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This study delves into the genomic characteristics and implications of SINEs within the genome, particularly their role in high-grade gliomas, such as diffuse intrinsic pontine glioma (DIPG) and glioblastoma multiforme (GBM). Genomic analysis revealed that SINEs constitute 8.43% of the human genome, with significant concentrations found within gene and promoter regions, particularly in areas up to 50kb from the transcription start site (TSS).

Focused transcriptomic analyses compared two DIPG samples with a healthy brain tissue control, identifying differential expression in 297 genes associated with DNA-templated transcription and nervous system development, which were predominantly upregulated in DIPG. In contrast, GBM samples compared with controls showed predominant disruptions in cell division pathways, along with a notable downregulation in the Keratin Filament pathway, similar to observations in DIPG samples.

Further, comparative Hi-C analyses provided insights into the 3D genomic architecture, showing differential chromatin interactions between DIPG and GBM samples when compared to controls, with correlation coefficients of 0.39 and 0.43, respectively. This suggests a variance in genetic expression profiles between the disease states and healthy controls, highlighted by RNA-seq analyses.

Additionally, the study identified specific chromatin regions with high contact frequencies and SINE presence, particularly noting a region within the Intermediate Filament (IntFil) gene cluster on chromosome 12, along with other significant bins across chromosomes 1, 5, 11, 17, and X. These findings highlight the intricate role of SINEs in modulating genomic architecture and suggest their potential impact on gene regulation and cancer progression.