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Related Concept Videos

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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Chromatin Packaging01:32

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, 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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Chromatin Packaging02:21

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Spreading of Chromatin Modifications02:25

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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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Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

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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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Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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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. 
Topologically Associated Domains (TADs)
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Related Experiment Video

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Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
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High resolution discovery of chromatin interactions.

Yuchun Guo1, Konstantin Krismer1,2, Michael Closser3

  • 1Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.

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|April 7, 2019
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Summary

A new method, Chromatin Interaction Discovery (CID), improves the detection of genome-wide chromatin interactions. CID enhances sensitivity and consistency, aiding the study of 3D genome organization and disease genetics.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is crucial for genome-wide de novo discovery of chromatin interactions.
  • Current computational methods often miss weak or dynamic interactions due to their reliance on peak-calling, which disregards paired-end linkage information.

Purpose of the Study:

  • To develop a novel computational method for unbiased chromatin interaction discovery.
  • To overcome limitations of existing methods in detecting weak or dynamic interactions.

Main Methods:

  • Developed Chromatin Interaction Discovery (CID), an unbiased clustering approach for interaction discovery.
  • Applied CID to ChIA-PET and HiChIP data.

Main Results:

  • CID demonstrates improved sensitivity, replicate consistency, and concordance with other chromatin interaction datasets compared to existing methods.
  • CID also shows superior performance in discovering chromatin interactions from HiChIP data.

Conclusions:

  • The CID method offers a more effective approach for characterizing 3D chromatin interactions.
  • CID is expected to advance the understanding of functional consequences of disease-associated genetic variations.