Microarray expression analyses following miRNA transfection/inhibition and, more recently, Argonaute cross-linked immunoprecipitation (CLIP)-seq assays have been used to detect miRNA target sites. CLIP and expression approaches measure differing stages of miRNA functioning-initial binding of the miRNP comple...
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"...
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...
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) ...
Identify MicroRNA Targets Using AGO2-CLASH (Cross-linking, Ligation, and Sequencing of Hybrids) and AGO2-CLIP (Cross-Linking and Immuno-Precipitation) in Cells with or Without the MicroRNA of Interest Depleted. In: Lin, RJ. (eds) RNA-Protein Complexes and Interactions. Methods in Molecular ...
Transcriptome-wide changes in AGO2-mRNA binding upon PUM knockdown were quantified by CLIP-seq, and the presence of PUM binding on the same 3′UTR corresponded with cooperative and antagonistic effects on AGO2 occupancy. In addition, PUM binding sites that overlap with AGO2 showed differential, ...
In this study, we explored the binding profile of AGO18b in maize tassel by UV cross-linking RNA immunoprecipitation, followed by deep sequencing of these cDNA libraries (cRIP-seq), and systematically studied AGO18b-associated small RNAs and mRNAs by bioinformatics analysis. By globally analyzing ...
starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (sRNAs) that regulate gene expression by targeting messenger RNAs. However, assign... JH Yang,JH Li,S Peng...
RNA-seq and cross-linking immunoprecipitation (CLIP)-based techniques from ENCODE and FANTOM consortia. We show that 3′UTR-derived RNAs present biochemical properties similar to their 5′ capped counterparts and that they can be as abundant as the protein-coding version of the host transcript, or...
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...