Table 1. Summary of high-throughput Ago-mRNA/DNA mapping in mammalian systems.
| Experimental approach | Experimental system | Ago member(s) studied | Antibody used | Key findings | Reference |
|---|---|---|---|---|---|
| HITS-CLIP | Mouse brain | Endogenous Ago | anti-pan-Ago (2A8) | Ago-bound tags fell in 3′UTR (40%), coding sequences (25%), introns (12%), and non-coding RNAs (5%). | Chi et al.33 |
| PAR-CLIP | Human embryonic fibroblasts (HEK293) | Tagged Ago1–4 |
anti-HA | Identified seed-dependent miRNA target sites and nearly 50% of the binding sites located in the CDS. | Hafner et al.36 |
| CLIP-seq | Mouse embryonic stem cells (wt vs. Dicer −/−) | Endogenous Ago2 | anti-Ago2 (2D5) | miRNA dependent and GC rich binding sites were identified in 3′ untranslated and coding regions. | Leung et al.35 |
| CLASH | HEK293 (Doxycycline inducible) | Tagged Ago1 | anti-FLAG | Widespread (> 63%) noncanonical miRNA-mRNA seed interactions via noncanonical Watson-Crick base pairing. | Helwak et al.37 |
| CLIP-seq | HEK293S | Endogenous Ago2 | anti-Ago2(11A9), anti-Ago2 (4F9), anti-Ago2(2E12–1C9) | Cellular stress induced by arsenite strengthens Ago2-mRNA interactions in 3′UTR and CDS of genes repressed during translation. | Karginov et al.34 |
| ChIP-chip | Primary human diploid fibroblasts (WI38) | Endogenous Ago2 | anti-pan-Ago, anti-Ago2(9E8.2) | Ago2, RB1 and miRNAs functionally interact to repress E2F regulated genes during senescence. | Benhamed et al.28 |
| ChIP-seq | Human prostate cancer cells (PC-3) | Endogenous Ago1 | anti-Ago1(2A7) | Ago1 bound sites are associated with transcriptionally active loci marked by H3K4me3. | Huang et al.22 |