>Tapbpl|NM_145391|3'UTR
   1 CCGCCTGCCTGCCTCCGAATACAAAGTAAAGTACTCCACATCCTGGCTACTTAAAGGACCCCGTGTGAGGTGTGGGGCTG
  81 AGCTGGGCCTGAAGGTGCCAGCACATTGGGAGTGCAGTACTGGCCCTGGACTGTACAAGTCTCTGCTTTCTGTGCTATTG
 161 AGAAGAGAGCCCTGGGCTGATGAAAAGGGACAGGACAAGAGGATGGCAGAATTATCAAAGTGGAAGCTAACACCATCTAT
 241 GTGAGGTATTAAGAAATCGGGGGTGGGGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTCTTCCGAAGATC
 321 TGGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCTGTAACGAGATCTGACTCCCTCTTCTGGAGTGTCTGA
 401 AGACAGCTACAGTGTACTTACATATAATAAATAAATAAATCTAATAAAAAAGAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uaCUAACGGUGUAAGACCUCAu 5' || | || | ||||||||| Target 5' ctGACTCCCTC-TTCTGGAGTg 3'	375 - 395	163.00	-16.90
2	miRNA 3' uacuAACGGUGUAAGACCUCAu 5' || | | : |||||||| Target 5' gctcTTCCGAAGATCTGGAGTt 3'	306 - 327	154.00	-15.60
3	miRNA 3' uaCUAACGGUGUAA----GACCUCAu 5' || ||| ::| | ||||| | Target 5' ggGAGTGCAGTACTGGCCCTGGACTg 3'	108 - 133	122.00	-9.51

- Nature structural & molecular biology, 2011

MicroRNAs (miRNAs) are 19-22-nucleotide noncoding RNAs that post-transcriptionally regulate mRNA targets. We have identified endogenous miRNA binding sites in mouse embryonic stem cells (mESCs), by performing photo-cross-linking immunoprecipitation using antibodies to Argonaute (Ago2) followed by deep sequencing of RNAs (CLIP-seq). 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 motif matches the seed of a miRNA family that constitutes ~68% of the mESC miRNA population. Unexpectedly, a G-rich motif was enriched in sequences cross-linked to Ago2 in both the presence and absence of miRNAs. Expression analysis and reporter assays confirmed that the seed-related motif confers miRNA-directed regulation on host mRNAs and that the G-rich motif can modulate this regulation.