Project description:To understand the function of gene CG7358 in Drosophila melanogaster, including indentification of those genes whose expression levels or alternative splicing are affected by CG7358.
Project description: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.
Project description:To address the global impact of PARP-1 on alternative splicing, we isolated total RNA in two biological replicates from control (non-treated), PARP-1 siRNA- and PJ-34-treated cells. Sequencing of these RNAs on an Illumina HiSeq 2500, yielded >56 million 100-bp paired-end RNA-seq reads. First we tested if PARP-1 KD was effective at the RNA-seq level. Read aligning to the entire gene body of PARP-1 shown 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, PARP-1 KD and PARylation inhibited) to assess whether these treatments resulted in changes in i) gene expression and ii) alternative splicing.
Project description:We sequenced mRNA from head tissue of females and male of Drosophila melanogaster to identify genes differentially expressed between the sexes and sex-specific alternative splicing events. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf