Genome-wide analysis of POLR2, CTCF, RAD21, and H3K9ac binding in N1E115 cells

Neuronal nitric oxide synthase 1 (NOS1) produces the gaseous signaling molecule nitric oxide (NO), which plays important roles in the development and function of the nervous system. The regulation of Nos1 gene expression is incompletely understood. Here, we explored the role of physiological hypoxia in the control of Nos1 transcription and the underlying mechanisms using N1E115 mouse neuroblastoma cells as a model. N1E115 cells were cultured for 3 days at high (20%) and low (4%) oxygen levels. Following the verification of upregulation of Nos1 mRNA and protein levels in response to 4% oxygen, we analyzed the genome-wide distribution of CTCF, RAD21, total and S2- or S5-phosphorylated RNA polymerase II, and the histone mark H3K9ac by chromatin immunoprecipitation-sequencing. Overall design: Libraries were made from chromatin-immunoprecipitated DNA isolated from N1E115 cells cultured in the presence of 20% or 4% oxygen (at ambient barometric pressure) using antibodies against CTCF, RAD21, H3K9ac, POLR2, POLR2S2p, and POLR2S5p and sequenced on Illumina HiSeq 4000 platform.