NETSeq Analysis of the Effect of PARP-1 Knockdown in Drosophila Melanogaster

Multiple roles for PARP1 have been elucidated including DNA damage repair, metabolic regulation, and cell cycle control. PARP1 also has an effect on chromatin structure, but this factor has not been well studied. Here, we strive to elucidate the effect of PARP1-mediated chromatin changes, specifically in the context of transcription and alternative splicing. Chromatin structure affects any process that occurs on the DNA, including transcription and splicing. Therefore, if PARP1 has an effect on chromatin structure, it will cause downstream changes in transcription and splicing. We investigated PARP1’s connection to splicing not only by evaluating splicing decisions, but also by studying its effect on splicing factors. We found that PARP1 has a multifaceted role in these processes. PARP1 presence influences splicing decisions by altering nucleosome deposition and histone post-translational modifications at exon-intron boundaries. Additionally, PARP1 occupancy modifies transcriptional elongation by hindering the rate of RNAPII movement. In this study, we show that through changes in chromatin structure, PARP1 is able to modify transcriptional elongation rates as well as alternative splicing decisions. Two conditions, wild type (WT) and PARP-1 knockdown (KD), were examined with two replicates per condition. In both cases, a high band and low band were extracted for sequencing, resulting in eight total samples.