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Chromatin Position Affects Gene Expression

Chromatin Position Affects Gene Expression

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...

Heterochromatin

Heterochromatin

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...

Heterochromatin

Heterochromatin

Euchromatin

Euchromatin

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...

Euchromatin

Euchromatin

Chromatin Immunoprecipitation- ChIP

Chromatin Immunoprecipitation- ChIP

Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...

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Related Experiment Video

Updated: Feb 27, 2026

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

Published on: September 20, 2018

CAGE: Chromatin Analogous Gene Expression.

Reza M Zadegan¹, William L Hughes¹

¹Micron School of Materials Science & Engineering, and ‡College of Innovation + Design, Boise State University , Boise, Idaho 83725, United States.

ACS Synthetic Biology

|June 29, 2017

Summary

This summary is machine-generated.

New DNA molecular machines react with cancer-specific miRNA mimics to control gene expression. This chromatin analogous gene expression (CAGE) technology offers potential for synthetic biology and personalized medicine.

Keywords:

CAGE RNA polymerase regulation gene expression molecular machine

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Last Updated: Feb 27, 2026

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

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Published on: September 20, 2018

Chromatin Immunoprecipitation ChIP using Drosophila tissue

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Published on: March 23, 2012

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

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

Published on: April 30, 2012

Area of Science:

Nanotechnology
Molecular Biology
Synthetic Biology

Background:

Self-assembled nucleic acids are crucial for nanoscale biological, chemical, and mechanical functions.
DNA-based molecular machines offer programmable control over biological processes.

Purpose of the Study:

To design DNA-based molecular machines capable of performing work by interacting with cancer-specific miRNA mimics.
To regulate gene expression in vitro through precise tuning of RNA polymerase activity.

Main Methods:

Development of DNA-based molecular machines.
In vitro experiments involving reactions with miRNA mimics.
Regulation of RNA polymerase activity to control gene expression.
Demonstration of chromatin analogous gene expression (CAGE).

Main Results:

The designed molecular machines successfully reacted with cancer-specific miRNA mimics.
Gene expression was regulated in vitro by tuning RNA polymerase activity.
The machines exhibited chromatin analogous gene expression (CAGE) due to topological constraints on RNA production.

Conclusions:

The developed CAGE technology is modular and tunable.
CAGE holds significant potential for applications in molecular biology, synthetic biology, and personalized medicine.