Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Chromatin immunoprecipitation of yeast to identify genomic binding locations of yeast transcription machinary factors Reb1, Rpb3, Rpo21, Rsc9, Sua7 and Swr1

ABSTRACT: High-resolution genome-wide mapping of the yeast transcription machinery. ChIP-chip was performed to identify the genomic binding locations for each factor.

Processed data files are also available on the FTP server for this experiment.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Bryan Venters

PROVIDER: E-MEXP-1676 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome.

Venters Bryan J BJ Pugh B Franklin BF

Genome research 20090105 3

The predominant organizational theme by which the transcription machinery and chromatin regulators are positioned within promoter regions or throughout genes in a genome is largely unknown. We mapped the genomic location of diverse representative components of the gene regulatory machinery in Saccharomyces cerevisiae to an experimental resolution of <40 bp. Sequence-specific gene regulators, chromatin regulators, mediator, and RNA polymerase (Pol) II were found primarily near the downstream bord ...[more]

PMID: 19124666

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Project description:Chromatin immunoprecipitation microarray (ChIP-chip) study using 3 human cell lines (K562, U937, CD14+); of 19 histone modifications across 1% of the human genome used in the pilot phase of the ENCODE project.<br>paper abstract: It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons ("exon-intron marking"), linking chromatin structure and function to co- transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing.

Dataset Information

Chromatin immunoprecipitation of yeast to identify genomic binding locations of yeast transcription machinary factors Reb1, Rpb3, Rpo21, Rsc9, Sua7 and Swr1

Publications

A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome.

Similar Datasets

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