LncRNAway

LncRNAway designs sgRNAs using the BESST strategy to enable precise knockout of long noncoding RNAs (lncRNAs) for functional studies while minimizing disruption to neighboring protein-coding genes and small RNAs.

Key Features:

• BESST sgRNA design: Employs the BESST (branchpoint to 3' splicing site targeting) method to design single-guide RNAs (sgRNAs) for lncRNA knockout.
• Targeting of complex loci: Supports design for natural antisense lncRNAs (NAT-lncRNAs) and other complex genomic loci to avoid perturbing adjacent elements.
• Primer generation: Produces genotyping primers and quantitative PCR (qPCR) primers for experimental validation of knockouts.
• Annotation integration: Leverages lncRNA annotations derived from high-throughput RNA sequencing datasets.
• Minimization of unintended disruption: Focuses on avoiding unintended disruption of neighboring protein-coding genes and small RNAs during knockout design.

Scientific Applications:

• Functional interrogation of lncRNAs: Enables design of knockouts to study lncRNA roles in gene regulation and cellular processes.
• NAT-lncRNA analysis: Facilitates specific interrogation of natural antisense lncRNAs without affecting overlapping coding genes.
• Knockout validation: Provides primer designs for genotyping and qPCR to assess knockout efficiency and transcript-level changes.
• Studies of biological processes and disease: Supports experiments aimed at elucidating lncRNA contributions to biological processes and diseases.

Methodology:

Uses the BESST (branchpoint to 3' splicing site targeting) method to design sgRNAs, generates genotyping and qPCR primers, and integrates lncRNA annotations from high-throughput RNA sequencing.