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Nucleosome Remodeling02:54

Nucleosome Remodeling

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Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
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Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
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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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Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
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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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Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning.

Drake A Donovan1, Johnathan G Crandall1, Orion G B Banks1

  • 1Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.

Cell Reports
|November 21, 2019
PubMed
Summary

Engineered chromatin remodeling proteins (E-ChRPs) precisely control nucleosome positioning. This technology enables targeted gene regulation and disruption of DNA-dependent processes in various chromatin contexts.

Keywords:
chromatin bindingchromatin engineeringchromatin remodelingdCas9nucleosometargeted nucleosome positioningtranscription factors

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Area of Science:

  • Molecular Biology
  • Epigenetics
  • Chromatin Biology

Background:

  • Chromatin structure regulates DNA accessibility for transcription factors.
  • Precise control over nucleosome positioning is crucial for gene regulation.

Purpose of the Study:

  • To develop and validate engineered chromatin remodeling proteins (E-ChRPs).
  • To demonstrate E-ChRPs' ability to induce programmable changes in nucleosome positioning.
  • To explore the effects of engineered nucleosome positioning on gene transcription.

Main Methods:

  • Development of engineered chromatin remodeling proteins (E-ChRPs).
  • In vitro and in vivo validation of E-ChRPs for nucleosome repositioning.
  • Utilizing targeting modalities like SpyCatcher and dCas9 for E-ChRP delivery.

Main Results:

  • E-ChRPs successfully reposition target nucleosomes and nucleosomal arrays in vitro and in vivo.
  • Systematic nucleosome positioning over Ume6 binding sites induced transcriptional activation.
  • Programmed loss of nucleosome-free regions at Reb1 targets showed repressive transcriptional effects.

Conclusions:

  • Engineered chromatin remodeling proteins offer a versatile tool for probing and manipulating DNA-dependent processes.
  • E-ChRPs provide a simple and robust method for controlling chromatin structure and gene expression.
  • This technology has broad applications in diverse chromatin contexts and future research.