Iterative correction of Hi-C data reveals hallmarks of chromosome organization
Open accessAbstract
Extracting biologically meaningful information from chromosomal interactions obtained with genome-wide chromosome conformation capture (3C) analyses requires the elimination of systematic biases. We present a computational pipeline that integrates a strategy to map sequencing reads with a data-driven method for iterative correction of biases, yielding genome-wide maps of relative contact probabilities. We validate this ICE (iterative correction and eigenvector decomposition) technique on published data obtained by the high-throughput 3C method Hi-C, and we demonstrate that eigenvector decomposition of the obtained maps provides insights into local chromatin states, global patterns of chromosomal interactions, and the conserved organization of human and mouse chromosomes.
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Restriction fragment biases were normalized by applying matrix balancing as previously reported.
“Finally, restriction fragment biases were normalized by applying matrix balancing as previously reported (Imakaev et al., 2012).”
From Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries (2018) · cites this paper as Imakaev et al., 2012
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- Authors
- Imakaev, M., Fudenberg, G., McCord, R. P., Naumova, N., Goloborodko, A., Lajoie, B. R., Dekker, J., & Mirny, L. A.
- Affiliations
- Massachusetts Institute of Technology (US)
- Harvard University (US)
- University of Massachusetts Chan Medical School (US)
- Corresponding author
- Dekker, Job
- Mirny, Leonid A
- ORCID
- Venue
- Nature Methods
- Published
- 2012-09-02
- Volume
- 9
- Issue
- 10
- Pages
- 999-1003
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC3816492
- OpenAlex
- W2097798909
- Cited by
- 1,423
- References
- 22
- Citations by year
- 2026: 86 · 2025: 98 · 2024: 134 · 2023: 133 · 2022: 132 · 2021: 145 · 2020: 149 · 2019: 120 · 2018: 119 · 2017: 106 · 2016: 61 · 2015: 74 · 2014: 37 · 2013: 24 · 2012: 4
- FWCI
- 17.88
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- The Journal of the American Medical Association (JAMA) Network (American Medical Association) (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- PMC
- Funders
- National Human Genome Research Institute (HG003143, R01HG003143)
- National Cancer Institute (U54CA143874)
- National Institute of General Medical Sciences (F32GM100617)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- Hi-C, chromosome conformation capture, bias correction, chromatin organization, human chromosomes, mouse chromosomes
- MeSH terms
- Chromatin, Chromosome Mapping, Chromosomes, Human, Humans, Nucleic Acid Conformation, High-Throughput Screening Assays
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