Fig. 3

piRNAs are differentially expressed between control- and PD-patient derived cells (a) Differentially expressed piRNAs between control- and PD-patient derived cells (log2FC ≥ 0.6, p-adj. < 0.1) in fibroblasts, iPSCs/ESCs and neurons. b Semiquantitative PCR of PIWIL2 and PIWIL4 in the neurons used for the analysis of small RNA expression patterns. Both genes are expressed in cultured neurons. GAPDH was used as a loading control. A 100 bp DNA-ladder (M) and a negative control (−) were loaded together with the PCRs from control (CTRL) and PD-patient (PD) neuronal samples. c Heatmap and hierarchical clustering based on the TOP100 differentially expressed piRNAs in neurons (sorted by adjusted p-value). PD-patient derived cells (salmon) are clearly separated from control-patient derived cells (azure). d Memory-related piRNAs (i.e. piRNAs already differentially expressed in parental fibroblasts) are present, but constitute a minor fraction (< 10%) of all deregulated piRNAs in iPSCs/ESCs and neurons. e Plot of cytosine content in all deregulated piRNAs over nucleotide positions 1 to 29. In the first 10 nucleotides, cytosines are overrepresented in the upregulated piRNAs (green line) as compared to all piRNAs analysed (dark red line). This observation does not apply to the downregulated piRNAs (blue line). f SINE- and LINE-derived piRNAs are highly enriched in the downregulated piRNA fraction in neurons. SINE- and LINE-derived piRNAs (but not LTR- or gene-derived piRNAs) are significantly enriched in the fraction of downregulated piRNAs as compared to their abundance in the genome (two-sided chi-square test, p < 0.0001 and p < 0.01, respectively)