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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

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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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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

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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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Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
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Mapping Open Chromatin in Trypanosoma brucei Using ATAC-Seq.

Ruth Shelton1, Keith Matthews2

  • 1Institute for Immunology and Infection Research, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh, UK. ruth.shelton@ed.ac.uk.

Methods in Molecular Biology (Clifton, N.J.)
|February 2, 2026
PubMed
Summary
This summary is machine-generated.

Researchers optimized the Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) for Trypanosoma brucei. This method reveals genome-wide chromatin accessibility, aiding gene regulation studies in these organisms.

Keywords:
ATAC-seqChromatin accessibilityDifferential accessibility analysisEpigenomicsNext-generation sequencingRNA-seqTranscriptional regulation

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Area of Science:

  • Molecular Biology
  • Genomics
  • Parasitology

Background:

  • Gene regulation in trypanosomatids is primarily understood as post-transcriptional.
  • Emerging evidence suggests a role for transcriptional control, challenging existing paradigms.
  • Chromatin accessibility is a key regulatory mechanism, but methods are limited in trypanosomatids.

Purpose of the Study:

  • To optimize and validate the Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) protocol for Trypanosoma brucei.
  • To provide a reliable method for assessing genome-wide chromatin accessibility in trypanosomatids.
  • To facilitate the study of transcriptional regulation in these organisms.

Main Methods:

  • Adaptation and optimization of the ATAC-seq protocol for Trypanosoma brucei (bloodstream and procyclic forms).
  • Application of ATAC-seq to generate genome-wide chromatin accessibility profiles.
  • Development of bioinformatic pipelines for data analysis and integration with RNA-seq.

Main Results:

  • An optimized ATAC-seq protocol effective in both bloodstream and procyclic forms of Trypanosoma brucei.
  • Successful generation of chromatin accessibility maps.
  • Guidance provided for bioinformatic analysis and integration with existing datasets.

Conclusions:

  • The optimized ATAC-seq protocol is a valuable tool for investigating chromatin accessibility and gene regulation in Trypanosoma brucei.
  • This method can be adapted for use in other Euglenozoa, expanding its applicability.
  • The findings support the potential role of transcriptional regulation in trypanosomatids.