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

Reymann S, Borlak J - BMC Genomics (2006)

Bottom Line: 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).

View Article: PubMed Central - HTML - PubMed

Affiliation: Fraunhofer Institute of Toxicology and Experimental Medicine (Fh-ITEM), Center for Drug Research and Medical Biotechnology, Nikolai-Fuchs-Str, 1, 30625 Hannover, Germany. reymann@item.fraunhofer.de

ABSTRACT

Background: 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.

Results: 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).

Conclusion: 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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Scheme of proposed network of transcription factors involved in regulation of gene expression under direct or indirect influence by the AhR. This network of transcription factors may explain the regulation of several genes that are not direct targets of AhR. Their regulation can be mediated through other TFs whose expression is regulated directly by AhR.
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Figure 6: Scheme of proposed network of transcription factors involved in regulation of gene expression under direct or indirect influence by the AhR. This network of transcription factors may explain the regulation of several genes that are not direct targets of AhR. Their regulation can be mediated through other TFs whose expression is regulated directly by AhR.

Mentions: Activation and repression of transcription factors and the ensuing changes in gene regulation seem to be hallmarks of the molecular mechanisms of Aroclor 1254. Many of them are candidates for being regulated directly by AhR, through its binding to the corresponding in silico-identified DNA binding sites in their promoters. This proposed network of transcription factors involved in regulation of gene expression under direct or indirect influence by the AhR is depicted in Figure 6.


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

Reymann S, Borlak J - BMC Genomics (2006)

Scheme of proposed network of transcription factors involved in regulation of gene expression under direct or indirect influence by the AhR. This network of transcription factors may explain the regulation of several genes that are not direct targets of AhR. Their regulation can be mediated through other TFs whose expression is regulated directly by AhR.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1590027&req=5

Figure 6: Scheme of proposed network of transcription factors involved in regulation of gene expression under direct or indirect influence by the AhR. This network of transcription factors may explain the regulation of several genes that are not direct targets of AhR. Their regulation can be mediated through other TFs whose expression is regulated directly by AhR.
Mentions: Activation and repression of transcription factors and the ensuing changes in gene regulation seem to be hallmarks of the molecular mechanisms of Aroclor 1254. Many of them are candidates for being regulated directly by AhR, through its binding to the corresponding in silico-identified DNA binding sites in their promoters. This proposed network of transcription factors involved in regulation of gene expression under direct or indirect influence by the AhR is depicted in Figure 6.

Bottom Line: 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).

View Article: PubMed Central - HTML - PubMed

Affiliation: Fraunhofer Institute of Toxicology and Experimental Medicine (Fh-ITEM), Center for Drug Research and Medical Biotechnology, Nikolai-Fuchs-Str, 1, 30625 Hannover, Germany. reymann@item.fraunhofer.de

ABSTRACT

Background: 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.

Results: 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).

Conclusion: 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.

Show MeSH
Related in: MedlinePlus