We also performed CLIP-seq in Dicer/ mESCs that lack mature miRNAs, allowing us to define whether the association of Ago2 with the identified sites was miRNA dependent. A significantly enriched motif, GCACUU, was identified only in wild-type mESCs in 3' untranslated and coding regions. This...
small_RNA_seq_counts_7D.txt Input table for Figure 7D Repository files navigation README AgoCLIP_2020 Code used for the manuscript: "Argonaute-CLIP delineates versatile, functional RNAi networks in Aedes aegypti, a major vector of human viruses"...
To determine if PUM proteins impact AGO2 binding behavior, AGO2 CLIP-seq was carried out in conditions of PUM1 or PUM2 knockdown with two distinct siRNAs each (average 82–91% knockdown, Fig. S1), and compared to control siRNA knockdowns. Three biological replicates of PUM1 KD and four ...
Li JH et al (2014) starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res 42(Database issue):D92–D97 Article CAS PubMed Google Scholar Chou C-H et al (2015) miRTarBase 2016: updates to the experimentally...
Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 39 untranslated region (UTR) ...
RNA-maps of iCLIP, eCLIP, eiCLIP and RNA-seq reads start/ends For the visualisation of all the CLIP based and RNA-seq methods, we used previously developed RNA-map approach [32,80] with small addition for RNA-seq read end positions by summarising the read start positions relative to the...
and atherosclerosis14,15(Supplementary Fig.6eand f). As AMPK is known as a critical regulator of energy metabolism, we further assessed the role of Ago2 inAmpka1expression. Analyzing a public database of photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) with Ago...
We used a combined AGO2 RIP-seq and AGO2 PAR-CLIP-seq (photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation) approach to determine the exact sites of interaction between the AGO2-bound miRNAs and their mRNA targets. Findings TP53 directly associated with AGO2, and induced ...
By using a combination of AGO2 enhanced individual nucleotide resolution UV crosslinking and immunoprecipitation (eiCLIP) and CAGE following siRNA treatment, we find that these 3′UTR-derived RNAs likely originate from AGO2-binding sites, and most often occur at locations with G-rich motifs bound...