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Fig. 2 | Genome Biology

Fig. 2

From: Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation

Fig. 2

Imp CLIP identifies CA-rich binding motifs in 3′ UTRs. a Standardized transcript profile showing the CLIP enrichment from short-wave (left panel) and long-wave (right panel) cross-linking approaches. The y-axis displays the mean enrichment per nucleotide in bins across the 5′ UTRs (20), coding regions (CDS; 50) and 3′ UTRs (50) on the x-axis. b UCSC genome browser tracks of normalized CLIP-tags on squid (sqd), chickadee (chic), pAbp, and visgun (vsg) primary transcripts (red depicts tags derived from minus-strand transcripts and green those from plus-strand transcripts). The blue boxes correspond to the coding region, whereas UTRs and introns are depicted with thick blue lines and thin blue lines, respectively. c Electrophoretic mobility-shift assay of RNA segments from the coding region and 3′ UTR of the sqd transcript (upper panel) and the pAbp transcript (lower panel) with recombinant Drosophila Imp protein (12.5 nM, 25 nM, 50 nM, and 100 nM). d Scatter plot displaying the Z-score of all tetramers in the cross-link region (x-axis) and flanking regions (y-axis) in the 3000 most enriched iCLIP clusters compared with background clusters. The words with the highest enrichment either in the cross-link region or in the flanking regions are highlighted in red (UAUA, AUAU, AUUU, UAUU, UUAU, UUUU) and blue (ACAC, CACA, AACA, ACAA, CAAA, AAAC, CAAC), respectively. e Plot of the running mean (over five nucleotides) of positional enrichment, showing the distribution of the CA-rich (blue line) and UA-rich (red line) motifs identified in panel (d) in highly enriched iCLIP clusters. The shaded area highlights the cross-link region. Enrichment of the same motifs in randomly selected (background) clusters from 3′ UTRs is depicted by the dashed light blue line (CA-rich motifs) and pink line (UA-rich motifs)

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