Dynamic recruitment of microRNAs to their mRNA targets in the regenerating liver

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.

A microRNA-Hippo pathway that promotes cardiomyocyte proliferation and cardiac regeneration in mice

“…Reads were aligned to the mouse genome (mm9), RefSeqs, and pre-miRNA (mirBase 13.0) using ELAND and allowing up to two mismatches. Significant CLIP tag cluster peaks located in the 3′UTR of mRNAs were identified, and potential miRNA regulators were identified as previously described (40). …”

ceRNA in cancer: possible functions and clinical implications

“…However, accurate prediction with these silicon-based tools remains challenging because the exact rules of miRNA-target binding are still not fully understood 3. High-throughput prediction methods can be used alone or in combination with silicon-based tools to increase prediction accuracy 81. MS2-tagged RNA affinity purification, for example, was aimed at identifying all miRNAs targeting a specific transcript,82 whereas high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation analysis was developed to identify genome-scale ceRNA binding for a specific miRNA 81…”

Transcriptome-wide Discovery of microRNA Binding Sites in Human Brain

“…Ago proteins (namely, Ago1 and Ago2) are the core components of miRNA-silencing complexes (Krol et al, 2010), and this powerful technique allows for sequencing of both the miRNAs and the mRNA target regions to which they bind. In mice, these approaches have been applied in brain and liver tissues (Chi et al, 2009; Schug et al, 2013); however, human data are only available for cultured cells (Chi et al, 2009; Haecker et al, 2012; Hafner et al, 2010). In order to advance our understanding of miRNA functions in humans, miRNA:target interactions must be further queried in primary tissues.…”