ArticleComputational and structural biotechnology journal2025
Transcriptional coordination between intergenic RNA polymerase II-bound regions and nearby genes reveals functional specialization and disease associations in peripheral blood.
Article in Computational and structural biotechnology journal, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Recent studies have shown that RNA polymerase II (RNAPII) frequently occupies regions outside conventional promoters and gene bodies, forming intergenic RNAPII-bound regions (iRNAPII-BRs) that are actively transcribed and involved in gene regulation. We assessed the transcriptional activity of 181,547 iRNAPII-BRs from a genome-wide atlas and their impact on the expression of nearby gene in peripheral blood. The iRNAPII-BRs were often associated with structurally complex longer genes located in gene deserts. Their strongest transcriptional activity peaks occurred within 10 kb upstream from transcription start sites (TSSs), indicating a close regulatory link. Genes were grouped into six categories according to their transcriptional coordination with the nearest iRNAPII-BRs. Housekeeping genes tended to be transcribed independently, whereas blood tissue-specific genes were highly coordinated with iRNAPII-BR transcription. Genes with neuronal functions were frequently transcribed without active iRNAPII-BRs, suggesting basal promoter-driven expression with potential regulation by iRNAPII-BRs in response to blood-brain cross-talk cues. We found that 4507 iRNAPII-BRs were positively correlated with gene expression, whereas 793 were negatively correlated with gene expression implying a possible role in repression. The presence of transcription factor binding sites common to iRNAPII-BRs and promoters suggests a cooperative regulatory mechanism. Finally, we observed a differential expression of iRNAPII-BRs and nearby genes-
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