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ARS Home » Pacific West Area » Hilo, Hawaii » Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center » Tropical Pest Genetics and Molecular Biology Research Unit » Research » Publications at this Location » Publication #422544
Research Project: Advancing Molecular Pest Management, Diagnostics, and Eradication of Fruit Flies and Invasive Species

Location: Tropical Pest Genetics and Molecular Biology Research Unit

Title: CiFi: Accurate long-read chromatin conformation capture sequencing with low-input requirements

Author
item MCGINTY, SEAN - University Of California, Davis
item GULHAN, KAYA - University Of California, Davis
item Sim, Sheina
item Corpuz, Renee
item QUAIL, MICHAEL - Wellcome Trust Sanger Institute
item LAWNICZAK, MARA - Wellcome Trust Sanger Institute
item Geib, Scott
item KORLACH, JONAS - Pacific Biosciences Inc
item DENNIS, MEGAN - University Of California, Davis

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 2/5/2025
Publication Date: 2/5/2025
Citation: Mcginty, S.P., Gulhan, K., Sim, S.B., Corpuz, R.L., Quail, M.A., Lawniczak, M.K., Geib, S.M., Korlach, J., Dennis, M.Y. 2025. CiFi: Accurate long-read chromatin conformation capture sequencing with low-input requirements. bioRxiv. Article 635566. https://doi.org/10.1101/2025.01.31.635566.
DOI: https://doi.org/10.1101/2025.01.31.635566

Interpretive Summary: Our ability to investigate chromatin conformation of intact nuclei has long relied on short-read sequencing of chromatin conformation capture libraries. Though highly accurate, the limitations of short-reads for this purpose is their inability to uniquely map to repetitive regions of the genome. We developed a new method, CiFi, for chromatin conformation capture library preparation that circumvents this through the preparation of a chromatin conformation capture library that creates proximity ligations of many long reads. This method are more efficient and thus requires less sample input, which can be applied to scaffolding the contig assemblies of small-bodied non-model organisms. The characterization of the chromatin conformation of highly repetitive regions have applications in human health research.

Technical Abstract: By coupling chromatin conformation capture (3C) with PacBio HiFi long-read sequencing, we have developed a new method (CiFi) that enables analysis of genome interactions across repetitive genomic regions with low-input requirements. CiFi produces multiple interacting concatemer segments per read, facilitating genome assembly and scaffolding. Together, the approach enables genomic analysis of previously recalcitrant low-complexity loci and of single individuals of tiny organisms, opening new and exciting avenues of research.