RNAcontacts

RNAcontacts predicts RNA-RNA contacts from high-throughput RNA proximity ligation assays (PLAs) and high-throughput sequencing data to identify spatial RNA interactions and distinguish ligation-induced sequence splits from pre-mRNA splicing.

Key Features:

• Two-pass alignment: Infers splice junctions from control RNA-seq in a first pass and treats inferred junctions as introns in a second pass to improve detection of ligation-induced splits.
• Splice-aware specificity: Distinguishes splits resulting from pre-mRNA splicing versus ligation of spatially proximate RNAs to reduce false positives.
• Contact extraction and clustering: Extracts contact points and clusters ligation sites from sequencing reads.
• Read support quantification: Computes read support for detected contacts.
• Visualization output: Generates visualization tracks compatible with the UCSC Genome Browser.
• Workflow implementation: Implemented with Snakemake to enable reproducible and scalable processing of multiple datasets.
• Applicability to proximity ligation methods: Applicable to any proximity ligation method where one interacting partner is RNA.

Scientific Applications:

• Mapping RNA spatial interactions: Detects pairwise RNA contacts from PLAs to map RNA spatial organization within cells.
• Reducing splicing-related false positives: Separates splicing-derived splits from ligation events to improve accuracy of contact calls.
• Comparative analysis across conditions: Processes multiple datasets reproducibly to compare RNA contact patterns across experimental conditions.
• Genome-browser visualization: Produces UCSC Genome Browser tracks for inspection and integration with genomic annotations.

Methodology:

Applies a two-pass alignment strategy with splice-junction inference from control RNA-seq in the first pass and treating inferred junctions as introns in the second pass; extracts contact points, clusters ligation sites, computes read support, and generates UCSC Genome Browser-compatible visualization tracks, implemented as a Snakemake workflow.