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In further CLIP analysis, the 5′-UTR region was divided into 2 fragments, J1 149 (SL I-SL II) and J127 360 (SL III-SL IV), according to the secondary structure, and the 3′-UTR region was divided into J9440 9578 (VSL2-polyU tract) and J9578 9678 (3′-X region).
A strong trend was observed for the clip analysis (p = 0.052, Table 4).
CLIP analysis of the neural specific splicing factor Nova identified a post-transcriptional regulatory network related to synaptic function.
CLIP analysis of SF2/ASF was performed as described by Ule et al.[32] with the following modifications relating to extract preparation and RNase treatment.
Purification of polyribosome for CLIP analysis of SF2/ASF was accomplished by pelleting polyribosomes through 10 25% sucrose gradients as previously described [8].
Alternatively an Ago CLIP analysis might be useful.
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HITS-CLIP analysis provide novel insights into global miRNA:mRNA relationships in the regenerating liver.
Transcriptome-wide HITS-CLIP analysis revealed widespread RBM47 binding to mRNAs, most prominently in introns and 3′UTRs.
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