Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Leishmania major promastigote ChIP-chip: TBP, SNAP50, acetylH3

ABSTRACT: The goal of this study is to identify likely sites of polycistronic transcription initiation in a kinetoplastid parasite. Peaks in histone H3 acetylations were found to mark these likely sites, with TBP and SNAP50 enriched upstream of these acetylation peaks. Acetylation peaks are greater in rapidly dividing cells than in stationary cells. Each ChIP sample was compared to an input chromatin sample that underwent a mock immunoprecipitation (without antiserum), or in the case of acetylH3 ChIPs, used an antiserum that recognized total H3 histones. Log ratios and raw scores for each probe are provided.

ORGANISM(S): Leishmania major

SUBMITTER: Amanda Green

PROVIDER: E-GEOD-13415 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Histone acetylations mark origins of polycistronic transcription in Leishmania major.

Thomas Sean S Green Amanda A Sturm Nancy R NR Campbell David A DA Myler Peter J PJ

BMC genomics 20090408

<h4>Background</h4>Many components of the RNA polymerase II transcription machinery have been identified in kinetoplastid protozoa, but they diverge substantially from other eukaryotes. Furthermore, protein-coding genes in these organisms lack individual transcriptional regulation, since they are transcribed as long polycistronic units. The transcription initiation sites are assumed to lie within the 'divergent strand-switch' regions at the junction between opposing polycistronic gene clusters. ...[more]

PMID: 19356248

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Project description:Samples from 20 children with B-cell precursor ALL, comprising ten with high hyperdiploidy and ten with the ETV6/RUNX1 fusion, were included in the study. Four Âµg of methylated and input fraction DNA were analyzed with a classic MeDIP assay and subsequent microarray hybridization using the NimbleGen CpG Island-Plus-Promoter Array (Roche NimbleGen, Madison, WI).<br><br>This array platform covers all 28,226 UCSC-annotated CpG islands and promoter regions for all RefSeq genes, including 385,000 probes of 50-75mer length per array, with an upstream and downstream promoter tiling of 800 bp and 200 bp, respectively. Signal intensity data were extracted from the scanned images. Each feature on the array has a corresponding log2 ratio, which is the ratio of the input signals for the methylated DNA and the input fraction DNA. The log2 ratio was scaled in order to center the ratio data around zero by subtracting the bi-weight mean for the log2 ratio values for all features on the array from each log2 ratio value. A modified ACME algorithm, where a fixed-length window (750 bp) is placed around each consecutive probe, and the one-sided Kolmogorov-Smirnov test were then applied on the scaled log2 ratio data to determine whether the probes were drawn from a significantly more positive distribution (peak) of intensity log2 ratios than the other probes in the array. The resulting score for each probe is the -log10 p-value from the windowed Kolmogorov-Smirnov test around that probe. Peak data were generated by searching for probes above a p-value minimum cut-off (-log10) of 2.<br><br>Peaks within 500 bp of each other were merged. Each annotated gene was subsequently searched for peaks appearing in a specified promoter region around the transcription start site. The region searched was design-specific, spanning from 5 kb upstream to 1 kb downstream of the transcription start site. Genes that had at least two probes with peaks above the p-value minimum cut-off were considered to have significant CpG island methylation scores for hypermethylation.

Dataset Information

Leishmania major promastigote ChIP-chip: TBP, SNAP50, acetylH3

Publications

Histone acetylations mark origins of polycistronic transcription in Leishmania major.

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