Dataset Information

Insights into distinct regulatory modes of nucleosome positioning.

ABSTRACT:

Background

The nucleosome is the fundamental unit of eukaryotic genomes. Experimental evidence suggests that the genomic DNA sequence and a variety of protein factors contribute to nucleosome positioning in vivo. However, how nucleosome positioning is determined locally is still largely unknown.

Results

We found that transcription factor binding sites (TFBSs) with particular nucleosomal contexts show a preference to reside on specific chromosomes. We identified four typical gene classes associated with distinct regulatory modes of nucleosome positioning, and further showed that they are distinguished by transcriptional regulation patterns. The first mode involves the cooperativity between chromatin remodeling and stable transcription factor (TF)-DNA binding that is linked to high intrinsic DNA binding affinities, evicting nucleosomes from favorable DNA sequences. The second is the DNA-encoded low nucleosome occupancy that is associated with high gene activity. The third is through chromatin remodeling and histone acetylation, sliding nucleosomes along DNA. This mode is linked to more cryptic sites for TF binding. The last consists of the nucleosome-enriched organization driven by other factors that overrides nucleosome sequence preferences. In addition, we showed that high polymerase II (Pol II) occupancy is associated with high nucleosome occupancy around the transcription start site (TSS).

Conclusions

We identified four different regulatory modes of nucleosome positioning and gave insights into mechanisms that specify promoter nucleosome location. We suggest two distinct modes of recruitment of Pol II, which are selectively employed by different genes.

SUBMITTER: Dai Z

PROVIDER: S-EPMC2799443 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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Publications

Insights into distinct regulatory modes of nucleosome positioning.

Dai Zhiming Z Dai Xianhua X Xiang Qian Q Feng Jihua J Deng Yangyang Y Wang Jiang J

BMC genomics 20091214

<h4>Background</h4>The nucleosome is the fundamental unit of eukaryotic genomes. Experimental evidence suggests that the genomic DNA sequence and a variety of protein factors contribute to nucleosome positioning in vivo. However, how nucleosome positioning is determined locally is still largely unknown.<h4>Results</h4>We found that transcription factor binding sites (TFBSs) with particular nucleosomal contexts show a preference to reside on specific chromosomes. We identified four typical gene c ...[more]

PMID: 20003404

Similar Datasets

Project description:BackgroundRecently, a number of high-resolution genome-wide maps of nucleosome locations in S. cerevisiae have been derived experimentally. However, nucleosome positions are determined in vivo by the combined effects of numerous factors. Consequently, nucleosomes are not simple static units, which may explain the discrepancies in reported nucleosome positions as measured by different experiments. In order to more accurately depict the genome-wide nucleosome distribution, we integrated multiple nucleosomal positioning datasets using a multi-angle analysis strategy.ResultsTo evaluate the contribution of chromatin structure to transcription, we used the vast amount of available nucleosome analyzed data. Analysis of this data allowed for the comprehensive identification of the connections between promoter nucleosome positioning patterns and various transcription-dependent properties. Further, we characterised the function of nucleosome destabilisation in the context of transcription regulation. Our results indicate that genes with similar nucleosome occupancy patterns share general transcription attributes. We identified the local regulatory correlation (LRC) regions for two distinct types of nucleosomes and we assessed their regulatory properties. We also estimated the nucleosome reproducibility and measurement accuracy for high-confidence transcripts. We found that by maintaining a distance of approximately 13 bp between the upstream border of the +1 nucleosome and the transcription start sites (TSSs), the stable +1 nucleosome may form a barrier against the accessibility of the TSS and shape an optimum chromatin conformation for gene regulation. An in-depth analysis of nucleosome positioning in normally growing and heat shock cells suggested that the extent and patterns of nucleosome sliding are associated with gene activation.ConclusionsOur results, which combine different types of data, suggest that cross-platform information, including discrepancy and consistency, reflects the mechanisms of nucleosome packaging in vivo more faithfully than individual studies. Furthermore, nucleosomes can be divided into two classes according to their stable and dynamic characteristics. We found that two different nucleosome-positioning characteristics may significantly impact transcription programs. Besides, some positioned-nucleosomes are involved in the transition from stable state to dynamic state in response to abrupt environmental changes.

Dataset Information

Insights into distinct regulatory modes of nucleosome positioning.

Background

Results

Conclusions

Publications

Insights into distinct regulatory modes of nucleosome positioning.

Similar Datasets

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