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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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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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The writer...
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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
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Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
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DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
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CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation.

Yichen Zhong1, Bishnu P Paudel2,3, Daniel P Ryan4

  • 1School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.

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Chromatin remodellers like CHD4 use ATP to move DNA. This study reveals CHD4

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Chromatin remodellers are ATP-dependent molecular machines.
  • They play crucial roles in DNA replication, transcription, and repair by repositioning nucleosomes.
  • The precise translocation mechanisms across different remodeller families remain incompletely understood.

Purpose of the Study:

  • To elucidate the mechanism of action of CHD4, a member of a poorly characterized chromatin remodeller family.
  • To investigate how CHD4 utilizes ATP hydrolysis to facilitate nucleosome sliding.

Main Methods:

  • Single-molecule assays were employed to monitor CHD4-nucleosome interactions in real-time.
  • Biophysical techniques were used to analyze DNA conformational changes and translocation dynamics.

Main Results:

  • CHD4 binding to nucleosomes, even without ATP, induces DNA conformational changes at the entry side, priming for remodelling.
  • Nucleosomal DNA translocation occurs with continuous entry and stepwise (4-6 bp) exit.
  • A mechanism involving strain accumulation and release during DNA expulsion is proposed.

Conclusions:

  • CHD4-mediated nucleosome sliding involves a unique mechanism with distinct entry and exit translocation dynamics.
  • This study provides novel insights into the functional diversity of chromatin remodellers.
  • The findings contribute to a broader understanding of ATP-dependent DNA-protein interactions in chromatin dynamics.