Identification of lncRNAs with PAX5-dependent expression in B-ALL cells. (A) Venn diagram depicting overlap between lncRNAs with sufficient read coverage to be included in this analysis (black), lncRNAs differentially expressed (DE) between B-ALL cells with and without doxycycline-induced Pax5 expression (red), and PAX5 transcription factor binding sites (TFBS) annotated in either pro-B cells or mature B cells (blue) that could not be associated with a protein-coding gene. A subset of lncRNAs is both DE and has PAX5 bound within the gene body or promoter region (peach). (B) Volcano plot depicting the fold-change in lncRNA expression between B-ALL cells vs B-ALL cells with doxycycline-induced Pax5 expression (see supplemental Table 7) plotted against the probability that this difference had occurred by chance (q value). Each dot represents a single lncRNA and is colored black unless it was DE (q < .05) and either near or not near a PAX5 binding site (peach or red, respectively). (C) Genome plot showing PAX5-bound eRNA loci (LNCGme00432, LNCGme00344, and LNCGme00345), together with their proximal protein-coding gene, the zinc finger protein gene B-cell lymphoma 11a (Bcl11a). All are DE in B-ALL cells upon induction of Pax5 expression. PAX5 binding sites in pro-B cells are indicated in peach. The other annotated lncRNA (LNCGme00346) is also an eRNA that is DE on induction of Pax5 expression, but it shows no evidence of PAX5 binding.