The CTCF insulator protein forms an unusual DNA structure
© MacPherson and Sadowski; licensee BioMed Central Ltd. 2010
Received: 9 August 2010
Accepted: 21 December 2010
Published: 21 December 2010
The CTCF insulator protein is a highly conserved zinc finger protein that has been implicated in many aspects of gene regulation and nuclear organization. The protein has been hypothesized to organize the human genome by forming DNA loops.
In this paper, we report biochemical evidence to support the role for CTCF in forming DNA loops. We have measured DNA bending by CTCF at the chicken HS4 β-globin FII insulator element in vitro and have observed a unique DNA structure with aberrant electrophoretic mobility which we believe to be a DNA loop. CTCF is able to form this unusual DNA structure at two other binding sites: the c-myc P2 promoter and the chicken F1 lysozyme gene silencer. We also demonstrate that the length though not the sequence of the DNA downstream of the binding site is important for the ability of CTCF to form this unusual DNA structure. We hypothesize that a single CTCF protein molecule is able to act as a "looper" possibly through the use of several of its zinc fingers.
CTCF is able to form an unusual DNA structure through the zinc finger domain of the protein. This unusual DNA structure is formed in a directional manner by the CTCF protein. The findings described in this paper suggest mechanisms by which CTCF is able to form DNA loops, organize the mammalian genome and function as an insulator protein.
The CTCF protein, formerly known as NeP1, is an eleven zinc finger protein that is highly conserved from fruit flies to man. The protein was first identified in the chicken as a negative regulator of the c-myc oncogene  and the lysozyme gene . The CTCF protein has a central zinc finger domain that shows 100% amino acid conservation between the chicken form and the human form of the protein. This central zinc finger domain is flanked by an NH2-terminal domain and a carboxy-terminal domain, both of which have an unknown structure. The CTCF protein has the ability to bind to different CTCF consensus sites by using different combinations of its eleven zinc fingers and is therefore frequently described as a multivalent protein . These binding studies were performed by deleting different CTCF zinc fingers and observing the effects the deletions had on the ability of the protein to bind to different consensus sites [4–8]. A more recent study has determined that CTCF uses 4 to 5 core zinc fingers to bind to CTCF consensus sites . Recent whole genome analyses of the CTCF binding sites in Drosophila and human cell lines support the idea that CTCF protein binds to a single consensus sequence [10, 11].
The molecular mechanisms regulating the many diverse functions of CTCF are in part governed by the posttranslational modification of the protein. Phosphorylation of CTCF has been shown to relieve its repressive activity at the c-myc P2 promoter [12, 13] and poly-(ADP)-ribosylation has been implicated in its role as an insulator protein . In addition, we have recently shown that the posttranslational modification of CTCF by the small ubiquitin-like modifier proteins (SUMOs) contributes to its role as a transcriptional repressor at the c-myc P2 promoter .
CTCF is implicated in a diverse number of biological roles including gene repression, gene activation, chromatin insulator function, X-chromosome inactivation and the maintenance of genomic imprinting [3, 16]. Recently, CTCF has been found to play a role in the organization of the mammalian genome and has been implicated in the genomic organization of the β-globin locus [17, 18], the H19/Igf2 imprinting control region [19–23], the major histocompatibility complex class II genes  and the cystic fibrosis transmembrane conductance regulator gene locus . The CTCF protein binds to approximately 15 000 sites in the human genome [11, 26–29] and is hypothesized to organize the genome by forming DNA loops [30, 31]. The evidence of CTCF's ability to loop DNA is the result of in vivo chromatin conformation capture assays (3C), and chromatin immunoprecipitation. The CTCF DNA binding site has been shown to be necessary for long-range chromatin interactions at the H19/IGF2 imprinting control region  and the knockdown of CTCF protein in chicken cells disrupts long-range chromatin interactions at the β-globin locus . It has also been suggested that CTCF forms loops in DNA by tethering DNA to the nucleolus through its interaction with the protein nucleophosmin .
Since CTCF has previously been shown to bend DNA , we asked whether its SUMOylation altered its bending ability. In the course of answering this question, we obtained some unexpected results. Although SUMOylation had no effect on CTCF's ability to bend DNA, we found that the CTCF protein does not act as a typical DNA bending protein. The CTCF protein forms an unusual structure in DNA that we believe to be a DNA loop. This unusual DNA structure forms at all three CTCF binding sites tested: the chicken β-globin FII insulator, the chicken lysozyme gene F1 silencer element and the human c-myc P2 promoter. We find that the SUMOylation of CTCF does not affect its ability to form this unusual DNA structure. We discuss the possible mechanisms of DNA looping by CTCF and their roles in genome organization.
The CTCF insulator protein forms an unusual directional DNA structure
In a typical DNA bending experiment, the DNA-protein complex has the slowest mobility when the DNA binding site is centrally located. Conversely, the fastest mobility occurs when the DNA binding site is located near either end of the probe. Therefore, we expected that the complexes formed by both the MluI probe and the BamHI probe would migrate more quickly than the EcoRV fragment containing the CTCF-binding site in the middle of the fragment (See Figure 1C). We tested the ability of CTCF to bend DNA using the well-characterized chicken HS4 β-globin FII insulator element. As expected, when the FII site was located near the right end of the probe (digestion with MluI), the complex migrated more quickly in the native gel than when the site was in the middle of the fragment (see Figure 1B, left). As the FII site was permuted to a more central location (digestion with BglII, NheI, SpeI and EcoRV), the mobility of the CTCF-probe complex decreased, as predicted. However, we expected that the probes generated by digestion with SmaI, SspI, KpnI and BamHI would yield complexes that would migrate progressively more quickly through the gel, mirroring the permuted probes on the opposite side of the EcoRV site as is usual in DNA bending assays. Instead, we saw even more slowly migrating complexes. We wondered if these results could be explained by CTCF binding to a second site in the pBEND2 probe itself. Therefore, we generated a probe that does not contain the FII CTCF binding site by digesting the parent pBEND2 plasmid with the enzyme BamHI. We observed no CTCF-DNA complexes with this substrate, indicating that CTCF does not bind DNA from the parent pBEND2 plasmid in the absence of the FII insulator site (data not shown).
Our original interest was to determine whether the SUMOylation of CTCF affected its ability to bend DNA; therefore, we SUMOylated CTCF quantitatively in vitro with SUMO1 . When SUMOylated CTCF was used in the EMSA assay, the DNA bending pattern was identical to that seen using unmodified CTCF (see Figure 1B, right). Hence, the modification of the CTCF protein by SUMO did not affect its ability to deform DNA containing a CTCF binding site. The relative electrophoretic mobility (μ) of a CTCF-probe complex was calculated as the mobility of the complex divided by the mobility of the free probe. The relative mobilities of the complexes were plotted as a function of the position (bp) from the middle of the left EcoRV site to the middle of the restriction enzyme used to generate the probe (Figure 1E). The graphs were fitted with the best fit polynomial curve using Microsoft Excel. Two CTCF DNA complexes were observed in these experiments. The top complex on the electrophoretic mobility gels corresponds to the probe bound by full length CTCF, whereas the bottom complex on the gels corresponds to the probe bound by a C-terminally truncated form of CTCF caused by premature termination during in vitro translation. The major SUMOylation site in CTCF is found in the C-terminal domain of the protein . The polynomial curves fitting the relative mobility of the top complexes of SUMOylated and unmodified CTCF are distinct, thus indicating that CTCF was efficiently SUMOylated due to the slower migration of the SUMOylated complexes (Figure 1E, bottom two curves). Conversely, when the protein is C-terminally truncated the bottom complexes exhibit similar relative electrophoretic mobilities since the C-terminally truncated CTCF is not being efficiently SUMOylated (Figure 1E, top two curves). The abnormal electrophoretic mobility exhibited by CTCF during circular permutation creates an unusual polynomial curve. Since we cannot extrapolate to the position at which the curve reaches a maximum relative mobility it was difficult to determine the centre of the CTCF-induced bend (see Figure 1C bottom). Likewise, we were unable to determine the possible differences in the bend angles induced by unmodified and SUMOylated forms of CTCF. The CTCF-induced bend is not a typical asymmetrical DNA bend (see Figure 1D). We refer to the DNA structure formed upon CTCF binding to the β-globin FII insulator element as an unusual DNA structure.
Although there are several explanations for the altered DNA structure, we believe that the unusual DNA structure formed by CTCF in our bending experiments is a small DNA loop. Some of the alternative models are dealt with in the Discussion.
The CTCF insulator protein forms a directional unusual DNA structure at two other CTCF binding sites
CTCF-DNA complexes do not involve intermolecular interactions between DNA molecules
The zinc finger domain of CTCF is sufficient for the formation of the unusual DNA structure
The formation of the unusual DNA structure by CTCF is not dependent on a specific DNA sequence downstream of the CTCF binding site
CTCF phases DNA in a manner dependent upon the orientation of the CTCF binding site
We believe that the complex multiphasic mobility pattern is due to a CTCF-induced directional bend towards the kinetoplast DNA in addition to an unusual DNA structure formed towards the PvuII restriction enzyme site. These complex DNA conformations may not phase because the unusual DNA structure is not a fixed structure. When the phasing analysis was done in the forward orientation, the unusual DNA structure may have been unable to form due to the topological constraints posed by the bent kinetoplast DNA. Therefore, the CTCF-induced bend alone is responsible for the DNA phasing.
In this paper we have presented biochemical evidence that shows CTCF is able to form an unusual DNA structure. We believe that this DNA structure is a CTCF-induced DNA loop and that CTCF acts as a DNA looping protein. We show that this unusual DNA structure is formed at the chicken β-globin FII insulator element and that its formation depends upon the orientation of the FII site. The unusual DNA structure also forms at two other well-characterized CTCF binding sites: the c-myc P2 promoter and the chicken lysozyme gene F1 silencer element. These results were unexpected since Arnold et al.  had previously characterized CTCF (formerly named NeP1) as a DNA bending protein. However, there are several differences between our circular permutation assay and those of these authors. We examined the effect of CTCF protein only on a circular permutation substrate that contained a single CTCF binding consensus sequence. Arnold et al.  examined a complex protein mixture of CTCF (NeP1), TR, and RXR in their circular permutation assays. The large number of protein-DNA complexes formed in their mobility shift assays may have obscured the aberrant electrophoretic mobilities of the CTCF-probe complexes alone. Careful re-examination of their data shows it to be consistent with our experiments.
There are several alternative models that could account for the unusual DNA topology caused by CTCF. One possible explanation might be that CTCF induces formation of single-stranded regions of DNA downstream of the FII binding site. However, when we probed the altered DNA structure with potassium permanganate or diethyl pyrocarbonate, the presence of single stranded DNA was not detected by DNA footprinting (not shown). Therefore, we conclude that the altered DNA structure is therefore not caused by melting of the DNA.
A second explanation is that the FII binding site nucleates the binding of multiple CTCF molecules downstream of the FII binding site. For example, multiple RecA protein molecules nucleate onto single stranded DNA in a unidirectional manner . Interestingly, a C-terminally truncated form of CTCF is present in the in vitro translation reaction. This complex was identified using "supershift" experiments in the presence of a C-terminal-specific antibody (data not shown). If the complexes formed at the FII binding site are caused by CTCF nucleation, we might have expected to detect a mixed protein-DNA complex containing both the truncated and full-length CTCF. Since we do not detect this mixed complex, we conclude that the CTCF-DNA complexes contain a single molecule of CTCF or its C-terminal truncation.
It is possible that the nucleation of other proteins present in the reticulocyte lysate accounts for the aberrant mobility of the CTCF-probe complexes. However, we note that the purified GST-zinc finger domain of CTCF exhibits the same overall electrophoretic mobility pattern as the in vitro translated CTCF lysates. The presence of such proteins in the GST-zinc finger protein purified from E. coli is unlikely.
A further possible explanation for the aberrant DNA structure is the wrapping of DNA around CTCF. Circular permutation experiments using the mitochondrial protein mtTF1, a DNA wrapping protein, show a protein-DNA mobility pattern similar to those observed in classical circular permutation experiments . While these other models may provide an explanation for the abnormal DNA structure formed by CTCF, the DNA looping model is the strongest explanation and fits well with the in vivo data describing CTCF's role in mediating long-range chromatin interactions.
Our bending results provide insight into the molecular mechanisms of the CTCF protein. It is of interest to note that the unusual DNA structure formed by CTCF is directional. CTCF uses DNA downstream of the binding site to form the structure while it does not appear to use DNA upstream of the binding site. Interestingly, the Drosophila insulator protein Su (Hw), which is also a zinc finger protein that binds to the gypsy insulator element, has also been studied in circular permutation experiments. Like CTCF, Su(Hw) protein is believed to contain twelve zinc fingers in a central protein domain and like CTCF, the Su(Hw) protein bends DNA in an unusual manner . These authors attributed the aberrant behaviour to either an increase in flexibility or a melting of the DNA by Su(Hw).
In our experiments, the zinc finger domain of CTCF is sufficient for both the bending and looping activities. Arnold et al.  used extracts from mammalian cells transfected with a CTCF zinc finger domain construct to conclude that CTCF's DNA bending ability resided outside the zinc finger domain of the protein. It is conceivable that our results differ from those of Arnold et al. since we used a partially purified zinc finger domain instead of a complex cell lysate. The Su(Hw) protein needs its zinc fingers to bind DNA but requires the presence of its acidic C-terminal domain for DNA bending. This suggests that the mechanism by which Su(Hw) forms an unusual DNA structure may differ from that used by CTCF.
We determined that the nucleotide sequence of the DNA outside the FII binding site is not critical for the formation of the DNA loop. We speculate that these results could provide mechanistic insight into the ability of CTCF to organize the human genome. If CTCF were to bind specifically to a core consensus sequence it might then make a DNA loop using any nucleotide sequence. The protein might conceivably be able to make a DNA loop at any of the 15 000 sites in the genome to which it has been shown to bind.
Previous studies have attributed CTCF's ability to bind to different CTCF consensus sites to its use of different combinations of its eleven zinc fingers . These studies were performed by deleting different CTCF zinc fingers and observing the effects the deletions had on the ability of the protein to bind to different consensus sites [4–8]. A more recent study has determined that CTCF uses 4 to 5 core zinc fingers (zinc fingers 4-8) that are critical to providing high affinity binding to a 12bp core sequence in CTCF consensus sites . Recent whole genome analyses of CTCF binding sites in Drosophila and human cell lines support the idea that CTCF protein binds to a single consensus sequence [10, 11].
If CTCF needs only 4 to 5 zinc fingers to bind to consensus sites (Figure 8), then the remaining six or seven zinc fingers might be free to bind DNA non-specifically to form a loop. A crystal structure of CTCF in the presence of DNA would add significant insight into its ability to form a DNA loop and its combinatorial use of zinc finger during DNA binding. The analysis of CTCF's DNA binding ability by surface plasmon resonance has shown that the binding of CTCF to DNA is a two-stage reaction . It is possible that the first stage of the binding reaction is due to the initial binding of CTCF to the consensus site followed by a second binding step whereby CTCF forms a DNA loop. Alternately, the initial binding may non-specific followed by binding to the consensus site.
The CTCF protein has been previously shown by other workers to act as a DNA bridging protein . In electrophoretic mobility shift assays, CTCF was able to form an intermolecular complex between two probes that contained target site 3 or 4, respectively, from the mouse IGF2/H19 imprinting control region. We were unable to detect bridged complexes between probes containing the FII insulator element and the c-myc P2 promoter. It is possible that CTCF acts in a different manner when binding to the IGF2/H19 ICR than at other CTCF consensus sites. It is also possible that our EMSA experiments did not contain sufficient amounts of CTCF protein to overcome the necessary entropic costs of forming bridged, cross-joined or sandwiched structures. Several proteins are known to form these DNA structures; however, sufficiently high binding energy is needed to achieve these DNA topologies. The lac repressor protein is known to form such structures only when the protein is present at sufficiently high concentrations . It is difficult to compare the amount of CTCF protein generated in our in vitro translation reaction to those obtained by Pant et al. for use in their gel shift experiments .
The experiments presented in our paper add biochemical evidence to CTCF's loop-forming ability. DNA looping is a central phenomenon in gene regulation in both prokaryotes and eukaryotes. There are several well-characterized models of DNA looping in the control of prokaryotic gene expression including the E. coli lac and deo operons as well as the integrase protein of the bacteriophage lambda [38, 39]. In all of these models protein:protein interactions either through the homodimerization of looping proteins or the heterodimerization of several looping proteins are required for DNA loop formation. The mechanism of CTCF DNA loop formation that we observed seems to be somewhat different. We propose a model of CTCF insulator function whereby a single CTCF protein molecule could form a DNA loop in an orientation dependent manner instead of the dimerization of two CTCF protein molecules or a bridging of two DNA molecules mediated by CTCF. By extension, a CTCF-dependent insulator element is a cis regulatory element that is the site of a DNA loop and the enhancer blocking ability of a DNA insulator function could be the result of the formation of the loop. It is interesting to note that Kyrchanova et al.  recently demonstrated that functional pairing interactions between Drosophila insulators was an orientation dependent interaction. Their findings fit nicely with our discovery of the orientation dependence of the unusual DNA structure formed by CTCF.
The results we have presented in this paper are a starting point towards a greater understanding of CTCF's DNA looping ability and the molecular mechanisms regulating this ability.
We conclude that the CTCF insulator protein is able to form an unusual DNA structure in vitro that we believe is a DNA loop. This unusual DNA structure is formed at several CTCF binding sites and is formed in a directional manner. The CTCF zinc finger domain is sufficient for the formation of the unusual DNA structure. CTCF uses DNA downstream of the CTCF binding site to form the unusual DNA structure but the sequence of this downstream DNA does not affect the formation of the structure. When the DNA sequence downstream of CTCF is topologically constrained, the unusual DNA structure is unable to form and CTCF acts as a DNA bending protein. The results of this study could provide mechanistic insights into CTCF's ability to mediate long-range chromatin interactions and form DNA loops.
Plasmids and Cloning
Oligonucleotides used in this study.
pK FII phasing vectors
pK FII phasing vectors
[tcgac]ttcctattatcgtccgaactccgaaccctctgtcttgtactgcc tggcacagcactagaggaatccctatcgttctggcatcaaccatgatt atacgctgctcggaatg[a]
[agctt]cattccgagcagcgtataatcatggttgatgccagaacgata gggattcctctagtgctgtgccaggcagtacaagacagagggttcgg agttcggacgataataggaa[g]
[tcgac]gattctgacagtgagatctgtgagatttcagttcgcggatca ccgtacttgatcccaggctaagacggaaagtaaggaaacgcctgct ccagctgtaccggtccccgta[a]
[agctt]tacggggaccggtacagctggagcaggcgtttccttactttc cgtcttagcctgggatcaagtacggtgatccgcgaactgaaatctca cagatctcactgtcagaatc[g]
To construct the shuffled clones, we randomized the original 115 nt DNA sequence from the SalI restriction enzyme site to the HindIII restriction enzyme site in the pBEND2 vector using the online Bioinformatics tool, the Sequence Manipulation Suite . The shuffled oligonucleotides pr2232 and pr2233 (Table 1) were annealed and phosphorylated using polynucleotide kinase (New England Biolabs). The primers were engineered to contain SalI and HindIII restriction enzyme sites for ligation into the SalI and HindIII sites in the pBEND2-FII-Forward or Reverse vectors. The result was the formation of the plasmids pBEND2-FII-Forward or Reverse-Shuffled in which the tandemly repeated restriction enzyme sites to the right of the XbaI site were replaced with the shuffled sequence. The random clones were constructed in a similar manner except that a random 115 nt DNA sequence of 50% A+T and 50% G+C base composition was generated using the Sequence Manipulation Suite . The random oligonucleotides pr2228 and pr2229 were cloned into pBEND2-FII-Forward or Reverse to form the plasmids pBEND2-FII-Forward or Reverse-Random as described above (see Figure 6A).
The phasing clones were constructed by excising the 156 bp BamHI-BamHI DNA fragment from the plasmids pK10, pK12, pK14, pK16, pK18 and pK20 and replacing it with annealed oligonucleotides that contained the chicken β-globin FII HS4 insulator element cut with BamHI (see Table 1 and Figure 7A). Clones in both orientations were isolated.
Purification of the zinc finger domain of CTCF
The zinc finger domain of CTCF was amplified by PCR from a mouse CTCF cDNA clone using the primers pr1964 (BamHI) and pr1965 (XhoI) (Table 1) and was cloned into the BamHI and XhoI restriction sites in the vector pGEX4T-1 (GE Healthcare) to create an NH2-terminal glutathione S-transferase (GST) fusion protein. The GST-fusion of the zinc finger domain was purified as previously described . The purity of the GST-ZnF-CTCF domain was determined to be about 37% pure by scanning a Coomassie stained SDS-PAGE using the program ImageJ.
In vitro transcription/translation of CTCF and in vitro SUMOylation
Full length CTCF was prepared by in vitro transcription/translation as described previously. The full length CTCF was posttranslationally modified by SUMO 1 in vitro using a SUMOylation control kit purchased from LAE Biotech International (catalogue no. K007) as described with the following modifications . Briefly, 2 μL of in vitro translated CTCF were incubated with the recommended amounts of E1 and E2 enzymes and 20 mM ATP with or without SUMO 1 protein in a 12 μL reaction mixture for one hour at 37°C. The SUMOylation of CTCF was quantitative as shown previously .
Circular Permutation Assay
Probes were prepared from the pBEND2 clones by digesting plasmid DNA with the following restriction enzymes: MluI, BglII, NheI, SpeI, EcoRV, SmaI, SspI, KpnI and BamHI. The digested probes were purified from an agarose gel using the MinElute Gel Purification Kit (Qiagen) and 5' labeled with γ-32P-ATP (Perkin Elmer) and T4 Polynucleotide Kinase (New England Biolabs). Electrophoretic mobility shift assays were carried out as described previously with the following modifications. Briefly, 2 μL of SUMOylated or unmodified CTCF from the SUMOylation reactions were used in each gel shift reaction. In experiments where the effects of SUMOylation were not being assayed, 0.5 μL to 1 μL of the in vitro translate was used in each gel shift reaction. In experiments using the GST-fusion of the zinc finger domain of CTCF, 250 ng of the purified protein domain was used in each gel shift reaction. The reactions were run on 4% native polyacrylamide gels in 0.25X TBE at 9 V/cm. The gel dimensions for the FII and F1 mobility shifts with full-length CTCF were 10 cm × 7 cm, while gels 19.5 cm × 16 cm were used to analyse the c-myc P2 promoter and the GST-zinc finger domain mobility shifts. The dried gels were exposed to a phosphor screen and imaged using a Phosphorimager. The electrophoretic mobilities of the CTCF-FII forward and reverse probe complexes and free probes were measured using ImageQuant software. The relative electrophoretic mobility (μ) of a CTCF-probe complex was calculated as the mobility of the complex divided by the mobility of the free probe. The relative mobilities of the complexes were plotted as a function of the position (bp) from the middle of the left EcoRV site to the middle of the restriction enzyme used to generate the probe and the graphs were fitted with the best fit polynomial curve using Microsoft Excel.
The fragments for the phasing experiments were prepared by digesting the pK10, pK12, pK14, pK16, pK18 and pK20 plasmids containing the FII insulator element in either the forward or reverse orientation, with the restriction enzymes RsaI, PvuII and NheI. Since the probes were not gel purified, we included the NheI restriction enzyme to digest a 464 bp RsaI vector fragment that would otherwise co-migrate with the FII insulator probes. The 391 bp to 401 bp RsaI to PvuII fragment contains the FII insulator element. Fragments were 5' labeled and electrophoretic mobility shifts were performed as described above, using 19.5 cm × 16 cm 4% native PAGE gels. The electrophoretic mobilities of the CTCF-FII forward and reverse phasing probe complexes and free probes were measured using ImageQuant software. The relative electrophoretic mobility (μ) of a CTCF-probe complex was calculated as the mobility of the complex divided by the mobility of the free probe. The relative mobilities of the complexes were plotted as a function of the linker length (bp). The graphs were fitted with the best fit polynomial curve using Microsoft Excel.
This work was supported in part by the Canadian Institutes of Health Research and the Department of Molecular Genetics at the University of Toronto. MJM is the recipient of a University of Toronto Open Fellowship. We thank Lori Frappier, Barbara Funnell and Linda Lee for their incisive comments on the manuscript. We thank Howard Lipshitz and Marc Shulman for their generous support of this work. We thank Dan Sadowski for drawing Figure 8.
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