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Histone Modification

Histone Modification

The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone...

Spreading of Chromatin Modifications

Spreading of Chromatin Modifications

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...

Chromatin Modification in iPS Cells

Chromatin Modification in iPS Cells

Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...

Covalently Linked Protein Regulators

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....

Nucleosome Remodeling

Nucleosome Remodeling

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
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...

Epigenetic Regulation

Epigenetic Regulation

Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
X-chromosome...

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Related Experiment Video

Updated: Jun 22, 2025

Site Specific Lysine Acetylation of Histones for Nucleosome Reconstitution using Genetic Code Expansion in Escherichia coli

Site Specific Lysine Acetylation of Histones for Nucleosome Reconstitution using Genetic Code Expansion in Escherichia coli

Published on: December 26, 2020

Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1.

Kwangwoon Lee^1,2, Marco Barone³, Amanda L Waterbury^4,5

¹Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.

Nature Chemical Biology

|July 4, 2024

Summary

Histone modification crosstalk, where one modification affects another, is key in epigenetics. Researchers engineered a mutant lysine-specific demethylase 1 (LSD1) enzyme to block this crosstalk, revealing its role in gene silencing.

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Published on: January 26, 2018

Area of Science:

Epigenetics
Molecular Biology
Biochemistry

Background:

Biochemical crosstalk between histone modifications is common in epigenetic regulation.
Lysine-specific demethylase 1 (LSD1) activity is inhibited by histone H3 Lysine 14 acetylation.
The functional significance of this crosstalk in cellular processes remains unclear.

Purpose of the Study:

To investigate the functional consequences of disconnecting histone modification crosstalk for LSD1.
To engineer a mutant LSD1 enzyme resistant to inhibition by H3 Lys14 acetylation.
To analyze the impact of this engineered enzyme on gene expression and chromatin states.

Main Methods:

Engineered a Y391K mutant form of LSD1, insensitive to H3 Lys14 acetylation.
Utilized CRISPR technology to knock in the Y391K LSD1 mutant into K562 cells.
Performed chromatin profiling to assess histone modifications and gene expression changes.

Main Results:

K562 cells with Y391K LSD1 showed decreased expression of genes involved in cellular adhesion and myeloid leukocyte activation.
Silenced genes' regulatory regions exhibited high H3 Lys14 acetylation.
Edited cells displayed reduced H3 mono-methyl Lys4 near silenced genes, indicating enhanced LSD1 demethylase activity.

Conclusions:

Disconnecting histone modification crosstalk for LSD1 impacts gene expression, specifically silencing genes related to cellular adhesion and myeloid leukocyte activation.
This study provides functional insights into the role of H3 Lys14 acetylation in regulating LSD1 activity and downstream gene expression.
The engineered LSD1 mutant serves as a valuable tool for dissecting epigenetic crosstalk mechanisms.