type and piwi1/piwi2 mutants. See also Figures S5 and S6 and Tables S2 and S3.
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Supplementary material: Includes references for known DV enhancers, ChIP-seq and ATAC-seq replicate correlations, and an overview of how some known DV enhancers were assigned to potential target genes. (DOCX 3548 kb)
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We find a high concordance between the binding of the Drosophila transcription factor Dorsal and the co-activator CBP during early embryogenesis. This relationship was furter examined by comparing CBP distribution in Drosophila embryos derived from wt and mutant flies lacking intranuclear Dorsal (gd7). Our data suggests a specific involvemet of CBP in initiating early dorsoventral patterning, but not in anterioposterior. CBP ChIP seq of 2-4 hours old Drosophila embryos derived from w1118 (wild-type) or gd7 homozygous mutant mothers
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Supplementary figures: Fig. S1: Gene names for the data shown in Fig. 1aâ c, Fig. S2: Transcription factor motifs enriched in top ChIP-seq and ATAC-seq regions, Fig. S3: Differential H3K27ac analysis of ATAC-seq regions is an effective method to identify tissue-specific enhancers, Fig. S4: Genes near putative ATAC-seq derived enhancers are differentially regulated across tissues, Fig. S5: The identified putative DV enhancer regions derived from ATAC-seq are enriched for known DV transcription factor motifs, Fig. S6: Number of genes with one or multiple assigned enhancers, Fig. S7: Transcription factor ChIP-seq signal is preferentially found at the expected corresponding binding motifs present within putative MEs and DEEs. (PDF 2673 kb)
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Enriched GO categories for human orthologs of Drosophila class I genes. ... Direct Nrf2 regulation of enhancers at Keap1 and SQSTM1 in human cells. (A) Human Nrf2 ChIP-seq peak and ARE sequence at the Keap1 locus; gene models and tested enhancer regions are indicated as described for Fig. 4A. (B) Human Nrf2 ChIP-seq peak and ARE sequence at the SQSTM1 locus; gene models and tested enhancer regions are indicated as described for Fig. 4A. (C) EMSA as described for Fig. 4B, with AREs from Keap1 and SQSTM1 enhancers used as cold competitors; both are able to compete with labeled NQO1 probe in an ARE-dependent manner (lost with mutation of ARE), though the Keap1 ARE is a weaker competitor than the SQSTM1 ARE. (D) Luciferase reporter assay as described for Fig. 4C, but with enhancer from the Keap1 locus. (E) Same as (D) with enhancer from the SQSTM1 locus. Both the Keap1 (D) and the SQSTM1 (E) enhancers are upregulated in Nrf2+ in an ARE-dependent manner. ... Deeply conserved human Nrf2 targets are upregulated by sulforaphane in human cells. (A) Percentage of Nrf2 target genes overlapping human orthologs of Drosophila class I, II, or III genes. Orthologs were identified using either the top-scoring ortholog only (best ortholog) or all orthologs scoring >2 as described in the text. ⁎p Drosophila class I genes) and gene expression changes after treatment of LCL cells with sulforaphane (SFN). ... Enhancers at deeply conserved human target genes are regulated by Nrf2 in human cells. (A) Human Nrf2 ChIP-seq signal from LCL cells treated with DMSO or SFN as indicated. Select ancient Nrf2 target genes with highly significant binding are represented (ChIP y-axis scale, 0–5000). (B) ChIP-seq signal as in (A) at select ancient Nrf2 target genes with moderate binding (ChIP y-axis scale, 0–500). (C) Heat map representing the response to SFN, tert-butylhydroquinone (tBHQ), overexpression of Nrf2, or overexpression of a dominant negative version of Nrf2 (Nrf2DN) for reporter constructs driven by the enhancer regions highlighted in (A) and (B). NQO1 is a positive control for human Nrf2, but is not a conserved target because insects do not have an orthologous gene; the remaining nine are enhancers at deeply conserved Nrf2 target genes. ... Drosophila... Drosophila class III genes and human orthologs.
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