Linc2function: A Comprehensive Pipeline and Webserver for Long Non-Coding RNA (lncRNA) Identification and Functional...

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Long non-coding RNAs (lncRNAs) are crucial regulators of cellular functions and potential disease biomarkers, yet their specific roles and transcript isoforms are largely uncharacterized.
• Current methods for lncRNA analysis primarily focus on gene-level investigations and sequence-based discrimination, limiting comprehensive functional annotation and cross-species applicability.

Purpose of the Study:

• To develop and validate a novel computational pipeline for high-throughput, isoform-level annotation of long non-coding RNAs (lncRNAs).
• To enhance the understanding of lncRNA mechanisms in pathological processes by integrating secondary structure and interactome information.
• To address challenges in annotating lncRNAs for new species and improve the generalizability of in silico prediction methods.

Main Methods:

• Developed a computational pipeline integrating transcript sequence, secondary structure, and interactome information for lncRNA annotation.
• Employed transcript-level analysis to discriminate lncRNAs from coding RNAs and predict functional motifs and target biomolecules.
• Validated the pipeline's effectiveness through comprehensive annotation of lncRNAs associated with two specific disease groups.

Main Results:

• The proposed pipeline enables comprehensive functional annotation of lncRNAs by incorporating diverse data types beyond primary sequence.
• Successfully demonstrated the pipeline's capability in annotating lncRNAs related to specific disease cohorts.
• The developed pipeline overcomes limitations of reference-based and sequence-only methods, improving accuracy and generalizability.

Conclusions:

• Integrating transcript sequence, secondary structure, and interactome data is essential for accurate and comprehensive lncRNA functional annotation.
• The developed pipeline provides a robust tool for isoform-level lncRNA identification and annotation, advancing our understanding of lncRNA roles in disease.
• The pipeline's open-source availability and web server interface promote accessibility for researchers and non-technical users alike.