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Updated: May 25, 2026
10:54
Extraction of Histones from Clinical Specimens for Epigenetic Profiling by Mass Spectrometry
Published on: November 21, 2025
Functional elements demarcated by histone modifications in breast cancer cells
Moon Kyung Choe1, Chang-Pyo Hong, Jihwan Park
1Division of Molecular and Life Sciences, POSTECH (Pohang University of Science and Technology), Pohang, Kyungbuk 790-784, Republic of Korea.
Biochemical and Biophysical Research Communications
|January 31, 2012
Summary
Histone modifications like H3K4me1, H3K4me3, and H3K9/14ac help identify gene regulatory elements. Analyzing these marks in breast cancer cells reveals distinct patterns linked to gene expression changes and enhancer activity.
Area of Science:
- Genomics
- Epigenetics
- Cancer Biology
Background:
- Histone modifications are key markers for DNA regulatory elements that control gene transcription.
- Altered histone modification levels are common in cancer development.
- Identifying functional regulatory elements is crucial for understanding gene regulation in disease.
Purpose of the Study:
- To identify regulatory elements in the MCF-7 human breast cancer cell line.
- To compare histone modification patterns (H3K4me1, H3K4me3, H3K9/14ac) between cancer and normal mammary cells (MCF-10A).
- To assess the functional role of histone-modified regions in gene transcription.
Main Methods:
- Chromatin immunoprecipitation sequencing (ChIP-Seq) was used to map histone modifications genome-wide.
- Comparative analysis of histone modification patterns in MCF-7 and MCF-10A cell lines.
- Functional assessment of selected genomic regions for transcriptional enhancer activity.
Main Results:
- H3K4me3 and H3K9/14ac were enriched at promoters, while H3K4me1 showed broader distribution.
- Significant differences in histone modification patterns were observed for differentially expressed genes in MCF-7 cells.
- Approximately 66% of tested regions in MCF-7 cells enhanced transcription, with H3K4me1 marks frequently indicating enhancer activity.
Conclusions:
- Comprehensive analysis of histone modification profiles is essential for defining functional regulatory elements.
- Cell type-specific chromatin environments influence regulatory element identification.
- Histone modification patterns provide insights into gene dysregulation in breast cancer.
Related Concept Videos
02:32Histone 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 deacetylase,...
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
02:32Histone 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 deacetylase,...
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
02:38Heterochromatin
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 9th...
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 9th...
02:25Spreading 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 is an enzyme that can...
Writers
The writer is an enzyme that can...
02:30Histone Variants at the Centromere
Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3 variants are also...
01:01Euchromatin
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 is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...