Genome-Wide Computational Prediction And Analysis Of Putative Promoters And Transcription Site: Derived In All Locus Of Whole Genome Present In Mus Musculus

Abstract

Dysregulation of transcriptional control is a central molecular event in carcinogenesis and neurodegenerative disorders, frequently arising from aberrant promoter architecture and altered transcription start site (TSS) usage. Genome-wide identification of promoter regions therefore provides critical insight into gene regulatory mechanisms underlying disease susceptibility. In the present study, we performed a comprehensive in silico analysis of the complete Mus musculus genome (GRCm39) to systematically predict and characterize putative RNA polymerase II promoters and transcription start sites across all genomic loci.

Whole-genome sequences were retrieved from the NCBI repository and analyzed using an integrated bioinformatics framework incorporating GeneRunner, DNASTAR, ExPASy, and the BDGP neural-network-based Promoter 2.0 algorithm. Chromosome-wise variation in genome size, GC content, and gene composition was evaluated, followed by strand-specific promoter prediction and transcription factor site enrichment analysis. Our results reveal extensive heterogeneity in promoter distribution across chromosomes, with significant enrichment of GC-rich and TATA-like motifs within upstream regulatory regions. Several high-confidence transcription start site hotspots were identified, indicating preferential loci of transcriptional initiation.

Notably, the predicted promoter regions exhibit architectural features consistent with estrogen receptor–responsive elements, suggesting potential regulatory relevance to hormone-dependent gene expression and carcinogenic pathways. Advanced graphical representations, including promoter density mapping and GC-content correlation analyses, further elucidated the structural determinants of transcriptional regulation. Collectively, this genome-wide promoter atlas provides a valuable computational resource for functional genomics and establishes a regulatory framework for investigating estrogen-mediated transcriptional dysregulation in cancer and neurological disorders.