Fig. 7

Activity dependent alternative splicing of Homer1. a Homer1 is encoded by 12 exons (yellow boxes, not to scale). Differential exon usage results in at least 5 splice variants (green). Larger boxes represent coding sequence and smaller boxes untranslated regions. b Visualization of the microarray data. The plot shows the log2 ratio calculated from mean normalized intensities of transformed expression values over the course of probesets per exon. Green lines represent expression kinetics of one time point. Blue boxes represent probesets per exon present on the microarrays. Red dotted circles highlight probesets corresponding to the second alternative 5′ exon which is featured in Homer1d, as well as probesets corresponding to the prolonged alternative 3′-end of exon 6, featured in Homer1a and probesets corresponding to the prolonged alternative 3′-end of exon 7, featured in Ania-3. c Validation of Homer1 variant expression in hippocampus of control mice or 1, 4 or 8 h after seizure onset by RNA sequencing. Shown are coverage plots (blue) from paired-end. The reference gene track is depicted below (black). d Sashimi plot of RNA sequencing data. Numbers indicate counts of RNA sequencing reads that span the respective exon junctions. e Validation of splicing events by RT-PCR. Numbers indicate exons. Exon-spanning primers (arrows) were used to assess expression in total RNA of hippocampi of control mice (−) and of mice sacrificed 4 h (+, 4 h) or 1 h after seizure onset (+, 1 h). Note that the product size in the upper left panel demonstrates exclusion of exon 2. The forward primer corresponding to exon 2 in the upper right panel is specific for the 5′-UTR. The reverse primer in the lower panels correspond to exon 6 and is specific for the coding region present in all transcripts (left) or specific for the 3′UTR of exon 6 present in Homer1a only (right)