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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.
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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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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 Packaging01:32

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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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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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An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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Spring Model - Chromatin Modeling Tool Based on OpenMM.

Michal Kadlof1, Julia Rozycka2, Dariusz Plewczynski3

  • 1Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland; Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.

Methods (San Diego, Calif.)
|December 3, 2019
PubMed
Summary
This summary is machine-generated.

This study introduces a new tool for 3D chromatin structure modeling. It helps visualize and analyze chromatin domains, gene loci, and structural variants using molecular mechanics.

Keywords:
3C3D nucleus structureBiophysical modelingChIA-PETChromatin 3D modelingChromatin higher order structureHi-CStructural variants

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Area of Science:

  • Computational Biology
  • Genomics
  • Structural Biology

Background:

  • The field of chromatin structure modeling is rapidly advancing.
  • There is an increasing demand for tools to build and visualize 3D genome structures, including nuclei, chromosomes, and chromatin domains.
  • Existing methods require robust computational tools for interpreting vast experimental datasets.

Purpose of the Study:

  • To present a novel computational tool for chromatin domain modeling.
  • To provide a user-friendly platform for generating and visualizing 3D chromatin structures based on experimental contact data.
  • To facilitate the analysis of structural variants and genomic interactions.

Main Methods:

  • The tool employs molecular mechanics principles, utilizing the OpenMM engine for 3D model generation.
  • Users input chromatin contacts (e.g., from BEDPE files) to guide structure generation.
  • The method allows adjustable parameters for fiber stiffness, initial structure, simulation resolution, refinement, and modeling within a spherical container.

Main Results:

  • The tool successfully generates 3D chromatin structures that satisfy user-defined contact constraints.
  • Generated structures can be downloaded in Protein Data Bank (PDB) format for downstream analysis.
  • The software enables visualization of datasets, analysis of structural variants, and measurement of genomic distances and local chromatin density.

Conclusions:

  • This chromatin modeling tool offers a versatile solution for researchers interested in 3D genome organization.
  • It supports diverse applications, from quick data visualization to detailed analysis of structural impacts.
  • The tool enhances the study of gene regulation and genome architecture by providing accessible 3D structural insights.