Whole Genome Expression Profiling Shows that BRG1 Transcriptionally Regulates UV Inducible Genes and Other Novel Targets in Human Cells

Abstract

UV irradiation is known to cause cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6–4) pyrimidone photoproducts (6-4PPs), and plays a large role in the development of cancer. Tumor suppression, through DNA repair and proper cell cycle regulation, is an integral factor in maintaining healthy cells and preventing development of cancer. Transcriptional regulation of the genes involved in the various tumor suppression pathways is essential for them to be expressed when needed and to function properly. BRG1, an ATPase catalytic subunit of the SWI/SNF chromatin remodeling complex, has been identified as a tumor suppressor protein, as it has been shown to play a role in Nucleotide Excision Repair (NER) of CPDs, suppress apoptosis, and restore checkpoint deficiency, in response to UV exposure. Although BRG1 has been shown to regulate transcription of some genes that are instrumental in proper DNA damage repair and cell cycle maintenance in response to UV, its role in transcriptional regulation of the whole genome in response to UV has not yet been elucidated. With whole genome expression profiling in SW13 cells, we show that upon UV induction, BRG1 regulates transcriptional expression of many genes involved in cell stress response. Additionally, our results also highlight BRG1's general role as a master regulator of the genome, as it transcriptionally regulates approximately 4.8% of the human genome, including expression of genes involved in many pathways. RT-PCR and ChIP were used to validate our genome expression analysis. Importantly, our study identifies several novel transcriptional targets of BRG1, such as ATF3. Thus, BRG1 has a larger impact on human genome expression than previously thought, and our studies will provide inroads for future analysis of BRG1's role in gene regulation.

Dynamic transcription of ubiquitin genes under basal and stressful conditions and new insights into the multiple UBC transcript variants

“…Besides the mutagenic, DNA damaging and cell cycle disturbing actions of UV, the ultraviolet stress response involves the transcriptional regulation of many target genes (Sesto et al, 2002;Zhang et al, 2014;Valéry et al, 2001).…”

“…No change in Ub genes expression was detected at these different UV doses at the two time points investigated, with respect to mock-treated cells (data not shown). To assess the efficacy of the treatment, we amplified as positive control interleukin 8 (IL-8), which was found to be a UV inducible gene in two whole genome expression studies (Sesto et al, 2002;Zhang et al, 2014): IL-8 mRNA markedly accumulated (~7.2-fold) 24 h after HeLa exposure to 100 J/m 2 . In the next experiments, HeLa cells were irradiated with higher UV doses (400 and 800 J/m 2 ), besides 100 J/m 2 , as above, and samples collected 4 h after treatment.…”

Dynamics of chromatin accessibility and epigenetic state in response to UV damage

“…Recent evidence has suggested that chromatin plays a major role in the UV-induced cellular response including regulation of gene expression changes (Andrade-Lima et al, 2015;Dawes et al, 2014;Dinant et al, 2013;Duan and Smerdon, 2014;Hassan et al, 2014;Izhar et al, 2015;Li et al, 2014;Sesto et al, 2002;Zhang et al, 2014). However, a detailed genomewide analysis to investigate the relationship of chromatin and gene expression changes was still missing.…”

“…Recent studies have revealed that epigenetic mechanisms also play a role in the transcriptional response following UV irradiation. For example, the components of the ATP-dependent SWI-SNF chromatin remodeling complex BRG1 and BRM (also known as SMARCA4 and SMARCA2, respectively) have been implicated in the transcriptional regulation of UV-induced genes (Hassan et al, 2014;Zhang et al, 2014). Furthermore, many posttranslational histone modifications have been shown to be modulated during the cellular response to DNA damage (Corpet and Almouzni, 2009;Kumar et al, 2012;Li et al, 2014;Tjeertes et al, 2009).…”

SMARCA4-inactivating mutations increase sensitivity to Aurora kinase A inhibitor VX-680 in non-small cell lung cancers

“…SWI/SNF complexes mobilize histone octamers in an ATP-dependent manner to allow or repress gene transcription1718. Loss of SMARCA4 expression changes approximately 5% of the mammalian transcriptome19, including changes in the expression of genes associated with NSCLC12, increasing the likelihood for loss of functions that might be redundant in normal cells and non-redundant in tumours lacking SMARCA4.…”