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Epigenetic silencing of the XAF1 gene is mediated by the loss of CTCF binding.

Victoria-Acosta G, Vazquez-Santillan K, Jimenez-Hernandez L, Muñoz-Galindo L, Maldonado V, Martinez-Ruiz GU, Melendez-Zajgla J - Sci Rep (2015)

Bottom Line: Here, we demonstrate that CTCF interacts with the XAF1 promoter in vivo in a methylation-sensitive manner.In addition, the absence of CTCF in the XAF1 promoter inhibits transcriptional activation induced by well-known apoptosis activators.We report for the first time that epigenetic silencing of the XAF1 gene is a consequence of the loss of CTCF binding.

View Article: PubMed Central - PubMed

Affiliation: Functional Cancer Genomics Laboratory, National Institute of Genomic Medicine, Mexico D.F., 14610, Mexico.

ABSTRACT
XAF1 is a tumour suppressor gene that compromises cell viability by modulating different cellular events such as mitosis, cell cycle progression and apoptosis. In cancer, the XAF1 gene is commonly silenced by CpG-dinucleotide hypermethylation of its promoter. DNA demethylating agents induce transcriptional reactivation of XAF1, sensitizing cancer cells to therapy. The molecular mechanisms that mediate promoter CpG methylation have not been previously studied. Here, we demonstrate that CTCF interacts with the XAF1 promoter in vivo in a methylation-sensitive manner. By transgene assays, we demonstrate that CTCF mediates the open-chromatin configuration of the XAF1 promoter, inhibiting both CpG-dinucleotide methylation and repressive histone posttranslational modifications. In addition, the absence of CTCF in the XAF1 promoter inhibits transcriptional activation induced by well-known apoptosis activators. We report for the first time that epigenetic silencing of the XAF1 gene is a consequence of the loss of CTCF binding.

No MeSH data available.


Related in: MedlinePlus

Epigenetic regulation by CTCF of the XAF1 promoter.(a) Methylation of the CTCF binding site in the XAF1 promoter, as occurs in cancer, inhibits its recognition by CTCF. This enriches repressive histone posttranslational modifications, contributing to XAF1 transcriptional silencing. (b) In demethylating conditions, CTCF is able to interact with its cognate DNA-binding site, inhibiting both CpG-dinucleotide methylation and repressive histone posttranslational modifications such as H3K9-2me. After treatment with transcriptional activators such as TNF-α or IFN-α, the association between CTCF and nucleophosmin/B23 is induced, allowing XAF1 promoter anchorage to the nuclear matrix and inducing transcriptional activation. Additionally, several subunits of CTCF could bridge additional genomic regions from interchromosomal or intrachromosomal locations to the same genomic anchor to which the XAF1 promoter is attached. The inhibition of CpG-dinucleotide methylation could be mediated by the inhibitory action of PARP-1 on DNMT1.
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f7: Epigenetic regulation by CTCF of the XAF1 promoter.(a) Methylation of the CTCF binding site in the XAF1 promoter, as occurs in cancer, inhibits its recognition by CTCF. This enriches repressive histone posttranslational modifications, contributing to XAF1 transcriptional silencing. (b) In demethylating conditions, CTCF is able to interact with its cognate DNA-binding site, inhibiting both CpG-dinucleotide methylation and repressive histone posttranslational modifications such as H3K9-2me. After treatment with transcriptional activators such as TNF-α or IFN-α, the association between CTCF and nucleophosmin/B23 is induced, allowing XAF1 promoter anchorage to the nuclear matrix and inducing transcriptional activation. Additionally, several subunits of CTCF could bridge additional genomic regions from interchromosomal or intrachromosomal locations to the same genomic anchor to which the XAF1 promoter is attached. The inhibition of CpG-dinucleotide methylation could be mediated by the inhibitory action of PARP-1 on DNMT1.

Mentions: It has been described that the nuclear matrix plays an important role in the regulation of gene transcription. Chromatin is anchored by short stretches of DNA sequences called matrix attachment regions (MARs). MARs range in size from 100 to 2000 bp and are rich in AT dinucleotide pairs and repetitive sequences. Both chromatin loop formation and the transcriptional activation of genes surrounded by MARs are dependent on nuclear matrix anchorage55. This is explainable by the fact that transcriptional factors are present in the nuclear matrix56. CTCF associates with the nuclear matrix5758 and mediates the anchoring of DNA sequences to it, as observed in the 5′-HS4 chicken β-globin insulator58. In addition, the association of CTCF with the nuclear matrix depends on nucleophosmin/B2359. However, it has been observed that IFN-γ induces transcriptional activation of major histocompatibility complex genes, which coincides with the reorganization of chromatin loops60. Interestingly, DNA anchorage to the nuclear matrix after IFN-γ exposure was associated with CTCF binding sites60. Therefore, CTCF reconfigures genomic regions by forming loops that affect the transcriptional gene landscape. In the present paper, we demonstrate that in cancer cells, CTCF is unable to associate with its cognate DNA-binding site in the XAF1 promoter if it is methylated (Fig. 7a), thus effectively rendering it unresponsive to well-known activators (Fig. 7a). However, after demethylating the cognate site, CTCF is now able to associate with the XAF1 promoter to enhance transcriptional activation (Fig. 2). One intriguing possibility is that CTCF could be able to attract DNA to the nuclear matrix, mediating faster chromatin loop formation in the nuclear matrix after exposure to exogenous stimuli. Although not tested, we envision that CTCF could be able to attract the XAF1 promoter to the nuclear matrix by its association with nucleophosmin/B23, thereby inducing both chromatin loop formation and transcriptional activation of the XAF1 gene (Fig. 7b). In cancer, this putative mechanism would not occur due to the absence of CTCF in its DNA-binding site via a methylation-sensitive mechanism (Fig. 7a).


Epigenetic silencing of the XAF1 gene is mediated by the loss of CTCF binding.

Victoria-Acosta G, Vazquez-Santillan K, Jimenez-Hernandez L, Muñoz-Galindo L, Maldonado V, Martinez-Ruiz GU, Melendez-Zajgla J - Sci Rep (2015)

Epigenetic regulation by CTCF of the XAF1 promoter.(a) Methylation of the CTCF binding site in the XAF1 promoter, as occurs in cancer, inhibits its recognition by CTCF. This enriches repressive histone posttranslational modifications, contributing to XAF1 transcriptional silencing. (b) In demethylating conditions, CTCF is able to interact with its cognate DNA-binding site, inhibiting both CpG-dinucleotide methylation and repressive histone posttranslational modifications such as H3K9-2me. After treatment with transcriptional activators such as TNF-α or IFN-α, the association between CTCF and nucleophosmin/B23 is induced, allowing XAF1 promoter anchorage to the nuclear matrix and inducing transcriptional activation. Additionally, several subunits of CTCF could bridge additional genomic regions from interchromosomal or intrachromosomal locations to the same genomic anchor to which the XAF1 promoter is attached. The inhibition of CpG-dinucleotide methylation could be mediated by the inhibitory action of PARP-1 on DNMT1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595840&req=5

f7: Epigenetic regulation by CTCF of the XAF1 promoter.(a) Methylation of the CTCF binding site in the XAF1 promoter, as occurs in cancer, inhibits its recognition by CTCF. This enriches repressive histone posttranslational modifications, contributing to XAF1 transcriptional silencing. (b) In demethylating conditions, CTCF is able to interact with its cognate DNA-binding site, inhibiting both CpG-dinucleotide methylation and repressive histone posttranslational modifications such as H3K9-2me. After treatment with transcriptional activators such as TNF-α or IFN-α, the association between CTCF and nucleophosmin/B23 is induced, allowing XAF1 promoter anchorage to the nuclear matrix and inducing transcriptional activation. Additionally, several subunits of CTCF could bridge additional genomic regions from interchromosomal or intrachromosomal locations to the same genomic anchor to which the XAF1 promoter is attached. The inhibition of CpG-dinucleotide methylation could be mediated by the inhibitory action of PARP-1 on DNMT1.
Mentions: It has been described that the nuclear matrix plays an important role in the regulation of gene transcription. Chromatin is anchored by short stretches of DNA sequences called matrix attachment regions (MARs). MARs range in size from 100 to 2000 bp and are rich in AT dinucleotide pairs and repetitive sequences. Both chromatin loop formation and the transcriptional activation of genes surrounded by MARs are dependent on nuclear matrix anchorage55. This is explainable by the fact that transcriptional factors are present in the nuclear matrix56. CTCF associates with the nuclear matrix5758 and mediates the anchoring of DNA sequences to it, as observed in the 5′-HS4 chicken β-globin insulator58. In addition, the association of CTCF with the nuclear matrix depends on nucleophosmin/B2359. However, it has been observed that IFN-γ induces transcriptional activation of major histocompatibility complex genes, which coincides with the reorganization of chromatin loops60. Interestingly, DNA anchorage to the nuclear matrix after IFN-γ exposure was associated with CTCF binding sites60. Therefore, CTCF reconfigures genomic regions by forming loops that affect the transcriptional gene landscape. In the present paper, we demonstrate that in cancer cells, CTCF is unable to associate with its cognate DNA-binding site in the XAF1 promoter if it is methylated (Fig. 7a), thus effectively rendering it unresponsive to well-known activators (Fig. 7a). However, after demethylating the cognate site, CTCF is now able to associate with the XAF1 promoter to enhance transcriptional activation (Fig. 2). One intriguing possibility is that CTCF could be able to attract DNA to the nuclear matrix, mediating faster chromatin loop formation in the nuclear matrix after exposure to exogenous stimuli. Although not tested, we envision that CTCF could be able to attract the XAF1 promoter to the nuclear matrix by its association with nucleophosmin/B23, thereby inducing both chromatin loop formation and transcriptional activation of the XAF1 gene (Fig. 7b). In cancer, this putative mechanism would not occur due to the absence of CTCF in its DNA-binding site via a methylation-sensitive mechanism (Fig. 7a).

Bottom Line: Here, we demonstrate that CTCF interacts with the XAF1 promoter in vivo in a methylation-sensitive manner.In addition, the absence of CTCF in the XAF1 promoter inhibits transcriptional activation induced by well-known apoptosis activators.We report for the first time that epigenetic silencing of the XAF1 gene is a consequence of the loss of CTCF binding.

View Article: PubMed Central - PubMed

Affiliation: Functional Cancer Genomics Laboratory, National Institute of Genomic Medicine, Mexico D.F., 14610, Mexico.

ABSTRACT
XAF1 is a tumour suppressor gene that compromises cell viability by modulating different cellular events such as mitosis, cell cycle progression and apoptosis. In cancer, the XAF1 gene is commonly silenced by CpG-dinucleotide hypermethylation of its promoter. DNA demethylating agents induce transcriptional reactivation of XAF1, sensitizing cancer cells to therapy. The molecular mechanisms that mediate promoter CpG methylation have not been previously studied. Here, we demonstrate that CTCF interacts with the XAF1 promoter in vivo in a methylation-sensitive manner. By transgene assays, we demonstrate that CTCF mediates the open-chromatin configuration of the XAF1 promoter, inhibiting both CpG-dinucleotide methylation and repressive histone posttranslational modifications. In addition, the absence of CTCF in the XAF1 promoter inhibits transcriptional activation induced by well-known apoptosis activators. We report for the first time that epigenetic silencing of the XAF1 gene is a consequence of the loss of CTCF binding.

No MeSH data available.


Related in: MedlinePlus