Comparison of Hi-C results using in-solution versus in-nucleus ligation
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BACKGROUND: Chromosome conformation capture and various derivative methods such as 4C, 5C and Hi-C have emerged as standard tools to analyze the three-dimensional organization of the genome in the nucleus. These methods employ ligation of diluted cross-linked chromatin complexes, intended to favor proximity-dependent, intra-complex ligation. During development of single-cell Hi-C, we devised an alternative Hi-C protocol with ligation in preserved nuclei rather than in solution. Here we directly compare Hi-C methods employing in-nucleus ligation with the standard in-solution ligation. RESULTS: We show in-nucleus ligation results in consistently lower levels of inter-chromosomal contacts. Through chromatin mixing experiments we show that a significantly large fraction of inter-chromosomal contacts are the result of spurious ligation events formed during in-solution ligation. In-nucleus ligation significantly reduces this source of experimental noise, and results in improved reproducibility between replicates. We also find that in-nucleus ligation eliminates restriction fragment length bias found with in-solution ligation. These improvements result in greater reproducibility of long-range intra-chromosomal and inter-chromosomal contacts, as well as enhanced detection of structural features such as topologically associated domain boundaries. CONCLUSIONS: We conclude that in-nucleus ligation captures chromatin interactions more consistently over a wider range of distances, and significantly reduces both experimental noise and bias. In-nucleus ligation creates higher quality Hi-C libraries while simplifying the experimental procedure. We suggest that the entire range of 3C applications are likely to show similar benefits from in-nucleus ligation.
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Low trans-chromosomal contacts are indicative of high library quality.
“indicative of high library quality13”
From Cell-cycle dynamics of chromosomal organization at single-cell resolution (2017) · cites this paper as [13]
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- Authors
- Nagano, T., Várnai, C., Schoenfelder, S., Javierre, B.-M., Wingett, S. W., & Fraser, P.
- Affiliations
- Babraham Institute (GB)
- Corresponding author
- Nagano, Takashi
- Fraser, Peter
- ORCID
- Venue
- Genome Biology
- Published
- 2015-08-26
- Volume
- 16
- Issue
- 1
- Pages
- 175-175
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC4580221
- OpenAlex
- W2116261028
- Cited by
- 166
- References
- 26
- Citations by year
- 2026: 4 · 2025: 5 · 2024: 8 · 2023: 8 · 2022: 11 · 2021: 20 · 2020: 17 · 2019: 23 · 2018: 25 · 2017: 27 · 2016: 12 · 2015: 5
- FWCI
- 9.99
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion, cc-by)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Funders
- European Research Council (111608)
- BBSRC (BBS/E/B/000C0405)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- Hi-C, chromosome conformation capture, 3D genome organization, topologically associating domains, single-cell Hi-C
- MeSH terms
- Animals, Cell Nucleus, Cells, Cultured, Chromatin, Humans, Mice, Inbred C57BL, Genomics, Mice
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