Figure 2. Neuron-specific splicing of PKM and OGDH.
(A) The upper panel shows the RNA-seq reads obtained from NPCs and neurons mapped to the PKM and OGDH chromosome locus using Integrative Genomics Viewer. The lower schematic diagram depicts the organization of exons near the cell type-specific splicing site. Red box and line represent exon splicing unique to NPCs; blue ones represent that unique to neurons. PKM2 and OGDH1 are unique to NPCs; PKM1 and OGDHneu are predominantly for neurons. (B) Validation of PKM, OGDH splicing by PCR. Primers were designed to amplify the unique splicing region and common region of PKM1/2 and OGDH1/neu mRNA. PCR was carried out with cDNA prepared from NPCs, neurons at 3 week and primary human astrocytes. (C) The fold changes of FPKM values of hnRNPI, hnRNPA1 and hnRNPA2 are shown. Bars represent mean ± SD of four RNA-seq replicates for NPCs and neurons differentiated at 1 and 3 week. (D) The RNA-seq reads obtained from purified mouse astrocytes and neurons mapped to the PKM and OGDH chromosome locus using Integrative Genomics Viewer. The original RNA-seq data were from Zhang et al. (2014). (E) Alignment of amino acid sequences encoded by the alternative exons of human and mouse OGDH1/neu. OGDH1 contains a calcium-binding motif underlined in red, absent in OGDHneu. (Figure 2—source data 1).
DOI: http://dx.doi.org/10.7554/eLife.13374.015