LIRBase

LIRBase catalogs long inverted repeats (LIRs) across eukaryotic genomes to support systematic study of their transcription into long hairpin RNAs (hpRNAs) and processing into small interfering RNAs (siRNAs).

Key Features:

• Systematic identification: Genome-wide identification of 6,619,473 LIRs across 424 eukaryotic genomes sourced from GenBank.
• Transcriptional annotation: Annotation of the transcriptional potential of LIRs into long hpRNAs and their processing into siRNAs.
• Sequence-based LIR detection: Identification of potential LIRs from input nucleotide sequences.
• sRNA alignment: Alignment of sRNA sequencing (sRNA-seq) data to LIR loci to assess expression of derived siRNAs.
• Differential expression analysis: Comparative analysis of LIR expression and derived siRNA abundance across conditions or species.
• mRNA target prediction: Prediction of mRNA targets for siRNAs derived from LIRs to infer potential gene-silencing interactions.
• Secondary structure analysis: Prediction and visualization of secondary structures of candidate long hpRNAs encoded by LIRs.

Scientific Applications:

• Cataloging and annotation: Comprehensive cataloging and annotation of LIRs across diverse eukaryotic genomes for comparative genomics studies.
• siRNA biogenesis studies: Investigation of biogenesis pathways from LIR transcription into hpRNAs and subsequent processing into siRNAs.
• Expression profiling: Analysis of differential expression of LIRs and LIR-derived siRNAs across developmental stages, treatments, or species.
• Functional inference: Prediction of mRNA targets to study potential regulatory roles and gene-silencing mechanisms of LIR-derived siRNAs.

Methodology:

Genome-wide identification of LIRs across eukaryotic genomes (424 genomes, 6,619,473 LIRs), annotation of transcriptional potential into hpRNAs and siRNAs, alignment of sRNA-seq data to LIR loci, differential expression analysis of LIRs, prediction of mRNA targets for derived siRNAs, and secondary-structure prediction/visualization of candidate long hpRNAs.