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Related Concept Videos

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
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Chromatin Modification in iPS Cells01:32

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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.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...
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Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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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.
Writers
The writer...
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Chromatin Packaging02:21

Chromatin Packaging

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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? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order...
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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.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
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Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

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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.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
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Capturing Common Fragile Site Breaks by Native &#947;H2A.X ChIP
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Emerging Chemistry Strategies for Engineering Native Chromatin.

Yael David1, Tom W Muir2

  • 1Chemical Biology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States.

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Chemists can help unravel epigenetics by developing new tools to precisely alter chromatin structure. This is crucial for moving beyond correlative data to understand molecular mechanisms in epigenetics.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Epigenetics

Background:

  • Chromosomes, comprising genomic DNA and nuclear factors, are complex substrates for biochemical study.
  • These factors stabilize DNA and regulate access to genetic information, a key aspect of epigenetics.
  • Current research in epigenetics often relies on correlative data, limiting molecular-level understanding.

Purpose of the Study:

  • To highlight the need for precise tools to manipulate chromatin's covalent structure.
  • To identify an opportunity for chemists to contribute to epigenetic research.
  • To bridge the gap between correlative observations and causal molecular mechanisms in epigenetics.

Main Methods:

  • The study is a perspective piece, outlining challenges and opportunities in the field.
  • It emphasizes the need for chemical approaches to modify chromatin structure.
  • It discusses the limitations of current methodologies in epigenetics.

Main Results:

  • There is a significant shortage of tools for precise covalent modification of chromatin.
  • Chemical methodologies are well-suited to address this gap.
  • Developing such tools will enable a deeper understanding of epigenetic regulation.

Conclusions:

  • Chemists are uniquely positioned to develop novel tools for chromatin manipulation.
  • Precise manipulation of chromatin structure is essential for establishing causal relationships in epigenetics.
  • This work presents an opportunity for interdisciplinary collaboration between chemistry and epigenetics.