ArticlebioRxiv : the preprint server for biology2025
Development of a long-read high-throughput chromatin conformation capture method for evaluating both
Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Authors and funding
6 authors.
Funding
Abstract
High-throughput chromatin conformation capture (Hi-C) has been utilized for characterizing the 3-dimensional (3D) interactome of the genome. However, short-read sequencing approaches have limited the information it provides, especially for integrated proviral DNAs. Herein we describe the development of a pipeline to investigate the 3D interactome associated with integrated Hepatitis B Virus (HBV) DNAs (iDNAs) to further understand the role of HBV iDNA in liver carcinogenesis. We employed long-read DNA sequencing combined with a novel target-pull-down library construction approach that protects against DNA shearage resulting in greatly improved sensitivity and specificity for the targeted HBV iDNA. Most importantly, we successfully increased the length of captured Hi-C library to the multi-kilobase-level and report Hi-C contacts based on a custom-developed informatics pipeline. We anticipate this combined laboratory-informatics pipeline will provide a more comprehensive view of HBV iDNA-host genomic interactions associated with their role in liver carcinogenesis, but even more importantly that it should be generalizable for the study of the geno-topological effects associated with any type of integrated DNA.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.