Related Experiment Video
Updated: May 26, 2026
10:41
An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
Published on: April 5, 2018
ChromCall: assigning chromatin status to defined genomic regions using epigenomic profiling data
Bo Wang1, Muna Al-Jabri1, Udayaraja Gk1,2
1University of Leeds, Leeds, LS9 7TF, United Kingdom.
Bioinformatics (Oxford, England)
|May 24, 2026
Summary
ChromCall is a new R package for analyzing chromatin enrichment at specific genomic regions. It reveals histone mark combinations in glioblastoma promoters linked to treatment resistance and potential therapeutic escape.
Area of Science:
- Epigenetics and Genomics
- Computational Biology
- Cancer Research
Background:
- Chromatin regulation is vital for gene expression and cellular function.
- Current methods lack region-specific chromatin annotation, hindering analysis.
- This gap necessitates tools for detailed epigenomic profiling.
Purpose of the Study:
- Introduce ChromCall, an R package for region-based chromatin enrichment analysis.
- Enable transparent and reproducible epigenomic profiling at predefined genomic regions.
- Facilitate comparative and integrative analyses across multiple factors and datasets.
Main Methods:
- Development of the ChromCall R package for region-based analysis.
- Application of ChromCall to ChIP-seq data from glioblastoma (GBM) samples.
- Statistical analysis of histone mark enrichment at predefined genomic regions.
Main Results:
- ChromCall provides robust and extensible epigenomic profiling.
- Analysis of GBM data identified specific histone mark combinations at gene promoters.
- These combinations are linked to genes involved in treatment resistance.
Conclusions:
- ChromCall facilitates detailed epigenomic analysis at functional genomic regions.
- Findings suggest a link between chromatin states and therapeutic resistance in glioblastoma.
- This highlights a potential mechanism for therapeutic escape in GBM.
Related Concept Videos
02:36Chromatin 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...
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...
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...
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...
02:35Chromatin 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 timing and level of...
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...
01:32Chromatin 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...
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...
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,...