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Curr. Issues Mol. Biol., Volume 47, Issue 6 (June 2025) – 1 article

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17 pages, 3712 KiB

Open AccessArticle

Genome-Wide Detection of Leukemia Biomarkers from lincRNA–Protein-Coding Gene Interaction Networks in the Three-Dimensional Chromatin Structure

by Yue Hou, Wei Ning, Muren Huhe and Chuanjun Shu

Curr. Issues Mol. Biol. 2025, 47(6), 384; https://doi.org/10.3390/cimb47060384 (registering DOI) - 22 May 2025

Abstract

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–promoter network/sub-network topological parameters. Full article

(This article belongs to the Special Issue The Contribution and Application of Molecular Biology in the Applied Biosciences—Focusing on Medicine, Biomaterials and Tissue Engineering Fields, 2nd Edition)

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Curr. Issues Mol. Biol., Volume 47, Issue 6 (June 2025) – 1 article

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