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Related Concept Videos

Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

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The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
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Heterochromatin02:38

Heterochromatin

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The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...
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Euchromatin01:01

Euchromatin

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The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
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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. 
Topologically Associated Domains (TADs)
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Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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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 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
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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
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The chromatin - triple helix connection.

Rodrigo Maldonado1, Gernot Längst2

  • 1Institute of Anatomy, Histology, and Pathology, Faculty of Medicine, Universidad Austral de Chile, 5090000 Valdivia, Chile.

Biological Chemistry
|July 28, 2023
PubMed
Summary

Mammalian genomes produce many nuclear RNAs (ncRNAs) that associate with chromatin. This review explores how RNA targets DNA via triple helices, influenced by nucleosomes and histone modifications for gene regulation.

Keywords:
RNA-DNA triple helixchromatinchromatin-associated RNAlncRNAnucleosome

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Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation
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Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation

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Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Mammalian genomes extensively transcribe coding and non-coding RNAs.
  • A significant portion of nuclear RNAs associates with chromatin, influencing gene regulation and genome organization.
  • Chromatin-associated RNAs (caRNAs) are tethered via RNA binding proteins, RNA polymerases, and R-loops.

Purpose of the Study:

  • To review the sequence-specific targeting of RNA to DNA through triple helix formation.
  • To describe the interplay between RNA-DNA triple helices and chromatin structure.
  • To discuss the role of nucleosomes and histone modifications in triple helix stability.

Main Methods:

  • Literature review focusing on RNA-DNA triple helix formation.
  • Analysis of mechanisms for RNA tethering to chromatin.
  • Examination of nucleosome positioning and histone tail interactions.

Main Results:

  • Nucleosome positioning and the nucleosome itself are critical for triple helix formation and stability.
  • The histone H3 tail significantly stabilizes RNA-DNA triple helices.
  • Epigenetic modifications of histone H3 tails influence triple helix stability.

Conclusions:

  • RNA-DNA triple helix formation is a key mechanism for sequence-specific RNA targeting to chromatin.
  • Nucleosomes and histone modifications play crucial roles in regulating triple helix formation and function.
  • This interaction is vital for understanding higher-order genome organization and gene regulation.