universal TTSs

universal TTSs identifies DNA regions capable of forming triple helices with diverse RNAs to enable systematic discovery of "universal triplex target sites" relevant to lncRNA-mediated chromatin interactions.

Key Features:

• Identification of Universal TTSs: Identifies DNA sequences that form triple helices with a majority (>90%) of analyzed transcripts, defining "universal TTSs" and reporting their genome-wide rarity (~0.5%) alongside increased frequency in specific regions.
• Statistical Significance Estimation: Estimates significance of predicted RNA–DNA triplex interactions using a novel statistical method with an adjusted p-value threshold of <0.01.
• Enrichment Analysis: Detects enrichment of universal TTSs in purine-rich low complexity regions, indicating specific sequence characteristics associated with triplex formation.
• Genomic Context and Frequency Reporting: Reports differential frequencies of universal TTSs across genomic contexts, including >15% prevalence among MEG3 binding sites and ~40% prevalence in shared Capture-seq peaks.

Scientific Applications:

• Chromatin Structure Analysis: Supports investigation of the role of RNA–DNA triple helices in three-dimensional chromatin organization and long-distance chromosomal contacts.
• Enhancer–Promoter Interactions: Enables exploration of potential contributions of universal TTSs to distal enhancer–promoter interactions involved in gene regulation.

Methodology:

Integrates computational analyses with experimental RNA–DNA interaction data to predict triplex-forming DNA regions and applies a novel statistical significance estimation with an adjusted p-value threshold of <0.01.