Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types

Abstract

To date, analyses of individual targets have provided evidence of a miRNA targetome that extends beyond the boundaries of messenger RNAs (mRNAs) and can involve non-Watson-Crick base pairing in the miRNA seed region. Here we report our findings from analyzing 34 Argonaute HITS-CLIP datasets from several human and mouse cell types. Investigation of the architectural (i.e. bulge vs. contiguous pairs) and sequence (Watson-Crick vs. G:U pairs) preferences for human and mouse miRNAs revealed that many heteroduplexes are “non-canonical” i.e. their seed region comprises G:U and bulge combinations. The genomic distribution of miRNA targets differed distinctly across cell types but remained congruent across biological replicates of the same cell type. For some cell types intergenic and intronic targets were more frequent whereas in other cell types mRNA targets prevailed. The findings suggest an expanded model of miRNA targeting that is more frequent than the standard model currently in use. Lastly, our analyses of data from different cell types and laboratories revealed consistent Ago-loaded miRNA profiles across replicates whereas, unexpectedly, the Ago-loaded targets exhibited a much more dynamic behavior across biological replicates.

The Emerging Function and Mechanism of ceRNAs in Cancer

“…This region, usually nucleotides 2–7, forms Watson–Crick (WC) pairs with the target mRNA 3’ untranslated region (UTR) [8, 10]. miRNAs have also been found to target the 5’UTR and coding sequence of the mRNAs as well as pseudogenes and lncRNAs [11–14]. Animal miRNAs post-transcriptionally repress target gene expression via transcript degradation and/or translation inhibition [15, 16].…”

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

“…Another comprehensive analysis of 34 Argonaute HITS-CLIP datasets from human and mouse cells revealed that many heteroduplexes are "non-canonical" i.e. their seed region comprises G:U and bulge combinations (Clark et al, 2014).…”

“…CLIP strategies are nowadays popular for high-throughput analysis of physiological miRNA targets (Chi et al, 2009;Hafner et al, 2010;Leung et al, 2011;Chi et al, 2012;Clark et al, 2014;Grosswendt et al, 2014;Haecker and Renne, 2014;Liu et al, 2014a;Imig et al, 2015) and it is accompanied with a number of algorithms and databases facilitating identification of miRNA targets in high-throughput CLIP data (Hsieh and Wang, 2011;Yang et al, 2011;Balaga et www.efsa.europa.eu/publications 254 EFSA Supporting publication 2017:EN-1246…”

TP53 regulates miRNA association with AGO2 to remodel the miRNA–mRNA interaction network

“…S9), and we used this information together with MRE conservation and length to prioritize the assignment of a single expressed miRNA to each AGO2 binding site where there was ambiguity due to multiple possible MREs (see Methods for further details). Since miRNAs also target genes in a "noncanonical" manner, through bulges and G:U pairs in the seed region (Chi et al 2012;Helwak et al 2013;Clark et al 2014), and given our novel findings of an increased association between let-7 and AGO2 following DNA damage, we wished to complement our analysis by taking into account potential noncanonical interactions between let-7 and their gene targets on AGO2. To achieve this, we used the miRNA-mRNA interaction data from Clark and coworkers (available at https://cm.jefferson.…”

“…To achieve this, we used the miRNA-mRNA interaction data from Clark and coworkers (available at https://cm.jefferson. edu/clip_2014/) that contains HITS-CLIP results from multiple cell lines (Clark et al 2014), focusing on let-7 interactions and selecting those that overlapped with our AGO2 binding sites (Supplemental Table S5). Finally, based on the analysis of AGO2 binding sites and their assignment to targeting miRNAs, we built a comprehensive miRNA-mRNA interaction network (Supplemental Fig.…”