Protein interactome of small RNA fragments: identification and functional implications

ABSTRACT: Populations of small eukaryotic RNAs, in addition to relatively well recognized molecules (such as miRNAs or siRNAs), also contain fragments derived from all classes of constitutively expressed non-coding RNAs. It has been recently demonstrated that the formation and accumulation of RNA fragments (RFs) is cell-/tissue-specific and depends on internal and external stimuli. Unfortunately, the mechanisms underlying RF biogenesis and function remain unclear. To better understand them, we employed RNA pull-down and mass spectrometry methods to characterize the interaction networks of seven RFs originating from tRNA, snoRNA and snRNA. In addition, we performed an in silico screen of the selected RFs against publicly available cross-linking and immunoprecipitation datasets. We determined that the RF interactome comprises a large number of proteins, which were generally different from those that interact with their parental full length RNAs. Proteins that were differentially bound by the RFs were involved in mRNA splicing, tRNA processing, DNA recombination/replication, protein biosynthesis and carbocyclic acid metabolism. Our data suggest that RFs can be endogenous aptamer-like molecules and potential players in emerging RNA-protein regulatory networks.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hepatocyte

DISEASE(S): Disease Free

SUBMITTER: Ireneusz Stolarek  

LAB HEAD: Marek Figlerowicz

PROVIDER: PXD010075 | Pride | 2018-10-24

REPOSITORIES: Pride