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Capturing Chromosome Conformation Across Length Scales
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CiFi: Accurate long-read chromatin conformation capture with low-input requirements.
Sean P McGinty1, Gulhan Kaya1, Sheina B Sim2
1Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA.
Biorxiv : the Preprint Server for Biology
|February 20, 2025
Summary
We developed CiFi, a new method combining chromatin conformation capture and long-read sequencing. This approach analyzes genome interactions in difficult repetitive regions, even with minimal samples.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Analyzing genome interactions in repetitive regions is challenging.
- Low-input requirements limit genomic studies in small organisms.
Purpose of the Study:
- To develop a novel method for analyzing genome interactions across repetitive genomic regions.
- To enable genomic analysis of low-complexity loci and small organisms.
Main Methods:
- Coupling chromatin conformation capture (3C) with PacBio HiFi long-read sequencing.
- Developing the CiFi method for low-input genome interaction analysis.
Main Results:
- CiFi enables analysis of genome interactions across repetitive regions with low-input DNA.
- The method generates multiple interacting concatemer segments per read, aiding genome assembly and scaffolding.
- CiFi successfully analyzes previously recalcitrant low-complexity loci and small organisms like single insects.
Conclusions:
- CiFi offers a powerful approach for high-resolution genome interaction analysis.
- This method overcomes limitations in studying repetitive and complex genomic regions.
- CiFi expands the scope of genomic research to include small or low-input samples.
