Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Ftz and Eve ChIP data

ABSTRACT: Genome wide mapping of Ftz and Eve transcription factor binding sites in early Drosophila embryos Ftz has one replicate and dyes swapping Eve has two replicates with one dye swap Mock IPs were used as controls Slides were hybridized with two color samples, but individual channels were uploaded seperately to GEO

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Kevin White

PROVIDER: E-GEOD-14289 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer.

Liu Jiang J Ghanim Murad M Xue Lei L Brown Christopher D CD Iossifov Ivan I Angeletti Cesar C Hua Sujun S Nègre Nicolas N Ludwig Michael M Stricker Thomas T Al-Ahmadie Hikmat A HA Tretiakova Maria M Camp Robert L RL Perera-Alberto Montse M Rimm David L DL Xu Tian T Rzhetsky Andrey A White Kevin P KP

Science (New York, N.Y.) 20090122 5918

We constructed a large-scale functional network model in Drosophila melanogaster built around two key transcription factors involved in the process of embryonic segmentation. Analysis of the model allowed the identification of a new role for the ubiquitin E3 ligase complex factor SPOP. In Drosophila, the gene encoding SPOP is a target of segmentation transcription factors. Drosophila SPOP mediates degradation of the Jun kinase phosphatase Puckered, thereby inducing tumor necrosis factor (TNF)/Ei ...[more]

PMID: 19164706

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Project description:Full title: Complex patterns of genome accessibility discriminate sites of PcG repression, H4K16 acetylation and replication initiation Histone modifications have been proposed to regulate gene expression in part by modulating DNA accessibility and higher-order chromatin structure. However, there is limited direct evidence to support structural differences between euchromatic and heterochromatic fibers in the nucleus. To ask how histone modifications relate to chromatin compaction, we measured DNA accessibility throughout the genome by combining M.SssI methylase footprinting with methylated DNA immunoprecipitation (MeDIP-footprint). In the Drosophila genome, we find that accessibility to DNA methylase is variable in a manner that relates to the differential distribution of active and repressive histone modifications. Active promoters are highly permissive to M.SssI activity, yet inactive chromosomal domains decorated with H3 lysine 27 trimethylation are least accessible providing in vivo evidence for Polycomb-mediated chromatin compaction. Conversely, DNA accessibility is increased at active chromosomal regions marked with H4 lysine 16 acetylation and at the dosage-compensated male X chromosome suggesting that Drosophila transcriptional dosage compensation is facilitated by more permissive chromatin structure. Interestingly early replicating chromosomal regions and sites of replication initiation show also higher accessibility linking temporal and spatial control of genome duplication to the structural organization of chromatin. In conclusion, using a novel protocol we generated a comprehensive view of DNA accessibility and uncover different levels of chromatin organization, which are delineated by distinct patterns of posttranslational histone modifications and replication. Keywords: cell type comparison, ChIP-chip, MeDIP-footprint, RNA-seq, ChIP-seq MeDIP-footprint and ChIP-chip: ChIP-chip was performed for H3K4me3, H3K36me2, H3K36me3, H3K27me3, and H3K9me2 in Kc cells. We measured DNA accessibility throughout the genome by combining M.SssI methylase footprinting with methylated DNA immunoprecipitation (MeDIP-footprint) in Kc and S2 cells. RNA-seq: cDNA from RNA from Drosophila Kc cells was sequenced using Illumina deep sequencing. Reads were mapped and the abundance of all transcripts was determined. ChIP-seq: PSC ChIP from Drosophila Kc cells was sequenced using Illumina deep sequencing in three lanes. Reads were mapped and the binding profile of PSC was determined.

Dataset Information

Ftz and Eve ChIP data

Publications

Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer.

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