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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? 
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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 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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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

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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. 
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The fineness of cement directly influences the rate of hydration, as the hydration begins at the surface of the cement particles. In addition to hydration, the fineness of cement is vital for various properties of concrete including workability, gypsum requirement, and long-term behavior. The fineness of cement is represented in terms of the specific surface of cement which is typically measured in square meters per kilogram, with several methods available for this determination.
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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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Fine mapping chromatin contacts in capture Hi-C data.

Christiaan Q Eijsbouts1,2,3, Oliver S Burren1, Paul J Newcombe2

  • 1Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK.

BMC Genomics
|January 25, 2019
PubMed
Summary

This study introduces a novel Bayesian method to precisely map direct chromatin contacts from Hi-C and capture Hi-C (CHi-C) data. The approach refines contact mapping, revealing true interactions within complex datasets.

Keywords:
Bayesian statisticsCapture Hi-CChromatin conformationVariable selection

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • High-throughput sequencing techniques like Hi-C and capture Hi-C (CHi-C) map physical chromatin contacts.
  • Current analysis methods treat fragment pairs independently, leading to long runs of apparent contacts.
  • This can obscure the identification of direct, functional interactions.

Purpose of the Study:

  • To develop a new computational method for high-resolution mapping of direct chromatin contacts.
  • To address the limitations of current analysis by identifying a subset of true contacts within CHi-C data.
  • To improve the interpretation of physical interactions in the cell nucleus.

Main Methods:

  • A novel Bayesian sparse variable selection approach was developed.
  • The method exploits the spatial pattern of counts within CHi-C data.
  • It focuses on identifying a minimal set of direct contacts from observed interaction data.

Main Results:

  • The proposed method successfully fine-maps direct chromatin contacts.
  • Prioritized fragments show expected biological properties, linking promoters to active chromatin and enhancers.
  • Long runs of apparent contacts can be explained by a significantly smaller subset of direct interactions (<10%).

Conclusions:

  • The Bayesian method offers enhanced resolution for mapping direct contacts in CHi-C experiments.
  • It provides complementary insights to existing per-fragment analysis approaches.
  • This technique can improve the understanding of 3D genome organization and function.