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<p>Long non-coding RNAs (lncRNAs) are increasingly recognized as important regulators of gene expression, yet their interactions with transcription factors (TFs) remain poorly understood. While previous studies have identified lncRNA-TF associations in specific biological contexts, a broader perspective on their evolutionary and functional relationships remains necessary. In this study, we systematically analyze the proximity and co-expression patterns of lncRNAs and TF-encoding genes in humans. We reveal consistent spatial associations and tissue-specific co-expression between lncRNAs and TFs using genome-wide annotations and transcriptomic data. Time-series analysis reveals interesting, but not definitive, dynamic correlations suggesting potential functional interactions. Additionally, our evolutionary analysis identified conserved pairs across species, particularly those related to developmental processes such as eye development, highlighting possible avenues for further investigation in evolutionary and developmental contexts. In summary, our findings provide new insights into the spatial and co-expression associations between lncRNAs and TF genes, and suggest directions for future research on the potential roles of lncRNAs in gene regulatory networks.</p>

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Bioinformatics analysis of regulatory relationships between long non-coding RNA genes and transcription factor coding genes

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年8月4日

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  • Taiju Yamada,
  • Martin Loza,
  • Izuho Hatada,
  • Kenta Nakai

摘要

Long non-coding RNAs (lncRNAs) are increasingly recognized as important regulators of gene expression, yet their interactions with transcription factors (TFs) remain poorly understood. While previous studies have identified lncRNA-TF associations in specific biological contexts, a broader perspective on their evolutionary and functional relationships remains necessary. In this study, we systematically analyze the proximity and co-expression patterns of lncRNAs and TF-encoding genes in humans. We reveal consistent spatial associations and tissue-specific co-expression between lncRNAs and TFs using genome-wide annotations and transcriptomic data. Time-series analysis reveals interesting, but not definitive, dynamic correlations suggesting potential functional interactions. Additionally, our evolutionary analysis identified conserved pairs across species, particularly those related to developmental processes such as eye development, highlighting possible avenues for further investigation in evolutionary and developmental contexts. In summary, our findings provide new insights into the spatial and co-expression associations between lncRNAs and TF genes, and suggest directions for future research on the potential roles of lncRNAs in gene regulatory networks.