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Related Concept Videos

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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Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
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The Nucleosome01:19

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Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
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In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
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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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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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Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
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Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

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How Do Nucleosome Dynamics Regulate Protein Search on DNA?

Sujeet Kumar Mishra1, Arnab Bhattacherjee1

  • 1School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.

The Journal of Physical Chemistry. B
|June 13, 2023
PubMed
Summary
This summary is machine-generated.

Nucleosome dynamics, including breathing and sliding, influence transcription factor search times on DNA. Understanding these mechanisms reveals key factors in gene regulation and cell fate determination.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • Nucleosomes, composed of histone proteins and DNA, package eukaryotic DNA and regulate gene accessibility.
  • Nucleosome dynamics are crucial for controlling DNA site accessibility for regulatory proteins, impacting cell identity and fate.

Purpose of the Study:

  • To develop an analytical framework for assessing nucleosome dynamics' impact on transcription factor target search.
  • To differentiate the effects of nucleosome breathing versus sliding on protein search efficiency.

Main Methods:

  • Utilizing a discrete-state stochastic model for transcription factor search dynamics.
  • Employing first-passage probability calculations with experimentally determined kinetic rates.
  • Validating analytical results through extensive Monte Carlo simulations.

Main Results:

  • Nucleosome breathing and sliding dynamics offer distinct mechanisms for DNA site access.
  • Substantial differences exist in transcription factor search strategies on nucleosomes undergoing breathing versus sliding.
  • Identified molecular factors significantly influence transcription factor search efficiency.

Conclusions:

  • Nucleosome dynamics create a dynamic landscape critical for gene regulation.
  • The interplay of protein and nucleosome dynamics governs the efficiency of transcription factor binding.
  • This framework provides insights into the molecular basis of cell fate determination.