Small RNA on Maragkakis Lab

cCLIP-Seq: Retrieval of Chimeric Reads from HITS-CLIP (CLIP-Seq) Libraries

Mon, 01 Jan 2018 00:00:00 +0000

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.

Kc167, a widely used Drosophila cell line, contains an active primary piRNA pathway

Sun, 01 Jan 2017 00:00:00 +0000

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.

Sequence-dependent but not sequence-specific piRNA adhesion traps mRNAs to the germ plasm

Thu, 17 Mar 2016 00:00:00 +0000

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.

Mitochondrial protein BmPAPI modulates the length of mature piRNAs

Tue, 01 Oct 2013 00:00:00 +0000

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.

Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis

Wed, 01 Aug 2012 00:00:00 +0000

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.