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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
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In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
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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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Dynamic enhancer function in the chromatin context.

Ido Goldstein1, Gordon L Hager1

  • 1Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.

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|May 26, 2017
PubMed
Summary
This summary is machine-generated.

New live-cell imaging reveals that enhancer-activating factors bind dynamically within milliseconds to seconds. This contrasts with older models suggesting slower, static binding, offering a real-time view of gene regulation.

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Area of Science:

  • Systems Biology
  • Molecular Biology
  • Genomics

Background:

  • Enhancers are crucial regulatory elements in eukaryotic gene expression.
  • Traditional genome-wide assays provide static, population-averaged views of enhancer function.
  • These methods often model enhancer-activating factor binding as slow and sequential.

Purpose of the Study:

  • To review the impact of advanced live-cell imaging techniques on understanding enhancer function.
  • To present a dynamic model of enhancer-activating factor binding in real time.
  • To highlight the utility of in vivo single-molecule tracking (SMT) for studying enhancers.

Main Methods:

  • Review of established genome-wide techniques (ChIP-seq, DNase-seq, 3C-based methods).
  • Analysis of advanced live-cell microscopy techniques (FRAP, FCS, SMT).
  • Re-evaluation of genomic footprinting data.

Main Results:

  • Live-cell microscopy reveals highly dynamic binding of enhancer factors.
  • Transcription factors may leave minimal or no footprints, challenging traditional models.
  • In vivo SMT emerges as a powerful tool for real-time enhancer analysis.

Conclusions:

  • Enhancer function is best understood as a dynamic process occurring on millisecond to second timescales.
  • Dynamic binding models provide a more accurate view of enhancer-activating factor action.
  • Integrating multiple methodologies offers a comprehensive understanding of enhancer regulation.