Summary This methods chapter describes cCLIP-seq, a computational approach for identifying and retrieving chimeric reads from HITS-CLIP libraries, where a small RNA and its target RNA are co-ligated and sequenced as a single molecule. By resolving these chimeric tags, cCLIP-seq enables direct identification of small RNA binding sites and precise base-pairing profiles at single-nucleotide resolution.
Summary This study characterizes the small RNA content of the Drosophila Kc167 cell line and demonstrates that it contains an active primary piRNA pathway. The findings establish Kc167 cells as a useful model system for studying piRNA biogenesis and function in vitro.
Summary This study shows that piRNAs promote germ plasm localization of mRNAs through a sequence-dependent but not sequence-specific adhesion mechanism. The findings reveal that the overall sequence composition, rather than specific complementarity, determines which mRNAs are retained in the germ plasm.
Summary This study identifies BmPAPI, a mitochondrial protein in the silkworm Bombyx mori, as a factor that modulates the length of mature piRNAs. The findings provide mechanistic insight into the piRNA 3’ end processing pathway and link mitochondria to piRNA biogenesis.
Summary Using CLIP-seq, this study maps the RNA targets of mouse PIWI proteins Mili and Miwi, providing insights into the mechanisms of piRNA biogenesis and the specific role of Miwi in regulating spermiogenesis through piRNA-mediated gene silencing.