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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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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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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 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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Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells
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A rapid and robust method for single cell chromatin accessibility profiling.

Xi Chen1, Ricardo J Miragaia1,2, Kedar Nath Natarajan1,3

  • 1Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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|December 19, 2018
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Summary
This summary is machine-generated.

We developed a simple plate-based assay for transposase-accessible chromatin using sequencing (ATAC-seq) at the single-cell level (scATAC-seq). This method identifies cell types and regulatory elements in complex tissues like the spleen.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Immunology

Background:

  • Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is crucial for identifying genomic regulatory regions.
  • Single-cell ATAC-seq (scATAC-seq) presents technical challenges, limiting its widespread application.
  • Previous scATAC-seq methods have faced limitations in robustness and applicability across diverse sample types.

Purpose of the Study:

  • To develop a simple, robust, and versatile plate-based scATAC-seq method.
  • To overcome existing technical hurdles in single-cell chromatin accessibility profiling.
  • To enable detailed analysis of regulatory landscapes in primary tissues.

Main Methods:

  • Developed a novel plate-based scATAC-seq protocol.
  • Integrated upfront bulk Tn5 enzyme tagging with subsequent single-nuclei sorting.
  • Validated the method on fresh and cryopreserved primary tissue samples, including splenocytes.

Main Results:

  • Demonstrated robust performance of the new scATAC-seq method across various sample types.
  • Successfully profiled over 3000 splenocytes, enabling high-resolution analysis.
  • Identified distinct immune cell populations within the spleen.
  • Revealed cell type-specific regulatory regions and associated transcription factors.

Conclusions:

  • The developed plate-based scATAC-seq method is simple, robust, and broadly applicable.
  • This technique facilitates the identification of cell-specific regulatory elements and transcription factors in complex biological systems.
  • The method advances single-cell genomics for studying immune cell heterogeneity and function.