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STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer.

Fleming JD, Giresi PG, Lindahl-Allen M, Krall EB, Lieb JD, Struhl K - Epigenetics Chromatin (2015)

Bottom Line: Transient induction of the Src oncoprotein in a non-transformed breast cell line can initiate an epigenetic switch to a cancer cell via a positive feedback loop that involves activation of the signal transducer and activator of transcription 3 protein (STAT3) and NF-κB transcription factors.Interestingly, STAT3 directly regulates the expression of NFKB1, which encodes a subunit of NF-κB, and IL6, a cytokine that stimulates STAT3 activity.These observations uncover additional complexities to the inflammatory feedback loop that are likely to contribute to the epigenetic switch.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA.

ABSTRACT

Background: Transient induction of the Src oncoprotein in a non-transformed breast cell line can initiate an epigenetic switch to a cancer cell via a positive feedback loop that involves activation of the signal transducer and activator of transcription 3 protein (STAT3) and NF-κB transcription factors.

Results: We show that during the transformation process, nucleosome-depleted regions (defined by formaldehyde-assisted isolation of regulatory elements (FAIRE)) are largely unchanged and that both before and during transformation, STAT3 binds almost exclusively to previously open chromatin regions. Roughly, a third of the transformation-inducible genes require STAT3 for the induction. STAT3 and NF-κB appear to drive the regulation of different gene sets during the transformation process. Interestingly, STAT3 directly regulates the expression of NFKB1, which encodes a subunit of NF-κB, and IL6, a cytokine that stimulates STAT3 activity. Lastly, many STAT3 binding sites are also bound by FOS and the expression of several AP-1 factors is altered during transformation in a STAT3-dependent manner, suggesting that STAT3 may cooperate with AP-1 proteins.

Conclusions: These observations uncover additional complexities to the inflammatory feedback loop that are likely to contribute to the epigenetic switch. In addition, gene expression changes during transformation, whether driven by pre-existing or induced transcription factors, occur largely through pre-existing nucleosome-depleted regions.

No MeSH data available.


Related in: MedlinePlus

Cooperation of STAT3 and FOS sites during transformation. (A) AP-1 factors during transformation and their transcriptional dependence on STAT3. Shown are the normalized RNA expression microarray levels at 4 and 24 h post EtOH or TAM treatment in samples transfected with siSCM (scrambled control) or siSTAT3. (B) Occupancy of FOS DNA binding site motifs, as a function of increasing motif quality score, within FAIRE-seq regions and in non-FAIRE regions. (C) All FOS and STAT3 sites from each time point that directly overlap or overlap only at FAIRE sites. (D) Transformation-dependent differential STAT3 sites directly overlapping all FOS sites from 4, 12, and 24 h post induction.
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Fig5: Cooperation of STAT3 and FOS sites during transformation. (A) AP-1 factors during transformation and their transcriptional dependence on STAT3. Shown are the normalized RNA expression microarray levels at 4 and 24 h post EtOH or TAM treatment in samples transfected with siSCM (scrambled control) or siSTAT3. (B) Occupancy of FOS DNA binding site motifs, as a function of increasing motif quality score, within FAIRE-seq regions and in non-FAIRE regions. (C) All FOS and STAT3 sites from each time point that directly overlap or overlap only at FAIRE sites. (D) Transformation-dependent differential STAT3 sites directly overlapping all FOS sites from 4, 12, and 24 h post induction.

Mentions: The bias of differential STAT3 sites towards distal intergenic regions is likely to reflect the presence of a cooperating factor(s). The enrichment of AP-1 motifs within FAIRE regions (Additional file 1: Figure S1) and the identification of FOS (a component of AP-1) as a cancer signature gene linking inflammation with metabolic syndrome in ER-Src and in a fibroblastic cell line [11] suggest the importance of AP-1 factors. AP-1 is composed of FOS (FOS, FOSL1, FOSL2, FOSB) and JUN family (JUN, JUNB, JUND) members, some of which are significantly differentially expressed during transformation (Figures 3C and 5A). FOS itself is one of the most differentially expressed STAT3-dependent TFs during transformation, and STAT3 sites are present in the FOS-proximal promoter region (not shown). In addition, in a STAT3-dependent manner, FOSL2 and JUNB are activated during transformation, whereas JUND is repressed (Figure 5A and Additional file 1: Figure S12).These observations prompted us to explore FOS binding genome-wide during transformation. FOS appears to be less dependent on its canonical motif for binding than STAT3 or NF-κB but shows an equally marked preference for open chromatin (FAIRE regions) (Figure 5B). Importantly, the increase in STAT3 occupancy across the genome during transformation is closely associated with FOS binding (Figure 5C, D). Of all STAT3 sites, 82% directly overlap a FOS site, with a higher overlap within FAIRE sites (95%), which persists throughout transformation. Nearly all (88%) differential STAT3 sites are directly associated with a FOS site (Figure 5D), with only 25% associating with a differential FOS site. The regulatory regions bound by FOS at genes differentially regulated during transformation highlight its importance to many STAT3-regulated processes such as G protein-coupled receptor signaling, NF-κB signaling, cellular movement, and cell death (not shown). These observations suggest that FOS may cooperate with STAT3 in many key processes of transformation.Figure 5


STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer.

Fleming JD, Giresi PG, Lindahl-Allen M, Krall EB, Lieb JD, Struhl K - Epigenetics Chromatin (2015)

Cooperation of STAT3 and FOS sites during transformation. (A) AP-1 factors during transformation and their transcriptional dependence on STAT3. Shown are the normalized RNA expression microarray levels at 4 and 24 h post EtOH or TAM treatment in samples transfected with siSCM (scrambled control) or siSTAT3. (B) Occupancy of FOS DNA binding site motifs, as a function of increasing motif quality score, within FAIRE-seq regions and in non-FAIRE regions. (C) All FOS and STAT3 sites from each time point that directly overlap or overlap only at FAIRE sites. (D) Transformation-dependent differential STAT3 sites directly overlapping all FOS sites from 4, 12, and 24 h post induction.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Fig5: Cooperation of STAT3 and FOS sites during transformation. (A) AP-1 factors during transformation and their transcriptional dependence on STAT3. Shown are the normalized RNA expression microarray levels at 4 and 24 h post EtOH or TAM treatment in samples transfected with siSCM (scrambled control) or siSTAT3. (B) Occupancy of FOS DNA binding site motifs, as a function of increasing motif quality score, within FAIRE-seq regions and in non-FAIRE regions. (C) All FOS and STAT3 sites from each time point that directly overlap or overlap only at FAIRE sites. (D) Transformation-dependent differential STAT3 sites directly overlapping all FOS sites from 4, 12, and 24 h post induction.
Mentions: The bias of differential STAT3 sites towards distal intergenic regions is likely to reflect the presence of a cooperating factor(s). The enrichment of AP-1 motifs within FAIRE regions (Additional file 1: Figure S1) and the identification of FOS (a component of AP-1) as a cancer signature gene linking inflammation with metabolic syndrome in ER-Src and in a fibroblastic cell line [11] suggest the importance of AP-1 factors. AP-1 is composed of FOS (FOS, FOSL1, FOSL2, FOSB) and JUN family (JUN, JUNB, JUND) members, some of which are significantly differentially expressed during transformation (Figures 3C and 5A). FOS itself is one of the most differentially expressed STAT3-dependent TFs during transformation, and STAT3 sites are present in the FOS-proximal promoter region (not shown). In addition, in a STAT3-dependent manner, FOSL2 and JUNB are activated during transformation, whereas JUND is repressed (Figure 5A and Additional file 1: Figure S12).These observations prompted us to explore FOS binding genome-wide during transformation. FOS appears to be less dependent on its canonical motif for binding than STAT3 or NF-κB but shows an equally marked preference for open chromatin (FAIRE regions) (Figure 5B). Importantly, the increase in STAT3 occupancy across the genome during transformation is closely associated with FOS binding (Figure 5C, D). Of all STAT3 sites, 82% directly overlap a FOS site, with a higher overlap within FAIRE sites (95%), which persists throughout transformation. Nearly all (88%) differential STAT3 sites are directly associated with a FOS site (Figure 5D), with only 25% associating with a differential FOS site. The regulatory regions bound by FOS at genes differentially regulated during transformation highlight its importance to many STAT3-regulated processes such as G protein-coupled receptor signaling, NF-κB signaling, cellular movement, and cell death (not shown). These observations suggest that FOS may cooperate with STAT3 in many key processes of transformation.Figure 5

Bottom Line: Transient induction of the Src oncoprotein in a non-transformed breast cell line can initiate an epigenetic switch to a cancer cell via a positive feedback loop that involves activation of the signal transducer and activator of transcription 3 protein (STAT3) and NF-κB transcription factors.Interestingly, STAT3 directly regulates the expression of NFKB1, which encodes a subunit of NF-κB, and IL6, a cytokine that stimulates STAT3 activity.These observations uncover additional complexities to the inflammatory feedback loop that are likely to contribute to the epigenetic switch.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA.

ABSTRACT

Background: Transient induction of the Src oncoprotein in a non-transformed breast cell line can initiate an epigenetic switch to a cancer cell via a positive feedback loop that involves activation of the signal transducer and activator of transcription 3 protein (STAT3) and NF-κB transcription factors.

Results: We show that during the transformation process, nucleosome-depleted regions (defined by formaldehyde-assisted isolation of regulatory elements (FAIRE)) are largely unchanged and that both before and during transformation, STAT3 binds almost exclusively to previously open chromatin regions. Roughly, a third of the transformation-inducible genes require STAT3 for the induction. STAT3 and NF-κB appear to drive the regulation of different gene sets during the transformation process. Interestingly, STAT3 directly regulates the expression of NFKB1, which encodes a subunit of NF-κB, and IL6, a cytokine that stimulates STAT3 activity. Lastly, many STAT3 binding sites are also bound by FOS and the expression of several AP-1 factors is altered during transformation in a STAT3-dependent manner, suggesting that STAT3 may cooperate with AP-1 proteins.

Conclusions: These observations uncover additional complexities to the inflammatory feedback loop that are likely to contribute to the epigenetic switch. In addition, gene expression changes during transformation, whether driven by pre-existing or induced transcription factors, occur largely through pre-existing nucleosome-depleted regions.

No MeSH data available.


Related in: MedlinePlus