Gene expression changes due to PARP knockdown in human cells

To address the global impact of PARP-1 on the transcriptome, we knocked down PARP1 using siRNA from Dharmacon. Total RNA in three biological replicates from control (non-treated) and PARP-1 siRNA-treated cells were isolated. Sequencing of these RNAs on an Illumina NextSeq 500 yielded >56 million 75-bp RNA-seq reads. First we tested if PARP-1 KD was effective at the RNA-seq level. Reads aligning to the entire gene body of PARP-1 show a reduction in PARP-1 expression of about 1.5-fold (P-value < 0.0003), confirming that indeed PARP-1 was depleted after PARP-1 siRNA treatment. We next used these RNA-seq data sets (control and PARP-1 KD) to assess whether these treatments resulted in changes in gene expression and alternative splicing. Overall design: mRNA profiles of three biological replicates (non-treated) and three PARP-1 siRNA knockdowns were compared using RNA-Seq on an IlluminaNextSeq 500.