{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T14:29:29Z","timestamp":1766068169862,"version":"build-2065373602"},"reference-count":54,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2025,5,22]],"date-time":"2025-05-22T00:00:00Z","timestamp":1747872000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Natural Science Foundation of Jiangsu Province","award":["BK20220313","22KJB180004","202205021"],"award-info":[{"award-number":["BK20220313","22KJB180004","202205021"]}]},{"name":"Natural Science Research Project of Colleges and Universities in Jiangsu Province","award":["BK20220313","22KJB180004","202205021"],"award-info":[{"award-number":["BK20220313","22KJB180004","202205021"]}]},{"name":"Nanjing Life and Health Science and Technology Special Project\u2014Preclinical Technology Breakthrough","award":["BK20220313","22KJB180004","202205021"],"award-info":[{"award-number":["BK20220313","22KJB180004","202205021"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["CIMB"],"abstract":"<jats:p>The human genome is widely transcribed, with part of these transcribed regions producing stably expressed protein-coding or non-coding RNAs. Long intergenic non-coding RNAs (lincRNAs) are significantly differentially expressed in various cell lines and tissues. However, the influence of their transcription events remains unclear. In this study, we constructed a human genomic interaction network and found frequent interactions between lincRNA genes and protein-coding genes that are highly related to the occupancy of RNA polymerase II on the lincRNA gene. Interestingly, in the human genome interaction networks, the degree of lincRNA genes was significantly higher than that of protein-coding genes. The promoter regions of the protein-coding genes interacting with the lincRNA genes are enriched with R-loop structures, indicating that lincRNA may influence the target genes through R-loop structures. These promoters were enriched in more transcription factor binding sites. Furthermore, the whole network and sub-network could be utilized to explore potential biomarkers of leukemia. We found that zinc finger protein 668 (ZNF668), eosinophil granule ontogeny transcript (EGOT), and glutamate metabotropic receptor 7 (GRM7) could serve as novel biomarkers for acute myeloid leukemia (LMAL). Pasireotide acetate (CAS No. 396091-76-2) represents a potential drug for LMAL patients. These results suggested that potential biomarkers and corresponding drugs for cancer could be identified based on lincRNA\u2013promoter network\/sub-network topological parameters.<\/jats:p>","DOI":"10.3390\/cimb47060384","type":"journal-article","created":{"date-parts":[[2025,5,22]],"date-time":"2025-05-22T04:32:37Z","timestamp":1747888357000},"page":"384","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Genome-Wide Detection of Leukemia Biomarkers from lincRNA\u2013Protein-Coding Gene Interaction Networks in the Three-Dimensional Chromatin Structure"],"prefix":"10.3390","volume":"47","author":[{"given":"Yue","family":"Hou","sequence":"first","affiliation":[{"name":"Military Medical Innovation Center, Fourth Military Medical University, Xi\u2019an 710032, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1648-3962","authenticated-orcid":false,"given":"Wei","family":"Ning","sequence":"additional","affiliation":[{"name":"Military Medical Innovation Center, Fourth Military Medical University, Xi\u2019an 710032, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Muren","family":"Huhe","sequence":"additional","affiliation":[{"name":"Military Medical Innovation Center, Fourth Military Medical University, Xi\u2019an 710032, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1427-2037","authenticated-orcid":false,"given":"Chuanjun","family":"Shu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,5,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1038\/s41580-022-00566-8","article-title":"Long non-coding RNAs: Definitions, functions, challenges and recommendations","volume":"24","author":"Mattick","year":"2023","journal-title":"Nat. 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