Figure 3

STAiR1 – a STAT3-controlled macroRNA. (A) STAiR1 is upregulated in response to STAT3 and was identified by manual inspection of TileShuffle tracks. After 1 h of restimulation with IL-6 (denoted 01 on the left), TileShuffle detects a 130-kB long region of significant upregulation compared to 13-h IL-6 withdrawn cells (13). In cells permanently cultured with IL-6 (P), the region extends to at least 300 kb. It overlaps H3K27me3 domains in ENCODE data identified in GM12878 lymphoblastoid cells and peripheral blood mononuclear cells (PBMCs) derived from healthy donors, which is missing in K562 leukemia cells [5], and several STAT3 binding sites (STAT3 BS). Please refer to the caption of Figure 1, for a definition of signal, H, and DE-TAR tracks and wiggle track scale bars. (B) STAiR1 contains highly conserved elements. STAiR1 was aligned to all vertebrate genomes provided by Ensembl using BLAST[64]. Several conserved elements throughout STAiR1 that did not overlap annotated repeat elements were selected for further analysis. The chart displays the relative location of elements E1 to E8, arbitrarily aligned by E6 for selected genomes. Hits in additional genomes, including those where no continuous scaffold was available for the interval E1 to E8, are shown in Additional file 1: Figure S14. (C)BLAST hits from (B) were initially aligned using Clustalw[65], submitted to RNAalifold[66] and trimmed to regions of conserved secondary structure. The depicted consensus RNA secondary structures were generated by applying LocARNA[67] followed by RNAalifold to the trimmed sequences. The number of different types of base pairs for a consensus pair, i.e. compensatory mutations supporting the structure, is given by the hue, the number of incompatible pairs by the saturation of the consensus base pair. ChIP, chromatin immunoprecipitation; Chr, chromosome; DE-TAR, significantly differentially expressed transcriptionally active region; EST, expressed sequence tag; kb, kilobase; Laurasiath, Laurasiatheria; MB, million base pairs; PBMC, peripheral blood mononuclear cell; PCR, polymerase chain reaction; qRT-PCR, quantitative real-time reverse transcriptase PCR; STAiR, STAT3-induced RNA; STAT3, signal transducer and activator of transcription-3.