CiFi: accurate long-read chromosome conformation capture with low-input requirements

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Hi-C is a key technique for studying 3D chromatin organization but struggles with complex genomic regions.
• Repetitive regions, centromeres, and segmental duplications pose challenges for standard Hi-C analysis.
• Existing methods require significant input DNA, limiting applications in low-input scenarios and small organisms.

Purpose of the Study:

• To develop a novel method for analyzing chromatin interactions in complex and repetitive genomic regions.
• To improve read mapping efficiency, coverage, and haplotype phasing in challenging genomic areas.
• To enable genome-wide chromatin interaction analysis from low-input samples and small organisms.

Main Methods:

• Coupling chromosome conformation capture (3C) with PacBio HiFi long-read sequencing to create the CiFi method.
• Generating multi-kilobasepair HiFi reads containing multiple interacting, concatenated segments.
• Applying CiFi to human lymphoblastoid cell lines and small insect genomes (Anopheles coluzzii, Ceratitis capitata).

Main Results:

• CiFi significantly enhances read-mapping efficiency and coverage in repetitive regions compared to short-read Hi-C.
• Improved assignment of topologically associating domains across centromeres, segmental duplications, and disease-associated hotspots.
• Successful characterization of chromatin interactions from a single mosquito and chromosome-scale assembly scaffolding from a fruit fly.

Conclusions:

• CiFi overcomes limitations of standard Hi-C in complex genomic regions.
• The method enables high-resolution chromatin interaction analysis with reduced input DNA requirements.
• CiFi opens new avenues for studying genome organization in diverse biological systems, including small organisms.