Limits...
FOXM1 binds directly to non-consensus sequences in the human genome.

Sanders DA, Gormally MV, Marsico G, Beraldi D, Tannahill D, Balasubramanian S - Genome Biol. (2015)

Bottom Line: Moreover, analysis of the protein interactome of wild-type versus DNA binding deficient FOXM1 shows that the reduced recruitment is not due to inhibition of protein-protein interactions.Even in FOXM1 mutants with almost complete loss of binding, the protein-protein interactions and pattern of phosphorylation are largely unaffected.These results strongly support a model whereby FOXM1 is specifically recruited to chromatin through co-factor interactions by binding directly to non-canonical DNA sequences.

View Article: PubMed Central - PubMed

Affiliation: Cancer Research UK, Cambridge Research Institute, Li Ka Shing Center, Robinson Way, Cambridge, CB2 0RE, UK. das1001@cam.ac.uk.

ABSTRACT

Background: The Forkhead (FKH) transcription factor FOXM1 is a key regulator of the cell cycle and is overexpressed in most types of cancer. FOXM1, similar to other FKH factors, binds to a canonical FKH motif in vitro. However, genome-wide mapping studies in different cell lines have shown a lack of enrichment of the FKH motif, suggesting an alternative mode of chromatin recruitment. We have investigated the role of direct versus indirect DNA binding in FOXM1 recruitment by performing ChIP-seq with wild-type and DNA binding deficient FOXM1.

Results: An in vitro fluorescence polarization assay identified point mutations in the DNA binding domain of FOXM1 that inhibit binding to a FKH consensus sequence. Cell lines expressing either wild-type or DNA binding deficient GFP-tagged FOXM1 were used for genome-wide mapping studies comparing the distribution of the DNA binding deficient protein to the wild-type. This shows that interaction of the FOXM1 DNA binding domain with target DNA is essential for recruitment. Moreover, analysis of the protein interactome of wild-type versus DNA binding deficient FOXM1 shows that the reduced recruitment is not due to inhibition of protein-protein interactions.

Conclusions: A functional DNA binding domain is essential for FOXM1 chromatin recruitment. Even in FOXM1 mutants with almost complete loss of binding, the protein-protein interactions and pattern of phosphorylation are largely unaffected. These results strongly support a model whereby FOXM1 is specifically recruited to chromatin through co-factor interactions by binding directly to non-canonical DNA sequences.

No MeSH data available.


Related in: MedlinePlus

Mutation of the FOXM1 DBD inhibits DNA binding. a Sequence alignments of the DBD for a number of Forkhead family members with the secondary structure shown schematically above. The residues used to generate point mutations are outlined in red. (*) conserved amino acids. H1-3 are α-helices, the orange arrows are β strands, and W1-2 are winged domains. b Plot showing relative change of polarization of a fluorescently-labeled (6FAM) dsDNA FKH consensus oligonucleotide upon addition of increasing concentrations of GST-FOXM1 WT or mutant DBD proteins. The FP assay provides a quantitative method and non-disruptive method to determine FOXM1 affinity for target by measuring the fluorescence polarization signals from the FAM-labeled FKH consensus (see Materials and methods). Data are plotted as % binding and show mean ± SD of triplicate experiments. (WT Kd = 1.10 ± 0.02 μM, H287A Kd = 3.04 ± 0.10 μM). c Plots showing relative luciferase activity of a 6X DB-TATA-luciferase reporter in cells transiently transfected with either WT or DBD mutant FOXM1 with the T596A mutation as a positive control. Data are shown as fold induction of luciferase activity following doxycycline induction. d Plot showing fold induction of a luciferase reporter containing a 200 bp sequence taken from the CCNB1 promoter following doxycycline induction of WT and mutant FOXM1 expression. Data represent triplicate experiments ± SD. (*) P <0.05, (**) P <0.01, (***) P <0.001
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4492089&req=5

Fig1: Mutation of the FOXM1 DBD inhibits DNA binding. a Sequence alignments of the DBD for a number of Forkhead family members with the secondary structure shown schematically above. The residues used to generate point mutations are outlined in red. (*) conserved amino acids. H1-3 are α-helices, the orange arrows are β strands, and W1-2 are winged domains. b Plot showing relative change of polarization of a fluorescently-labeled (6FAM) dsDNA FKH consensus oligonucleotide upon addition of increasing concentrations of GST-FOXM1 WT or mutant DBD proteins. The FP assay provides a quantitative method and non-disruptive method to determine FOXM1 affinity for target by measuring the fluorescence polarization signals from the FAM-labeled FKH consensus (see Materials and methods). Data are plotted as % binding and show mean ± SD of triplicate experiments. (WT Kd = 1.10 ± 0.02 μM, H287A Kd = 3.04 ± 0.10 μM). c Plots showing relative luciferase activity of a 6X DB-TATA-luciferase reporter in cells transiently transfected with either WT or DBD mutant FOXM1 with the T596A mutation as a positive control. Data are shown as fold induction of luciferase activity following doxycycline induction. d Plot showing fold induction of a luciferase reporter containing a 200 bp sequence taken from the CCNB1 promoter following doxycycline induction of WT and mutant FOXM1 expression. Data represent triplicate experiments ± SD. (*) P <0.05, (**) P <0.01, (***) P <0.001

Mentions: The Forkhead DBD [27] adopts a structure consisting of three α helices, three β sheets, and two wings with the main contact points with the DNA major groove located in helix H3. Amino acid residues involved in the base-specific contacts are highly conserved among all Forkhead members [28]. To investigate the importance of direct interaction of the FOXM1 DBD with the FKH consensus on in vitro binding, four highly conserved H3 amino acids were chosen to generate mutations that are predicted to interfere with DNA binding. (Fig. 1a; H3 residues selected for mutation are indicated with red box). Four point mutations, N283A, R286A, H287A, S290A. and one double mutant N283A/H287A (Fig. 1a) were engineered and used to generate FOXM1 DBD-GST-tagged proteins.Fig. 1


FOXM1 binds directly to non-consensus sequences in the human genome.

Sanders DA, Gormally MV, Marsico G, Beraldi D, Tannahill D, Balasubramanian S - Genome Biol. (2015)

Mutation of the FOXM1 DBD inhibits DNA binding. a Sequence alignments of the DBD for a number of Forkhead family members with the secondary structure shown schematically above. The residues used to generate point mutations are outlined in red. (*) conserved amino acids. H1-3 are α-helices, the orange arrows are β strands, and W1-2 are winged domains. b Plot showing relative change of polarization of a fluorescently-labeled (6FAM) dsDNA FKH consensus oligonucleotide upon addition of increasing concentrations of GST-FOXM1 WT or mutant DBD proteins. The FP assay provides a quantitative method and non-disruptive method to determine FOXM1 affinity for target by measuring the fluorescence polarization signals from the FAM-labeled FKH consensus (see Materials and methods). Data are plotted as % binding and show mean ± SD of triplicate experiments. (WT Kd = 1.10 ± 0.02 μM, H287A Kd = 3.04 ± 0.10 μM). c Plots showing relative luciferase activity of a 6X DB-TATA-luciferase reporter in cells transiently transfected with either WT or DBD mutant FOXM1 with the T596A mutation as a positive control. Data are shown as fold induction of luciferase activity following doxycycline induction. d Plot showing fold induction of a luciferase reporter containing a 200 bp sequence taken from the CCNB1 promoter following doxycycline induction of WT and mutant FOXM1 expression. Data represent triplicate experiments ± SD. (*) P <0.05, (**) P <0.01, (***) P <0.001
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4492089&req=5

Fig1: Mutation of the FOXM1 DBD inhibits DNA binding. a Sequence alignments of the DBD for a number of Forkhead family members with the secondary structure shown schematically above. The residues used to generate point mutations are outlined in red. (*) conserved amino acids. H1-3 are α-helices, the orange arrows are β strands, and W1-2 are winged domains. b Plot showing relative change of polarization of a fluorescently-labeled (6FAM) dsDNA FKH consensus oligonucleotide upon addition of increasing concentrations of GST-FOXM1 WT or mutant DBD proteins. The FP assay provides a quantitative method and non-disruptive method to determine FOXM1 affinity for target by measuring the fluorescence polarization signals from the FAM-labeled FKH consensus (see Materials and methods). Data are plotted as % binding and show mean ± SD of triplicate experiments. (WT Kd = 1.10 ± 0.02 μM, H287A Kd = 3.04 ± 0.10 μM). c Plots showing relative luciferase activity of a 6X DB-TATA-luciferase reporter in cells transiently transfected with either WT or DBD mutant FOXM1 with the T596A mutation as a positive control. Data are shown as fold induction of luciferase activity following doxycycline induction. d Plot showing fold induction of a luciferase reporter containing a 200 bp sequence taken from the CCNB1 promoter following doxycycline induction of WT and mutant FOXM1 expression. Data represent triplicate experiments ± SD. (*) P <0.05, (**) P <0.01, (***) P <0.001
Mentions: The Forkhead DBD [27] adopts a structure consisting of three α helices, three β sheets, and two wings with the main contact points with the DNA major groove located in helix H3. Amino acid residues involved in the base-specific contacts are highly conserved among all Forkhead members [28]. To investigate the importance of direct interaction of the FOXM1 DBD with the FKH consensus on in vitro binding, four highly conserved H3 amino acids were chosen to generate mutations that are predicted to interfere with DNA binding. (Fig. 1a; H3 residues selected for mutation are indicated with red box). Four point mutations, N283A, R286A, H287A, S290A. and one double mutant N283A/H287A (Fig. 1a) were engineered and used to generate FOXM1 DBD-GST-tagged proteins.Fig. 1

Bottom Line: Moreover, analysis of the protein interactome of wild-type versus DNA binding deficient FOXM1 shows that the reduced recruitment is not due to inhibition of protein-protein interactions.Even in FOXM1 mutants with almost complete loss of binding, the protein-protein interactions and pattern of phosphorylation are largely unaffected.These results strongly support a model whereby FOXM1 is specifically recruited to chromatin through co-factor interactions by binding directly to non-canonical DNA sequences.

View Article: PubMed Central - PubMed

Affiliation: Cancer Research UK, Cambridge Research Institute, Li Ka Shing Center, Robinson Way, Cambridge, CB2 0RE, UK. das1001@cam.ac.uk.

ABSTRACT

Background: The Forkhead (FKH) transcription factor FOXM1 is a key regulator of the cell cycle and is overexpressed in most types of cancer. FOXM1, similar to other FKH factors, binds to a canonical FKH motif in vitro. However, genome-wide mapping studies in different cell lines have shown a lack of enrichment of the FKH motif, suggesting an alternative mode of chromatin recruitment. We have investigated the role of direct versus indirect DNA binding in FOXM1 recruitment by performing ChIP-seq with wild-type and DNA binding deficient FOXM1.

Results: An in vitro fluorescence polarization assay identified point mutations in the DNA binding domain of FOXM1 that inhibit binding to a FKH consensus sequence. Cell lines expressing either wild-type or DNA binding deficient GFP-tagged FOXM1 were used for genome-wide mapping studies comparing the distribution of the DNA binding deficient protein to the wild-type. This shows that interaction of the FOXM1 DNA binding domain with target DNA is essential for recruitment. Moreover, analysis of the protein interactome of wild-type versus DNA binding deficient FOXM1 shows that the reduced recruitment is not due to inhibition of protein-protein interactions.

Conclusions: A functional DNA binding domain is essential for FOXM1 chromatin recruitment. Even in FOXM1 mutants with almost complete loss of binding, the protein-protein interactions and pattern of phosphorylation are largely unaffected. These results strongly support a model whereby FOXM1 is specifically recruited to chromatin through co-factor interactions by binding directly to non-canonical DNA sequences.

No MeSH data available.


Related in: MedlinePlus