Abstract
BackgroundValidation of physiologic miRNA targets has been met with significant challenges. We employed HITS-CLIP to identify which miRNAs participate in liver regeneration, and to identify their target mRNAs.ResultsmiRNA recruitment to the RISC is highly dynamic, changing more than five-fold for several miRNAs. miRNA recruitment to the RISC did not correlate with changes in overall miRNA expression for these dynamically recruited miRNAs, emphasizing the necessity to determine miRNA recruitment to the RISC in order to fully assess the impact of miRNA regulation. We incorporated RNA-seq quantification of total mRNA to identify expression-weighted Ago footprints, and developed a microRNA regulatory element (MRE) prediction algorithm that represents a greater than 20-fold refinement over computational methods alone. These high confidence MREs were used to generate candidate ‘competing endogenous RNA’ (ceRNA) networks.ConclusionHITS-CLIP analysis provide novel insights into global miRNA:mRNA relationships in the regenerating liver.
Highlights
Validation of physiologic miRNA targets has been met with significant challenges
We have demonstrated here that the HITS-CLIP assay can be applied to a complex model of growth and proliferation
We demonstrate that dynamic changes in miRNA recruitment to the RISC in most cases did not correlate with overall expression patterns in the regenerating liver, indicating that assessment of expression levels alone does not reflect miRNA activity
Summary
Validation of physiologic miRNA targets has been met with significant challenges. We employed HITS-CLIP to identify which miRNAs participate in liver regeneration, and to identify their target mRNAs. microRNAs (miRNAs), 22–23 nucleotide noncoding RNAs, contribute to the control of diverse developmental, growth, and disease processes [1,2]. MicroRNAs decrease expression of mRNA targets by either destabilization of mRNA or inhibition of protein translation [3]. MicroRNAs are thought to target mRNAs through binding of nucleotides at position 2–8 of the miRNAs (the so-called ‘seed region’) to a complementary sequence in the mRNA [4,5]. While differential expression of miRNAs has been determined in multiple contexts, the validation of physiologic miRNA targets has proven to be difficult. Modulation of miRNA levels using gain- and loss-of-function approaches
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
