Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Molecular landscape of modified histones in Drosophila heterochromatin

ABSTRACT: The aim of this study is to analyze the distribution of the modified histones in and around peri-centromeric heterochromatin at high resolutions for understanding the molecular nature of the heterochromatic genes and euchromatin-heterochromatin transition. Since heterochromatin is repeat-rich, stringent repeat-filtering was applied in the genome-tiling array design. When possible, parallel analyses were performed with two different types of reference controls, namely total genomic DNA and histone H3 C-terminus ChIP.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Barbara Wakimoto

PROVIDER: E-GEOD-7839 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Molecular landscape of modified histones in Drosophila heterochromatic genes and euchromatin-heterochromatin transition zones.

Yasuhara Jiro C JC Wakimoto Barbara T BT

PLoS genetics 20071213 1

Constitutive heterochromatin is enriched in repetitive sequences and histone H3-methylated-at-lysine 9. Both components contribute to heterochromatin's ability to silence euchromatic genes. However, heterochromatin also harbors hundreds of expressed genes in organisms such as Drosophila. Recent studies have provided a detailed picture of sequence organization of D. melanogaster heterochromatin, but how histone modifications are associated with heterochromatic sequences at high resolution has not ...[more]

PMID: 18208336

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Project description:The goals of the study were to assess array platform performance and analysis algorithm performance. The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated. Keywords: ChIP-chip, competition, artificial DNA For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf DNA samples had spike-in DNA added to simulate peaks in ChIP-chip experiments. Same DNA samples used in the arrays in this Series; these are technical array replicates.

Dataset Information

Molecular landscape of modified histones in Drosophila heterochromatin

Publications

Molecular landscape of modified histones in Drosophila heterochromatic genes and euchromatin-heterochromatin transition zones.

Similar Datasets

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