Combinatorial patterns of histone acetylations and methylations in the human genome

@article{Wang2008CombinatorialPO,
  title={Combinatorial patterns of histone acetylations and methylations in the human genome},
  author={Zhibin Wang and Chongzhi Zang and Jeffrey A. Rosenfeld and Dustin E. Schones and Artem Barski and Suresh Cuddapah and Kairong Cui and Tae-Young Roh and Weiqun Peng and Michael Q. Zhang and Keji Zhao},
  journal={Nature Genetics},
  year={2008},
  volume={40},
  pages={897-903}
}
Histones are characterized by numerous posttranslational modifications that influence gene transcription. However, because of the lack of global distribution data in higher eukaryotic systems, the extent to which gene-specific combinatorial patterns of histone modifications exist remains to be determined. Here, we report the patterns derived from the analysis of 39 histone modifications in human CD4+ T cells. Our data indicate that a large number of patterns are associated with promoters and… 

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References

SHOWING 1-10 OF 51 REFERENCES

Histone acetylation and an epigenetic code.

  • B. Turner
  • Biology
    BioEssays : news and reviews in molecular, cellular and developmental biology
  • 2000
Recent evidence raises the interesting possibility that an acetylation-based code may operate through both mitosis and meiosis, providing a possible mechanism for germ-line transmission of epigenetic changes.

Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping.

High-resolution genome-wide mapping of diacetylation of histone H3 at Lys 9 and Lys 14 in resting and activated human T cells by genome- wide mapping technique (GMAT) shows that high levels of the H3 acetylation are detected in gene-rich regions.

Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns.

This study exploits the highly conserved nature of epigenetic modifications to identify potential transcriptional enhancers and establishes a novel genome-wide method for identifying regulatory elements not discernable by comparative genomics alone.

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

Insight is given into the connections between chromatin modifications and transcriptional regulatory activity and a novel functional enhancer for the carnitine transporter SLC22A5 (OCTN2) is uncovered, providing a new tool for the functional annotation of the human genome.

Quantitative Proteomic Analysis of Post-translational Modifications of Human Histones*

Histone proteins are subject to a range of post-transcriptional modifications in living cells. The combinatorial nature of these modifications constitutes the “histone code” that dictates chromatin

High-Resolution Profiling of Histone Methylations in the Human Genome

Roles of histone acetyltransferases and deacetylases in gene regulation

  • M. KuoC. Allis
  • Biology
    BioEssays : news and reviews in molecular, cellular and developmental biology
  • 1998
Recent developments in histone acetylation and transcriptional regulation are reviewed, suggesting the possibility that internal lysine acetylations of multiple proteins exists as a rapid and reversible regulatory mechanism much like protein phosphorylation.

The language of covalent histone modifications

It is proposed that distinct histone modifications, on one or more tails, act sequentially or in combination to form a ‘histone code’ that is, read by other proteins to bring about distinct downstream events.

The genomic landscape of histone modifications in human T cells

Investigation of the genomic landscape of activating histone modifications in primary human T cells reveals that rapidly inducible genes are associated with the H3 acetylation and H3K4me3 modifications, suggesting they assume a chromatin structure poised for activation.
...