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Histone Modification02:32

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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
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An integrative approach to understanding the combinatorial histone code at functional elements.

William K M Lai1, Michael J Buck

  • 1Department of Biochemistry, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA.

Bioinformatics (Oxford, England)
|July 4, 2013
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Summary
This summary is machine-generated.

We developed a novel nucleosome alphabet to interpret complex chromatin modifications. This framework reveals distinct chromatin motifs and their associations with genomic features and transcription factor binding.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Genomic technology reveals the complexity of chromatin modifications.
  • Interpreting the combinatorial nature of chromatin is challenging.

Purpose of the Study:

  • To develop a novel method for integrating chromatin datasets.
  • To create a "nucleosome alphabet" for interpreting chromatin architecture.

Main Methods:

  • Integrated multiple chromatin datasets into distinct nucleosome types.
  • Applied the nucleosome alphabet approach to Saccharomyces cerevisiae.
  • Utilized chromatin alignment and global word search for motif discovery.

Main Results:

  • Generated a nucleosome alphabet for yeast, forming chromatin motifs.
  • Defined motifs for introns, origins of replication, tRNAs, and other genomic elements.
  • Distinguished genes by expression level and found associations between transcription factor binding and nucleosome types.

Conclusions:

  • The nucleosome alphabet provides a functional framework for chromatin analysis.
  • This approach facilitates the interpretation of chromatin complexity and architecture.
  • Demonstrated the utility of the nucleosome alphabet in understanding genomic organization.