FANTOM-ZENBU lncRNA annotation

FANTOM-ZENBU lncRNA annotation provides an annotation of nuclear long non-coding RNAs based on chromatin interactions and Hi-C data, identifying potential target genes and regulatory factors.

Key Features:

• Hi-C-based target gene identification: Uses Hi-C chromatin conformation data to identify potential target genes of nuclear lncRNAs based on local chromatin 3D conformation.
• Regulatory factor prediction: Incorporates RNA-protein interaction data to infer that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers.
• Spatial proximity analysis: Analyzes the role of nuclear lncRNAs in directing regulatory factors to locations spatially close to the lncRNA gene.

Scientific Applications:

• Nuclear lncRNA functional annotation: Annotates nuclear lncRNAs with potential target genes and regulatory factors based on chromatin interaction data.
• 3D chromatin structure integration: Integrates Hi-C data to link nuclear lncRNAs with genes in spatial proximity for regulatory inference.
• lncRNA-protein interaction analysis: Uses RNA-protein interaction data to understand how nuclear lncRNAs recruit regulatory proteins to chromatin.

Methodology:

Uses Hi-C chromatin conformation data to identify potential target genes of lncRNAs, and RNA-protein interaction data to infer recruitment of regulatory proteins to target promoters and enhancers.