Genome-wide and Cell-type Selective Profiling of In Vivo Small Noncoding RNA:Target RNA Interactions by Chimeric RNA Sequencing

Small noncoding RNAs (sncRNAs) can regulate biological processes by impacting posttranscriptional gene expression through repressing the levels and translation of targeted transcripts. Despite clear biological importance of sncRNAs, developed approaches to unambiguously define sncRNA:target RNA interactions in a genome-wide manner remain challenging and have not been widely adopted. We present CIMERA-seq, a robust strategy that incorporates covalent ligation of sncRNAs to their target RNAs within the RNA-induced silencing complex (RISC) and direct detection of the in vivo interactions by sequencing the resulting chimeric RNAs. Modifications are incorporated that increase the capacity for processing low abundance samples and which permit cell-type selective profiling of sncRNA:target RNA interactions, as demonstrated in mouse brain cortex. CIMERA-seq represents a cohesive and optimized method for unambiguously characterizing the in vivo network of sncRNA:target RNA interactions in numerous biological contexts and even subcellular fractions. Genome wide and cell-type selective CIMERA-seq enhances researchers’ ability to study the role of sncRNAs in mediating post-transcriptional gene regulation in diverse model systems and tissue types. sex and age matched C57BL/6 mice forebrain; genome-wide and cell-type selective miRNA:target RNA seq from Ago-CLIP, IgG for negative control.