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Related Concept Videos

Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

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In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
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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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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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Nucleosome Remodeling02:54

Nucleosome Remodeling

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Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
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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)
The 3-dimensional positioning of chromatin in the nucleus influences the...
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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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Related Experiment Video

Updated: Jul 31, 2025

CRISPR Epigenome Editing in Human Cells using Plasmid DNA Transfection and mRNA Nucleofection Delivery
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CRISPR Epigenome Editing in Human Cells using Plasmid DNA Transfection and mRNA Nucleofection Delivery

Published on: May 30, 2025

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Chromatin structure and context-dependent sequence features control prime editing efficiency.

Somang Kim1,2, Jimmy B Yuan1,2, Wendy S Woods3

  • 1Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

Biorxiv : the Preprint Server for Biology
|May 10, 2023
PubMed
Summary
This summary is machine-generated.

This study develops statistical models to optimize prime editor (PE) guide-RNA (pegRNA) designs for enhanced CRISPR-Cas9 genome editing efficiency. Findings reveal key sequence and epigenomic features that improve editing outcomes and reduce experimental optimization.

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A Method to Study de novo Formation of Chromatin Domains
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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Prime editing (PE) is a versatile CRISPR-Cas9 genome editing tool.
  • Current PE constructs exhibit variable efficiency, necessitating optimization.
  • Understanding target site features is crucial for improving PE performance.

Conclusions:

  • The study provides crucial insights into optimizing PE pegRNA design by considering sequence and epigenomic features.
  • Identified context-dependent features clarify previous conflicting observations and guide future PE development.
  • This work facilitates more efficient and predictable genome editing using prime editors.