ChromCall: assigning chromatin status to defined genomic regions using epigenomic profiling data.
Overview
- University of Leeds, Leeds, LS9 7TF, United Kingdom
- Aarhus University, Aarhus, 8000, Denmark
- University of York, York, YO10 5DD, United Kingdom
Abstract
Motivation: Chromatin regulation is crucial for modulating gene expression and cellular function by altering DNA accessibility. Defining and understanding chromatin regulation across diverse biological conditions, including health and disease, requires quantification of both the presence and enrichment level of diverse DNA-binding factors and chromatin modifications across defined genomic regions. Existing approaches mainly rely on peak-based or genome-wide models, which identify high-signal regions but do not annotate chromatin status at predefined functional genomic regions, such as promoters or enhancers. This lack of region-based annotation limits downstream comparative and integrative analyses across multiple factors and datasets, prompting us to create ChromCall.
Results: ChromCall is an R package for region-based chromatin enrichment analysis that provides a robust and extensible foundation for transparent and reproducible epigenomic profiling at predefined genomic regions. We applied ChromCall to ChIP-seq data from glioblastoma (GBM) brain tumours and found that the promoters of genes implicated in treatment resistance are significantly more likely to exhibit a combination of histone marks associated with phenotypic plasticity. This highlights a potential novel mechanism of therapeutic escape in these deadly tumours.
Availability and Implementation: The R package is available on https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Code
The paper links to its data, not to its authors' code: see the Data section.
Availability and Implementation
The R package is available on https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Tracing map
A tracing map links a paper to the code its authors published: this paper has none, so it has no map.
Data
Datasets cited
- bioproject:PRJNA391756, at NCBI BioProject; found in “Data availability”
Data availability
ChIPseq data from primary GBM tumors was acquired from the Sequencing Read Archive (https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 9 MeSH terms, 3 funders, 17 references.
Cite
This paper
Wang, B., Al-Jabri, M., GK, U., Droop, A., & Stead, L. F. (2026). ChromCall: assigning chromatin status to defined genomic regions using epigenomic profiling data. Bioinformatics (Oxford, England), 42(6), btag336. https://
BibTeX
@article{wang2026chromca
author = {Wang, Bo and Al-Jabri, Muna and GK, Udayaraja and Droop, Alastair and Stead, Lucy F},
title = {{ChromCall: assigning chromatin status to defined genomic regions using epigenomic profiling data}},
journal = {Bioinformatics (Oxford, England)},
year = {2026},
month = jun,
volume = {42},
number = {6},
pages = {btag336},
publisher = {Oxford University Press},
issn = {1367-4803},
doi = {10.1093/
url = {https://
pmid = {42178345},
pmcid = {PMC13238738}
}
RIS
TY - JOUR
AU - Wang, Bo
AU - Al-Jabri, Muna
AU - GK, Udayaraja
AU - Droop, Alastair
AU - Stead, Lucy F
TI - ChromCall: assigning chromatin status to defined genomic regions using epigenomic profiling data
T2 - Bioinformatics (Oxford, England)
J2 - Bioinformatics
PY - 2026
DA - 2026/
VL - 42
IS - 6
SP - btag336
SN - 1367-4803
PB - Oxford University Press
DO - 10.1093/
UR - https://
LA - en
ER -
CSL-JSON
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"family": "Wang",
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