Distinct nuclear and cytoplasmic transcriptomic signatures reveal-transcription alone is insufficient to determine glucose-induced transcriptomic dynamics
1 Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland OH 44115, USA
2 Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland OH 44115, USA
3 Department of Biological Sciences, Biola University, La Mirada CA 90639, USA
  • Volume
  • Citation
    Bagheri A, Kim J, Jiang P. Distinct nuclear and cytoplasmic transcriptomic signatures reveal-transcription alone is insufficient to determine glucose-induced transcriptomic dynamics. Biomed. Inform. 2025(2):0006, https://doi.org/10.55092/bi20250004. 
  • DOI
    10.55092/bi20250004
  • Copyright
    Copyright2025 by the authors. Published by ELSP.
Abstract

Glucose profoundly influences cellular transcriptomes, but whether these changes are primarily driven by transcription remains unclear. Traditional bulk RNA sequencing, which interrogates total mRNA from whole cells, obscures distinct dynamics of nuclear and cytoplasmic transcriptomes. Nuclear RNA levels primarily reflect transcriptional activity but are also influenced by nuclear export, whereas cytoplasmic RNA abundances result from transcription, nuclear export, RNA stability (i.e., RNA half-life), and active RNA degradation mechanisms. In this study, we systematically investigate glucose-induced transcriptomic responses in a subcellular location-and cell type-specific manner using three cell lines: FHC (normal colonic epithelial cells), MCF10A (normal breast epithelial cells), and MCF7 (metastatic breast cancer cells). Our findings reveal that, although nuclear and cytoplasmic mRNA levels show strong global correlations, glucose-induced changes in mRNA abundance exhibit minimal concordance between the nucleus and cytoplasm. Additionally, glucose-induced changes in exon inclusion levels often diverge between the nucleus and cytoplasm, underscoring the importance of post-transcriptional processes in shaping the cytoplasmic transcriptome response to glucose level changes. Glucose-induced differentially expressed genes (DEGs) and differentially spliced exons (ΔPSI) are enriched in distinct pathways exhibiting unique enrichment patterns depending on the subcellular location and cell line. These findings underscore the complexity of glucose-induced transcriptomic regulation, demonstrating that transcription alone is insufficient to explain the observed dynamics.

Keywords

nucleus; cytoplasm; mRNA levels; alternative splicing; transcriptomic dynamics

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