Genome organisation research, spanning chromatin architecture, epigenomics, transcription factor binding, and 3D genome structure, routinely produces large, multi-modal datasets deposited in repositories such as GEO, SRA, ENCODE, and the 4D Nucleome. Yet FAIR compliance across these resources varies considerably, and integration between datasets generated by different platforms or research groups remains technically challenging.
This Research Topic invites contributions addressing the practical implementation of FAIR principles in genome organisation research, including metadata harmonisation across sequencing technologies, ontologies for chromatin state annotation, and interoperability between 3D genome data formats such as .hic and .cool. Contributions addressing pipeline standardisation and parameter reporting — ensuring that published analyses can be reproduced from raw reads — are of particular importance. Contributions addressing the deposition of intermediate processed files alongside raw reads, to maximise the range of researchers who can engage with shared data, are of particular importance.
We also welcome submissions on FAIR-compliant sharing of single-cell epigenomics data, TAD and enhancer-promoter interaction datasets, and regulatory element catalogues. Studies demonstrating novel insights enabled by cross-study data integration, and FAIR² Data Articles presenting curated, analysis-ready genomics datasets, are especially encouraged. Reproducible bioinformatics workflows built entirely on open data, and designed so that others can rerun analyses from raw reads to biological interpretation, are of high interest.
KEY THEMES
Metadata harmonisation across Hi-C, ATAC-seq, ChIP-seq, and CUT&RUN datasets
Interoperability between 3D genome data formats (.hic, .cool, .pairs)
Ontologies and controlled vocabularies for chromatin state and regulatory element annotation
FAIR-compliant deposition of TAD, enhancer-promoter, and insulator interaction data
Reproducible bioinformatics workflows built on openly deposited raw data
FAIR practices for single-cell epigenomics and multi-modal genome data
Cross-tissue and cross-condition integration of genome organisation datasets
Linking genome organisation data to gene expression and disease-relevant phenotypes
Article types and fees
This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:
Brief Research Report
Editorial
FAIR² Data
General Commentary
Hypothesis and Theory
Methods
Mini Review
Opinion
Original Research
Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.
Article types
This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:
Brief Research Report
Editorial
FAIR² Data
General Commentary
Hypothesis and Theory
Methods
Mini Review
Opinion
Original Research
Perspective
Review
Technology and Code
Keywords: FAIR data, genome organisation, chromatin architecture, epigenomics, Hi-C, ATAC-seq, ChIP-seq, 3D genome, TAD, ENCODE, 4D Nucleome, reproducible bioinformatics, open data, regulatory elements
Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.
