Fig. 2

Conserved elements in the Cyrano lncRNA. a Outline of the genomic organization of Cyrano exons in select species. b Sequence elements identified by LncLOOM to be conserved in Cyrano in at least 17 species. The region containing elements found in the region alignable by BLAST between human and zebrafish Cyrano sequences is circled. Numbers between elements indicate the range distances between the elements in the 18 species. The circled number above each element indicates the element number used in the text and in the other panels. c Pairing between the predicted binding elements in Cyrano and the miR-25/92 and miR-7 miRNAs. d Evidence for binding of PUM1 and PUM2 to the UGUAUAG motif (shaded region) in the human genome. ENCODE project CLIP data (top, K562 cells) and [15] (bottom, HCT116 cells). Shading is based on strength of binding evidence, as defined by the ENCODE project. e Binding and regulation of the mouse Cyrano sequence by Pum1/2 and Rbfox1/2. Top: Pum1/2 CLIP and RNA-seq data from [16]. Middle: Rbfox1 CLIP from mouse brain [17] and from mESCs [18]. Binding motifs for Pumilio and Rbfox are highlighted in yellow and blue, respectively. PhyloP sequence conservation scores are from the UCSC genome browser. Bottom: Binding of Ago2 in the mouse brain to the region of the miR-153 binding site near the 3′ end of Cyrano. CLIP data from [19]. f Top left: Alignment of the region surrounding the conserved AUGGCG motif near the 5′ end of Cyrano. Top right and bottom: Composite Ribo-seq and RNA-seq data from multiple datasets curated in [20]. ChIP-seq data for YY1 in the K562 cell line from the ENCODE project. Shown is the read coverage and the IDR peaks