Intron-derived RNA platforms coordinate inflammatory gene networks through the Intronic Signaling Pathways System (ISPS)

This repository contains all datasets, structural analyses, computational outputs, and supplementary materials generated in support of the manuscript: "Intron-derived RNA platforms coordinate inflammatory gene networks through the Intronic Signaling Pathways System (ISPS)" The study investigates the potential regulatory organization of spliceosome-generated intronic RNAs using human TNF intron 1 as a model system. The repository includes: • TNF intron 1 sequence datasets and reconstructed lariat RNA sequences. • RNA secondary structure predictions generated using ViennaRNA/RNAfold and FORNA visualization tools. • Structural cluster annotations (C1–C7) and associated accessibility analyses. • Transcription factor binding site (TFBS) analyses generated using FIMO and JASPAR databases. • RNA-binding protein (RBP) interaction datasets compiled from ATtRACT, POSTAR3, CISBP-RNA, and related resources. • Integrated structural-regulatory maps used to identify asymmetrical regulatory organization across the TNF intron 1 scaffold. • Figures, supplementary materials, and computational resources associated with the manuscript. These materials support the proposed Intronic Signaling Pathways System (ISPS) framework, which explores the possibility that spliceosome-generated intronic RNAs may function as structured regulatory platforms capable of participating in dynamic transcription factor and RNA-binding protein interaction landscapes. All files are provided to ensure transparency, reproducibility, and future reuse of the analyses described in the associated manuscript.