Supplementary Figure 10: Identification, expression and localization of ALE, a long noncoding RNA in DUX4/ERG ALL.
From: Deregulation of DUX4 and ERG in acute lymphoblastic leukemia
(a) UCSC WGL plot of transcriptome sequencing data at ERG for a representative case, SJERG003, showing peaks of coverage representing ERG exons, and a region of coverage proximal to the ERG isoform 1 (NM_182918) locus. (b,c) Stranded total RNA–seq data for the same case. (b) The sense strand shows coverage corresponding to a four-exon noncoding RNA, with exon junctions shown below the WGL plot as red bars and the numbers to the left of each bar corresponding to the number of exon–exon junctions. (c,d) Antisense sequencing data corresponding to coding ERG transcripts (c) and the number of annotated (green) and non-annotated (red) junctions shown as bars (d). Note the high number of reads corresponding to ERG alt (exon 6 alt to exon 7) junctions. (e) RT–PCR for expression of ALE (antisense long noncoding RNA associated with ERG) showing two spliced isoforms. (f) Sequential RNA and DNA FISH showing that expressed ALE transcripts are retained at the ERG locus, in contrast to coding ERG transcripts, which are dispersed throughout the nucleus.
