Transcriptome profiling of human hepatocytes treated with Aroclor 1254 reveals transcription factor regulatory networks and clusters of regulated genes

Fraunhofer Institute of Toxicology and Experimental Medicine (Fh-ITEM), Center for Drug Research and Medical Biotechnology, Nikolai-Fuchs-Str, 1, 30625 Hannover, Germany.
BMC Genomics (Impact Factor: 3.99). 02/2006; 7(1):217. DOI: 10.1186/1471-2164-7-217
Source: PubMed


Aroclor 1254 is a well-known hepatotoxin and consists of a complex mixture of polychlorinated biphenyls (PCBs), some of which have the ability to activate the aryl hydrocarbon receptor (AhR) and other transcription factors (TFs). Altered transcription factor expression enables activation of promoters of many genes, thereby inducing a regulatory gene network. In the past, computational approaches were not applied to understand the combinatorial interplay of TFs acting in concert after treatment of human hepatocyte cultures with Aroclor 1254. We were particularly interested in interrogating promoters for transcription factor binding sites of regulated genes.
Here, we present a framework for studying a gene regulatory network and the large-scale regulation of transcription on the level of chromatin structure. For that purpose, we employed cDNA and oligomicroarrays to investigate transcript signatures in human hepatocyte cultures treated with Aroclor 1254 and found 910 genes to be regulated, 52 of which code for TFs and 47 of which are involved in cell cycle and apoptosis. We identified regulatory elements proximal to AhR binding sites, and this included recognition sites for the transcription factors ETS, SP1, CREB, EGR, NF-kB, NKXH, and ZBP. Notably, ECAT and TBP binding sites were identified for Aroclor 1254-induced and E2F, MAZ, HOX, and WHZ for Aroclor 1254-repressed genes. We further examined the chromosomal distribution of regulated genes and observed a statistically significant high number of gene pairs within a distance of 200 kb. Genes regulated by Aroclor 1254, are much closer located to each other than genes distributed randomly all over the genome. 37 regulated gene pairs are even found to be directly neighbored. Within these directly neighbored gene pairs, not all genes were bona fide targets for AhR (primary effect). Upon further analyses many were targets for other transcription factors whose expression was regulated by Aroclor 1254 (secondary effect).
We observed coordinate events in transcript regulation upon treatment of human hepatocytes with Aroclor 1254 and identified a regulatory gene network of different TFs acting in concert. We determined molecular rules for transcriptional regulation to explain, in part, the pleiotropic effect seen in animals and humans upon exposure to Aroclor 1254.

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    • "Moreover, we found that the module 106 (Fig. 4D) identified three candidate genes associated with alcoholism (PDE11A, HCP9 and TTN) and that all of these genes have plausible biological bases for being involved in alcoholism, such as being part of the calcium signalling pathway, regulation of the actin cytoskeleton and focal adhesion. Although PDE11A and TTN did not directly interact with each other in the protein–protein interaction network and the distance between them is 417,650 bp, which is larger than the threshold of colocalised genes used in Susanne Reymann et al. (Reymann and Borlak, 2006) (other modules' ranges are given in Table S12), they still exhibit significant synergistic effects. In agreement with previous studies, this result indicates that synergetic effects of genes located in biochemically distinct circuits are common (Hartman et al., 2001; Wagner et al., 2008). "
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    • "However, the Hif1 and Foxn1 TFBS showed enrichment within the 1893 regions that showed significant AHR binding and did not co-occur with the AHR. In an in silico analysis of promoter regions from genes showing differential expression in primary human hepatocytes following exposure to Aroclor 1254, the TFBS for Nrf1 (V$NRF1) and Npas2 (V$HIFF) co-occurred with the AHR TFBS (Reymann and Borlak, 2006). In our study, the AHR and Nrf1 module was identified. "
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