Detecting hierarchical genome folding with network modularity
Open accessPublished version of a preprint
Abstract
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Here, we describe 3DNetMod, a graph theory-based method for sensitive and accurate detection of chromatin domains across length scales in Hi-C data. We identify nested, partially overlapping TADs and subTADs genome wide by optimizing network modularity and varying a single resolution parameter. 3DNetMod can be applied broadly to understand genome reconfiguration in development and disease.
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Many other daSTRs are co-localized to subTAD boundaries, which are known to be dynamically reconfigured across cell state transitions in development.
“By contrast, many other daSTRS are co-localized to subTAD boundaries, which are known to be dynamically reconfigured across cell state transitions in development (Norton et al., 2018).”
From Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries (2018) · cites this paper as Norton et al., 2018
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References 85 · Cited by 146
- Authors
- Norton, H. K., Emerson, D. J., Huang, H., Kim, J., Titus, K. R., Gu, S., Bassett, D. S., & Phillips-Cremins, J. E.
- Affiliations
- University of Pennsylvania (US)
- ORCID
- Venue
- Nature Methods
- Published
- 2018-01-15
- Volume
- 15
- Issue
- 2
- Pages
- 119-122
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC6029251
- OpenAlex
- W2784063494
- Cited by
- 146
- References
- 85
- Citations by year
- 2026: 6 · 2025: 16 · 2024: 13 · 2023: 13 · 2022: 16 · 2021: 31 · 2020: 16 · 2019: 23 · 2018: 11 · 2017: 1
- FWCI
- 7.52
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Science Foundation (1321851, 1562665, 1R01HD086888-01, 1631550, 1554488, 1441502)
- John D. and Catherine T. MacArthur Foundation (BCS-1631550, 1R01HD086888-01, BCS-1441502, PHY-1554488)
- Alfred P. Sloan Foundation (BCS-1631550, BCS-1441502, PHY-1554488, 1R01HD086888-01)
- New York Stem Cell Foundation
- National Institutes of Health (BCS-1631550, PHY-1554488, DGE-1321851, BCS-1441502, 1r01hd086888-01)
- National Heart, Lung, and Blood Institute (U01HL129998)
- National Institute of Mental Health (1DP2MH11024701, DP2MH110247)
- National Institute of General Medical Sciences
- National Institute of Child Health and Human Development (1R01HD086888-01)
- Division of Mathematical Sciences
- Common Fund
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- topologically associating domains, chromatin folding, 3D genome organization, network modularity, Hi-C data, chromatin domains, graph theory
- MeSH terms
- Chromatin, Computer Graphics, Humans, Genome, Human, Computational Biology, High-Throughput Nucleotide Sequencing
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