{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T01:46:59Z","timestamp":1768528019831,"version":"3.49.0"},"posted":{"date-parts":[[2025,10,21]]},"group-title":"Genomics","reference-count":54,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T00:00:00Z","timestamp":1761004800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,10,21]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>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\u00adinformatics 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. (word count: 164\/250)<\/jats:p>","DOI":"10.1101\/2025.10.21.683758","type":"posted-content","created":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T04:05:18Z","timestamp":1761105918000},"source":"Crossref","is-referenced-by-count":0,"title":["Development of a long-read high-throughput chromatin conformation capture method for evaluating both\n                  <i>cis<\/i>\n                  and\n                  <i>trans<\/i>\n                  interactions between integrated Hepatitis B Virus and host genomes"],"prefix":"10.64898","author":[{"given":"Yih-Ping","family":"Su","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joshua P.","family":"Earl","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Azad A.","family":"Ahmed","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bhaswati","family":"Sen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel","family":"Czerski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Garth D.","family":"Ehrlich","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2025102407400872000_2025.10.21.683758v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/282615a0"},{"key":"2025102407400872000_2025.10.21.683758v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/286533a0"},{"key":"2025102407400872000_2025.10.21.683758v1.3","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0216697"},{"key":"2025102407400872000_2025.10.21.683758v1.4","doi-asserted-by":"crossref","first-page":"676957","DOI":"10.3389\/fmolb.2021.676957","article-title":"Pacbio sequencing of PLC\/PRF\/5 cell line and clearance of HBV integration through CRISPR\/Cas-9 system","volume":"8","year":"2021","journal-title":"Frontiers in molecular biosciences"},{"key":"2025102407400872000_2025.10.21.683758v1.5","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.85.15.5693"},{"key":"2025102407400872000_2025.10.21.683758v1.6","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"2025102407400872000_2025.10.21.683758v1.7","doi-asserted-by":"publisher","DOI":"10.3390\/v14020445"},{"key":"2025102407400872000_2025.10.21.683758v1.8","doi-asserted-by":"crossref","first-page":"e1003065","DOI":"10.1371\/journal.pgen.1003065","article-title":"Recurrent targeted genes of hepatitis B virus in the liver cancer genomes identified by a next-generation sequencing\u2013based approach","volume":"8","year":"2012","journal-title":"PLoS genetics"},{"key":"2025102407400872000_2025.10.21.683758v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/286535a0"},{"key":"2025102407400872000_2025.10.21.683758v1.10","doi-asserted-by":"crossref","first-page":"1515","DOI":"10.4014\/jmb.2208.08020","article-title":"Dynamics of viral and host 3D genome structure upon infection","volume":"32","year":"2022","journal-title":"Journal of Microbiology and Biotechnology"},{"key":"2025102407400872000_2025.10.21.683758v1.11","doi-asserted-by":"crossref","first-page":"e29614","DOI":"10.1002\/jmv.29614","article-title":"Multi omics panoramic analysis of HBV integration, transcriptional regulation, and epigenetic modifications in PLC\/PRF\/5 cell line","volume":"96","year":"2024","journal-title":"Journal of Medical Virology"},{"key":"2025102407400872000_2025.10.21.683758v1.12","doi-asserted-by":"crossref","first-page":"1161522","DOI":"10.3389\/fimmu.2023.1161522","article-title":"Three-dimensional and single-cell sequencing of liver cancer reveals comprehensive host-virus interactions in HBV infection","volume":"14","year":"2023","journal-title":"Frontiers in Immunology"},{"key":"2025102407400872000_2025.10.21.683758v1.13","doi-asserted-by":"crossref","first-page":"661","DOI":"10.3390\/genes11060661","article-title":"Analysis of HBV genomes integrated into the genomes of human hepatoma PLC\/PRF\/5 cells by HBV sequence capture-based next-generation sequencing","volume":"11","year":"2020","journal-title":"Genes"},{"key":"2025102407400872000_2025.10.21.683758v1.14","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1099\/0022-1317-57-1-95","article-title":"Detection of hepatitis B virus-specific DNA in the genomes of human hepatocellular carcinoma and liver cirrhosis tissues","volume":"57","year":"1981","journal-title":"Journal of General Virology"},{"key":"2025102407400872000_2025.10.21.683758v1.15","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.41.8.1715"},{"key":"2025102407400872000_2025.10.21.683758v1.16","unstructured":"Li H . 2012. Seqtk: a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. GitHub"},{"key":"2025102407400872000_2025.10.21.683758v1.17","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"2025102407400872000_2025.10.21.683758v1.18","first-page":"4572\u00ad4574","article-title":"New strategies to improve minimap2 alignment accuracy","volume":"37","year":"2021","journal-title":"Bioinformatics"},{"key":"2025102407400872000_2025.10.21.683758v1.19","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhep.2013.12.014"},{"key":"2025102407400872000_2025.10.21.683758v1.20","doi-asserted-by":"publisher","DOI":"10.1126\/science.1181369"},{"key":"2025102407400872000_2025.10.21.683758v1.21","doi-asserted-by":"publisher","DOI":"10.1016\/j.livres.2025.09.002"},{"key":"2025102407400872000_2025.10.21.683758v1.22","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.33.2.795-806.1980"},{"key":"2025102407400872000_2025.10.21.683758v1.23","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0409332102"},{"key":"2025102407400872000_2025.10.21.683758v1.24","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1099\/jgv.0.001387","article-title":"Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences","volume":"101","year":"2020","journal-title":"Journal of General Virology"},{"key":"2025102407400872000_2025.10.21.683758v1.25","doi-asserted-by":"crossref","first-page":"1371","DOI":"10.1534\/g3.118.200900","article-title":"TSD: a computational tool to study the complex structural variants using PacBio targeted sequencing data","volume":"9","year":"2019","journal-title":"G3: Genes, Genomes, Genetics"},{"key":"2025102407400872000_2025.10.21.683758v1.26","doi-asserted-by":"crossref","first-page":"4268","DOI":"10.1038\/s41467-018-06739-4","article-title":"Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin","volume":"9","year":"2018","journal-title":"Nature communications"},{"key":"2025102407400872000_2025.10.21.683758v1.27","doi-asserted-by":"publisher","DOI":"10.1136\/gut.2004.054452"},{"key":"2025102407400872000_2025.10.21.683758v1.28","doi-asserted-by":"publisher","DOI":"10.1099\/0022-1317-69-10-2575"},{"key":"2025102407400872000_2025.10.21.683758v1.29","doi-asserted-by":"publisher","DOI":"10.1002\/ijc.21731"},{"key":"2025102407400872000_2025.10.21.683758v1.30","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"2025102407400872000_2025.10.21.683758v1.31","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.00299-00221"},{"key":"2025102407400872000_2025.10.21.683758v1.32","doi-asserted-by":"publisher","DOI":"10.1101\/2020.05.03.075499"},{"key":"2025102407400872000_2025.10.21.683758v1.33","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-17-0337"},{"key":"2025102407400872000_2025.10.21.683758v1.34","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1754"},{"key":"2025102407400872000_2025.10.21.683758v1.35","doi-asserted-by":"publisher","DOI":"10.1136\/gut.24.7.618"},{"key":"2025102407400872000_2025.10.21.683758v1.36","doi-asserted-by":"publisher","DOI":"10.1056\/NEJM198110293051807"},{"key":"2025102407400872000_2025.10.21.683758v1.37","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0163962"},{"key":"2025102407400872000_2025.10.21.683758v1.38","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1635109100"},{"key":"2025102407400872000_2025.10.21.683758v1.39","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.72.11.4597"},{"key":"2025102407400872000_2025.10.21.683758v1.40","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2295"},{"key":"2025102407400872000_2025.10.21.683758v1.41","doi-asserted-by":"crossref","unstructured":"Tang D , Zhao H , Wu Y , Peng B , Gao Z , Sun Y , Duan J , Qi Y , Li Y , Zhou Z . 2021. Transcriptionally inactive hepatitis B virus episome DNA preferentially resides in the vicinity of chromosome 19 in 3D host genome upon infection. Cell Reports 35.","DOI":"10.1016\/j.celrep.2021.109288"},{"key":"2025102407400872000_2025.10.21.683758v1.42","unstructured":"Team DD. 2020. DigestDNA: A function for simulating DNA digestion in the DECIPHER R package. RDrr.io."},{"key":"2025102407400872000_2025.10.21.683758v1.43","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbs017"},{"key":"2025102407400872000_2025.10.21.683758v1.44","doi-asserted-by":"crossref","first-page":"2147","DOI":"10.2147\/JHC.S420603","article-title":"Updates in Characteristics and Survival Rates of Hepatocellular Carcinoma in a Nationwide Cohort of Real-World US Patients, 2003\u20132021","volume":"10","year":"2023","journal-title":"Journal of Hepatocellular Carcinoma"},{"key":"2025102407400872000_2025.10.21.683758v1.45","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.02007-02017"},{"key":"2025102407400872000_2025.10.21.683758v1.46","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1128\/jvi.37.1.239-243.1981","article-title":"Integration pattern of hepatitis B virus DNA sequences in human hepatoma cell lines","volume":"37","year":"1981","journal-title":"Journal of virology"},{"key":"2025102407400872000_2025.10.21.683758v1.47","unstructured":"Van der Auwera GA , O\u2019Connor BD . 2020. Genomics in the cloud: using Docker, GATK, and WDL in Terra. O\u2019Reilly Media."},{"key":"2025102407400872000_2025.10.21.683758v1.48","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aan0241"},{"key":"2025102407400872000_2025.10.21.683758v1.49","doi-asserted-by":"crossref","unstructured":"Wright ES . 2016. Using DECIPHER v2. 0 to analyze big biological sequence data in R. R Journal 8.","DOI":"10.32614\/RJ-2016-025"},{"key":"2025102407400872000_2025.10.21.683758v1.50","doi-asserted-by":"crossref","first-page":"4665","DOI":"10.62347\/KKLE8602","article-title":"Identification of novel genomic hotspots and tumor-relevant genes via comprehensive analysis of HPV integration in Chinese patients of cervical cancer","volume":"14","year":"2024","journal-title":"Am J Cancer Res"},{"key":"2025102407400872000_2025.10.21.683758v1.51","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/s41421-020-00218-1","article-title":"3D landscape of Hepatitis B virus interactions with human chromatins","volume":"6","year":"2020","journal-title":"Cell Discovery"},{"key":"2025102407400872000_2025.10.21.683758v1.52","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.73.12.9710-9717.1999"},{"key":"2025102407400872000_2025.10.21.683758v1.53","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1007\/s00535-023-02053-z","article-title":"Three\u00addimensional chromatin landscapes in hepatocellular carcinoma associated with hepatitis B virus","volume":"59","year":"2024","journal-title":"Journal of Gastroenterology"},{"key":"2025102407400872000_2025.10.21.683758v1.54","doi-asserted-by":"crossref","first-page":"12992","DOI":"10.1038\/ncomms12992","article-title":"Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma","volume":"7","year":"2016","journal-title":"Nature communications"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.10.21.683758","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T09:51:46Z","timestamp":1768470706000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.10.21.683758"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,21]]},"references-count":54,"URL":"https:\/\/doi.org\/10.1101\/2025.10.21.683758","relation":{},"subject":[],"published":{"date-parts":[[2025,10,21]]},"subtype":"preprint"}}