TTS mapping

TTS mapping identifies and annotates potential triplex target sites (pTTSs) within specified regions of the human genome to characterize their co-localization with regulatory elements and inform studies of DNA triplex formation and disease-related genomic modules.

Key Features:

• Identification and annotation: Locates pTTSs in user-specified genomic regions and reports descriptive statistics and sequence context for each site.
• Integration with regulatory elements: Maps annotation tracks from the UCSC Genome Browser and other databases to identify overlaps with TTS-overlapping gene regions, G-quadruplexes (G4), CpG Islands, miRNA precursors and targets, transcription factor binding sites (TFBSs), SNPs, snoRNAs, and repeat elements.
• Unique sequence verification: Uses BLASTN to verify uniqueness of identified pTTSs within the human genome.
• Enrichment analysis: Performs analyses that revealed significant enrichment of pTTSs in recombination- and mutation-prone genes such as EVI-1 and MYC.
• Structural insights: Reports cases of natural triplex formation, including miR-483 transcribed from IGF2 intron 2, and documents polypurine/polypyrimidine sequence complementarity forming triplexes via Hoogsteen or reverse Hoogsteen hydrogen bonds and co-localization with factors such as TF MZF1.
• Visualization and analysis outputs: Produces visual and analytical outputs to explore pTTS co-localization and complex structural–functional modules within genes (for example, IGF2 with mir-483 and MZF1 sites).

Scientific Applications:

• Genomic architecture studies: Enables mapping of pTTSs relative to regulatory elements to investigate genome organization and structural-functional modules.
• Gene regulation research: Supports investigation of how triplex formation and pTTS co-localization with G4, TFBSs, and ncRNA precursors influence transcriptional regulation.
• Disease mechanism and genomic stability: Facilitates analysis of pTTS involvement in recombination- and mutation-prone genes (e.g., EVI-1, MYC) to study links to genomic instability and disease.
• Anti-gene experimental design: Informs selection of target sites and experimental strategies for anti-gene treatments by providing annotated pTTSs and sequence-context information.

Methodology:

Identification of pTTSs in genomic regions; mapping of annotation tracks using data from the UCSC Genome Browser and other databases; calculation of descriptive statistics and sequence context; BLASTN-based uniqueness verification; and enrichment analyses of pTTS distribution across genes.