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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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The coordinate events which resulted in gene regulation in response to Aroclor 1254. 1) The Aroclor 1254-activated nuclear transcription factor AhR influences the expression of different transcription factors by binding to AhR recognition sites in corresponding promoters. These transcription factors constitute the basis of a regulatory gene network that again influences the expression of different genes. Other transcription factors could also be primary targets of Aroclor 1254. 2) The Aroclor 1254-activated nuclear transcription factor AhR seems to act in concert with other transcription factors, because a common framework of the corresponding binding sites could be identified proximal to AhR in the Aroclor 1254-regulated gene promoters. The combination of co-acting transcription factors might be one reason for the level of gene expression being either induced or repressed. Other transcription factors whose sites are found in the neighborhood of AhR binding sites could well be primary targets of Aroclor 1254. 3) Chromosomal localization seems to be important in the large-scale regulation of mRNA transcripts in response to Aroclor 1254. Hence, genes in neighborhood of direct Aroclor 1254-induced transcriptional regulation (primary effect), might be co-expressed through the accessibility of their promoters for transcription factors whose transcription was altered by Aroclor 1254 (secondary effect).
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Figure 7: The coordinate events which resulted in gene regulation in response to Aroclor 1254. 1) The Aroclor 1254-activated nuclear transcription factor AhR influences the expression of different transcription factors by binding to AhR recognition sites in corresponding promoters. These transcription factors constitute the basis of a regulatory gene network that again influences the expression of different genes. Other transcription factors could also be primary targets of Aroclor 1254. 2) The Aroclor 1254-activated nuclear transcription factor AhR seems to act in concert with other transcription factors, because a common framework of the corresponding binding sites could be identified proximal to AhR in the Aroclor 1254-regulated gene promoters. The combination of co-acting transcription factors might be one reason for the level of gene expression being either induced or repressed. Other transcription factors whose sites are found in the neighborhood of AhR binding sites could well be primary targets of Aroclor 1254. 3) Chromosomal localization seems to be important in the large-scale regulation of mRNA transcripts in response to Aroclor 1254. Hence, genes in neighborhood of direct Aroclor 1254-induced transcriptional regulation (primary effect), might be co-expressed through the accessibility of their promoters for transcription factors whose transcription was altered by Aroclor 1254 (secondary effect).

Mentions: Taken collectively, global gene regulation in response to Aroclor 1254 seems to be the result of different coordinate events (see Figure 7).


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)

The coordinate events which resulted in gene regulation in response to Aroclor 1254. 1) The Aroclor 1254-activated nuclear transcription factor AhR influences the expression of different transcription factors by binding to AhR recognition sites in corresponding promoters. These transcription factors constitute the basis of a regulatory gene network that again influences the expression of different genes. Other transcription factors could also be primary targets of Aroclor 1254. 2) The Aroclor 1254-activated nuclear transcription factor AhR seems to act in concert with other transcription factors, because a common framework of the corresponding binding sites could be identified proximal to AhR in the Aroclor 1254-regulated gene promoters. The combination of co-acting transcription factors might be one reason for the level of gene expression being either induced or repressed. Other transcription factors whose sites are found in the neighborhood of AhR binding sites could well be primary targets of Aroclor 1254. 3) Chromosomal localization seems to be important in the large-scale regulation of mRNA transcripts in response to Aroclor 1254. Hence, genes in neighborhood of direct Aroclor 1254-induced transcriptional regulation (primary effect), might be co-expressed through the accessibility of their promoters for transcription factors whose transcription was altered by Aroclor 1254 (secondary effect).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: The coordinate events which resulted in gene regulation in response to Aroclor 1254. 1) The Aroclor 1254-activated nuclear transcription factor AhR influences the expression of different transcription factors by binding to AhR recognition sites in corresponding promoters. These transcription factors constitute the basis of a regulatory gene network that again influences the expression of different genes. Other transcription factors could also be primary targets of Aroclor 1254. 2) The Aroclor 1254-activated nuclear transcription factor AhR seems to act in concert with other transcription factors, because a common framework of the corresponding binding sites could be identified proximal to AhR in the Aroclor 1254-regulated gene promoters. The combination of co-acting transcription factors might be one reason for the level of gene expression being either induced or repressed. Other transcription factors whose sites are found in the neighborhood of AhR binding sites could well be primary targets of Aroclor 1254. 3) Chromosomal localization seems to be important in the large-scale regulation of mRNA transcripts in response to Aroclor 1254. Hence, genes in neighborhood of direct Aroclor 1254-induced transcriptional regulation (primary effect), might be co-expressed through the accessibility of their promoters for transcription factors whose transcription was altered by Aroclor 1254 (secondary effect).
Mentions: Taken collectively, global gene regulation in response to Aroclor 1254 seems to be the result of different coordinate events (see Figure 7).

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