Peril

Peril characterizes enhancer activity of long intergenic noncoding RNAs (lincRNAs) and links lincRNA gene-body regulatory elements to distal gene expression.

Key Features:

• Massively Parallel Reporter Assay (MPRA): Employs MPRA to quantitatively assess enhancer activity across lincRNA loci and neighboring protein-coding genes and identifies significant MPRA peaks within gene bodies of Lincp21, LincEnc1, Peril, and in mRNA loci such as Morc2a.
• Enhancer versus promoter distinction: Distinguishes promoter regions from gene-body enhancer activities and identifies MPRA peaks within gene bodies that may function as long-range enhancers.
• In vivo validation with knockout models: Uses RNA sequencing from knockout mouse models to validate functional impacts of specific enhancer regions on distant gene expression and shows Peril locus regulation of genes in neighboring TADs via DNA-dependent mechanisms independent of Peril transcription.
• Chromosome conformation capture (Hi-C) integration: Integrates Hi-C data to confirm long-range chromatin interactions between the Peril gene body and adjacent TADs and to detect disruption of those interactions upon Peril knockout.

Scientific Applications:

• Enhancer–target gene linking: Connects enhancers discovered within lincRNA gene bodies to their target genes across different genomic regions, including across TAD boundaries.
• Non-localized lincRNA regulation: Provides evidence and insight into non-localized regulatory functions of lincRNAs, indicating gene-body elements can exert long-range regulatory effects beyond local TADs.

Methodology:

Peril applies MPRA to map and quantify enhancer activities, performs RNA sequencing in knockout mouse models to measure changes in gene expression, and integrates Hi-C chromosome conformation capture data to analyze and confirm long-range chromatin interactions and their disruption.