RNA-Seq analysis of de-repressed chimeric transcripts in erythroid cells in the absence of KLF3. Tracks represent merged data for triplicate Klf3+/+ (WT) and Klf3−/− (KO) E14.5 TER119+ fetal liver cell samples. Four loci are shown: the Pu.1/Sfpi1 gene (A), the Thsd7b gene (B), the Pqlc3 gene (C), and a region on chromosome 10 (D). In each panel, sequencing reads are shown for WT (top) and KO (bottom). Within each panel, the intensity scale is consistent for both genotypes and is shown on the left. Underneath the reads, detected splicing events are shown in red (sense) or purple (anti-sense). Similarly, directionality of genes has been denoted as being on either the sense (+) or anti-sense (−) strand. The positions of ORR1A0 and ORR1A0-int elements are shown at the bottom of each panel. In (A and B), internal ORR1A0s are transcribed and spliced to downstream genic exons which show a marked increase in expression in KO samples. In (C), an ORR1A0 element serves as an upstream promoter and transcripts are spliced to genic exons. In (D), an ORR1A0 is transcribed solely in KO cells and is spliced to unannotated exons.
Mak et al. Genome Biology 2014 15:R58 doi:10.1186/gb-2014-15-4-r58