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Spreading of Chromatin Modifications02:25

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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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Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
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Chromatin Immunoprecipitation ChIP to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells
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TALE proteins bind to both active and inactive chromatin.

James N F Scott1, Adam P Kupinski1, Christopher M Kirkham1

  • 1*School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.

The Biochemical Journal
|January 21, 2014
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Summary

Transcription activator-like effector (TALE) proteins can bind DNA targets within chromatin. Studies show TALEs bind accessible sites on nucleosomes in vitro and in vivo, even in repressed chromatin, suggesting broad applicability.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Epigenetics

Background:

  • Transcription activator-like effector (TALE) proteins offer customizable DNA binding for genome engineering.
  • TALE functionality relies on their ability to access target DNA sequences within the complex chromatin environment.
  • Understanding TALE binding dynamics in chromatin is crucial for optimizing their use in research and therapeutics.

Purpose of the Study:

  • To systematically evaluate the binding characteristics of TALEs to chromatin substrates.
  • To determine the preferred binding locations of TALEs on nucleosomes.
  • To assess the impact of transcriptional activity on TALE binding in vivo.

Main Methods:

  • In vitro assays using purified nucleosomes and TALEs.
  • In vivo chromatin immunoprecipitation (ChIP) experiments.
  • Quantitative analysis of TALE binding to different chromatin states.

Main Results:

  • In vitro, TALEs preferentially bind to the entry/exit DNA regions of nucleosomes, avoiding the dyad.
  • In vivo, TALEs demonstrate binding to transcriptionally repressed chromatin.
  • Increased transcriptional activity resulted in only a modest (2-fold) increase in TALE binding.

Conclusions:

  • TALE proteins can access their target DNA sites within chromatin, irrespective of transcriptional status.
  • The binding preference for accessible nucleosome regions suggests TALEs can function even in tightly packed chromatin.
  • These findings support the utility of TALEs for genome editing and gene regulation in diverse chromatin contexts.