Homo sapiens epigenomics project. Homo sapiens strain:SH-SY5Y cells

Source of DNA used for sequencing was ChIP samples from SH-SY5Y cells using anti-DJ-1 antibody and anti-rabbit IgG as a negative control. DJ-1/PARK7, a cancer- and Parkinson's disease-associated protein, works as a coactivator to various transcription factors, including the androgen receptor, p53 tumor suppressor, PSF and Nrf2. Genes or sequences that are regulated by DJ-1 are, however, poorly identified. Of DNA sequence technologies recently developed, the next-generation DNA sequencers are one of the powerful tools for identifying transcription factors and their recognition sequences by using a chromatin immunoprecipitation (ChIP) sequence method. In this study, DNA fragments that bind to DJ-1 complexes were obtained by the ChIP sequencing with an anti-human DJ-1 antibody using nuclear extracts from human neuroblastoma SH-SY5Y cells in the presence or absence of oxidative stress, and their sequences were determined using Genome Analyzer II (GAII, Illumina). DNA fragments sequenced were then aligned on the human genome using ELAND software. We identified 60 sequences as potential DJ-1 complex-binding sites and found that DJ-1 recognized genes encoding almost all of the categories of their encoding proteins. After SH-SY5Y cells had been subjected to oxidative stress with 6-OHDA, numbers of DJ-1-recognized sites were reduced more than 7 fold on chromosomes 4, 6, 7, 14 and 19 compared to those in non-treated cells. By RT-PCR analysis, we found that expression levels of DJ-1-binding site-containing genes for DNA polymerase N, estrogen receptor alpha and KIAA0828 as known S-adenosylhomocysteine hydrolase like-2 on chromosomes 4, 6 and 7, respectively, were decreased in DJ-1-knockdown cells. Expression levels of these genes were also decreased in cells treated with 6-OHDA. In this study, we identified 60 DJ-1-binding sites on genes by ChIP sequences using a next-generation DNA sequencer and found that DJ-1 or its complexes regulate the expression of versatile genes at the transcriptional level and that some of the genes are regulated by DJ-1 in an oxidative status-dependent manner.