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• W2088661602 abstract "Article1 April 2003free access Thyroid hormone-regulated enhancer blocking: cooperation of CTCF and thyroid hormone receptor Marcus Lutz Marcus Lutz Present address: University of Frankfurt Medical School, Medical Clinic III, Molecular Hematology, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany Search for more papers by this author Les J. Burke Les J. Burke Institute for Genetics, Justus-Liebig-Universitaet Giessen, Heinrich-Buff-Ring 58–62, D-35392 Giessen, Germany Search for more papers by this author Pascal LeFevre Pascal LeFevre Molecular Medicine Unit, University of Leeds, St James's University Hospital, Leeds, LS9 7TF UK Search for more papers by this author Fiona A. Myers Fiona A. Myers Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, Faculty of Science, University of Portsmouth, Portsmouth, PO1 2DT UK Search for more papers by this author Alan W. Thorne Alan W. Thorne Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, Faculty of Science, University of Portsmouth, Portsmouth, PO1 2DT UK Search for more papers by this author Colyn Crane-Robinson Colyn Crane-Robinson Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, Faculty of Science, University of Portsmouth, Portsmouth, PO1 2DT UK Search for more papers by this author Constanze Bonifer Constanze Bonifer Molecular Medicine Unit, University of Leeds, St James's University Hospital, Leeds, LS9 7TF UK Search for more papers by this author Galina N. Filippova Galina N. Filippova Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109 USA Search for more papers by this author Victor Lobanenkov Victor Lobanenkov Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892-0760 USA Search for more papers by this author Rainer Renkawitz Corresponding Author Rainer Renkawitz Institute for Genetics, Justus-Liebig-Universitaet Giessen, Heinrich-Buff-Ring 58–62, D-35392 Giessen, Germany Search for more papers by this author Marcus Lutz Marcus Lutz Present address: University of Frankfurt Medical School, Medical Clinic III, Molecular Hematology, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany Search for more papers by this author Les J. Burke Les J. Burke Institute for Genetics, Justus-Liebig-Universitaet Giessen, Heinrich-Buff-Ring 58–62, D-35392 Giessen, Germany Search for more papers by this author Pascal LeFevre Pascal LeFevre Molecular Medicine Unit, University of Leeds, St James's University Hospital, Leeds, LS9 7TF UK Search for more papers by this author Fiona A. Myers Fiona A. Myers Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, Faculty of Science, University of Portsmouth, Portsmouth, PO1 2DT UK Search for more papers by this author Alan W. Thorne Alan W. Thorne Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, Faculty of Science, University of Portsmouth, Portsmouth, PO1 2DT UK Search for more papers by this author Colyn Crane-Robinson Colyn Crane-Robinson Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, Faculty of Science, University of Portsmouth, Portsmouth, PO1 2DT UK Search for more papers by this author Constanze Bonifer Constanze Bonifer Molecular Medicine Unit, University of Leeds, St James's University Hospital, Leeds, LS9 7TF UK Search for more papers by this author Galina N. Filippova Galina N. Filippova Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109 USA Search for more papers by this author Victor Lobanenkov Victor Lobanenkov Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892-0760 USA Search for more papers by this author Rainer Renkawitz Corresponding Author Rainer Renkawitz Institute for Genetics, Justus-Liebig-Universitaet Giessen, Heinrich-Buff-Ring 58–62, D-35392 Giessen, Germany Search for more papers by this author Author Information Marcus Lutz2, Les J. Burke1, Pascal LeFevre3, Fiona A. Myers4, Alan W. Thorne4, Colyn Crane-Robinson4, Constanze Bonifer3, Galina N. Filippova5, Victor Lobanenkov6 and Rainer Renkawitz 1 1Institute for Genetics, Justus-Liebig-Universitaet Giessen, Heinrich-Buff-Ring 58–62, D-35392 Giessen, Germany 2Present address: University of Frankfurt Medical School, Medical Clinic III, Molecular Hematology, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany 3Molecular Medicine Unit, University of Leeds, St James's University Hospital, Leeds, LS9 7TF UK 4Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, Faculty of Science, University of Portsmouth, Portsmouth, PO1 2DT UK 5Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109 USA 6Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892-0760 USA ‡M.Lutz and L.J.Burke contributed equally to this work *Corresponding author. E-mail: [email protected] The EMBO Journal (2003)22:1579-1587https://doi.org/10.1093/emboj/cdg147 PDFDownload PDF of article text and main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info The highly conserved, ubiquitously expressed, zinc finger protein CTCF is involved in enhancer blocking, a mechanism crucial for shielding genes from illegitimate enhancer effects. Interestingly, CTCF-binding sites are often flanked by thyroid hormone response elements (TREs), as at the chicken lysozyme upstream silencer. Here we identify a similar composite site positioned upstream of the human c-myc gene. For both elements, we demonstrate that thyroid hormone abrogates enhancer blocking. Relief of enhancer blocking occurs even though CTCF remains bound to the lysozyme chromatin. Furthermore, chromatin immunoprecipitation analysis of the lysozyme upstream region revealed that histone H4 is acetylated at the CTCF-binding site. Loss of enhancer blocking by the addition of T3 led to increased histone acetylation, not only at the CTCF site, but also at the enhancer and the promoter. Thus, when TREs are adjacent to CTCF-binding sites, thyroid hormone can regulate enhancer blocking, thereby providing a new property for what was previously thought to be constitutive enhancer shielding by CTCF. Introduction CTCF is a highly conserved, ubiquitously expressed, 11-zinc finger phospho-protein that was first identified as a transcription factor that binds to silencer elements in the chicken c-myc and lysozyme genes (Baniahmad et al., 1990; Lobanenkov et al., 1990). The conservation of CTCF between man, mouse, rat, chicken and frog is such that the 11-zinc finger DNA-binding domain is almost identical, and the overall amino acid identity of the full length protein is in the range of 83–84% (Burke et al., 2002). Its ubiquitous expression profile and the above conservation argue for important functions at the cellular level. In addition to CTCF-mediated repression (Baniahmad et al., 1990; Lobanenkov et al., 1990) and activation (Quitschke et al., 1996) of promoters, enhancer blocking activity of CTCF on insulator elements has also been demonstrated. In fact, CTCF is the only mammalian protein so far identified that exhibits enhancer blocking activity (Bell et al., 1999). Enhancers can communicate over long distances with promoter elements, both from upstream and downstream sites. Specific mechanisms therefore had to evolve to control enhancer activity so that only the appropriate promoters are activated. Insulator elements with enhancer blocking activity fulfil this purpose (for reviews, see Mueller, 2000; Wolffe, 2000; Ohlsson et al., 2001; West et al., 2002). Constitutive enhancer blocking function has been found, for example, in the locus control region of β-globin genes (Bell et al., 1999). In contrast, CpG containing CTCF-binding sites have been shown to lose binding activity when methylated (Bell and Felsenfeld, 2000; Hark et al., 2000; Kanduri et al., 2000; Szabo et al., 2000; Filippova et al., 2001; Takai et al., 2001; Chao et al., 2002; Kanduri et al., 2002a). This activity is crucial for the proper function of the imprinting control region at the Igf2/H19 locus. Functional regulatory elements in eukaryotic genomes are often built from modules consisting of individual sites for DNA-binding factors. Such a modular structure has been shown for the lysozyme upstream silencer that consists of a CTCF-binding site together with a thyroid hormone response element (TRE) (Arnold et al., 1996; Lutz et al., 2000a). The thyroid hormone receptor (TR) binds as a homodimer or as a heterodimer with the retinoid-X-receptor (RXR) to the two TRE half sites, which are arranged as an inverted palindrome. For this composite CTCF/TR element, synergy in repression in the absence of thyroid hormone (T3), as well as in gene activation in the presence of T3, has been demonstrated (Lutz et al., 2000a). Similarly, a TRE-containing rat genomic DNA segment (element 144) is found next to a CTCF-binding site (Awad et al., 1999). This TRE is a so-called negative response element, mediating transcriptional repression in the presence of T3. This repression is critically dependent on CTCF binding next to the TRE. Another example of a composite CTCF/TR-binding site is site A, downstream of the mouse c-myc gene, which is flanked by a TRE (Perez-Juste et al., 2000). This element also confers transcriptional repression in the presence of T3. Here we addressed the question of whether composite CTCF/TR-binding sites confer their repressive effect directly on promoters, or whether the enhancer blocking activity of CTCF on insulator elements can also be modulated by TR and T3. We tested the composite binding site that lies upstream of the chicken lysozyme gene and a newly identified composite element upstream of the human c-myc gene. For both composite elements we demonstrate that enhancer blocking activity can be regulated, since in the presence of T3, enhancer blocking is abrogated. This is the first demonstration that enhancer blocking in vertebrates is not only a constitutive property or an activity regulated by long-term changes in DNA methylation, but, in the case of CTCF/TR composite elements, can also be regulated by ligand. Results CTCF sites are often found next to binding sites for the thyroid hormone receptor Thyroid hormone response elements can be grouped into so-called positive TREs and negative TREs (for a review, see Dotzlaw and Baniahmad, 2002). In several cases, binding sites for CTCF and for TR have been found in close proximity (Figure 1A and B). For the 144 element, T3-dependent repression of this negative TRE is strictly dependent on the presence of a functional CTCF-binding site (Awad et al., 1999). The F2 sequence in the F1/F2 silencer element 2.4 kb upstream of the chicken lysozyme gene is a positive TRE and synergy with CTCF in repression in the absence of T3 has been seen (Lutz et al., 2000a). Encouraged by the frequent occurrence of adjacent TR- and CTCF-binding sites, we wondered whether a new CTCF site at position −2.1 kb upstream of the human c-myc gene (N-site; G.Filippova, D.Loukinov, Y.Hu, T.Awad, B.Penn, S.Tapscott, E.Klenova, P.Neiman, S.Collins, H.Morse III, R.Ohlsson, R.Renkawitz and V.Lobanenkov, submitted for publication) is also flanked by a TR-binding site. Sequence inspection indeed revealed a potential TR-binding site (Figure 1). This sequence element, TRE(myc-N), is a direct repeat element spaced by four nucleotides (DR4), the distance between the DR4 element and the border of the CTCF-binding site N being 10 bp (Figure 1). This arrangement is similar to the lysozyme F1 and F2 sequences, which show a 13 bp spacing between elements. TR binding to TRE(myc-N) was analysed by electrophoretic mobility shift experiments (EMSA). Addition of TR and RXR proteins resulted in a prominent shift in mobility of the TRE, demonstrating protein binding to this sequence (Figure 1C). This binding was specific, since competition with a bona fide TRE (DR4) efficiently removed protein binding, whereas competition with a CTCF-binding site (F1) did not. Furthermore, EMSAs in the presence of T3 displayed a slight increase in the mobility of DNA-bound TR/RXR, which is characteristic for the hormone-loaded receptor–DNA complex (Arnold et al., 1996). The direct repeat arrangement of the TRE(myc-N) half sites spaced by 4 nucleotides, as shown for other TREs, allows only heterodimeric TR/RXR binding, and not homodimeric TR/TR or RXR/RXR binding. Addition of CTCF induced the formation of a specific complex, which is abrogated by excess F1 DNA, but not by a DR4 element. Simultaneous addition of all binding components (TR, RXR, CTCF) generates all the possible shifts: TR/RXR, CTCF and TR/RXR plus CTCF. Inspection of the binding efficiency in the absence of DNA competitors indicates that TR/RXR and CTCF binding occur independently without any positive or negative cooperativity. Thus the myc-N/TRE, 2 kb upstream of the human c-myc gene, is another example of adjacent TRE and CTCF sites (Figure 1A and B). Figure 1.CTCF sites are often found close to binding sites for TR. Five different cases of CTCF/TR composite elements are listed: the human c-myc upstream elements N and TRE(myc-N) (see text), the chicken lysozyme upstream F1 and F2 sequences (Baniahmad et al., 1990), the human 144 CTCF- and TR-binding sites (Bigler and Eisenman, 1995; Awad et al., 1999), the promoter region of the human APP gene (Quitschke et al., 1996; Belandia et al., 1998) and the mouse c-myc site with the CTCF site A and the TRE (Filippova et al., 1996; Perez-Juste et al., 2000). (A) Alignment of the 10 different TRE half sites from the five different CTCF/TR composite elements and their arrangement as direct repeats spaced by 4 or 5 nucleotides (DR4 and DR5), or as inverted palindromes spaced by 3, 6 or 7 nucleotides (IP3, IP6 and IP7) is indicated. (B) Alignment of the five different CTCF-binding sites with their spacing (in bp) from their respective TREs, upstream (left hand side) or downstream (right hand side) of the CTCF binding sequence. (C) Gel retardation with the c-myc upstream composite element N and TRE(myc-N) as probe. TRα, RXRα or CTCF were added as indicated, in the absence or presence of T3. Competitors, DR4 to compete specifically for TR/RXR binding and F1 to compete CTCF binding, were added as indicated. Download figure Download PowerPoint CTCF/TR-mediated enhancer blocking by the chicken lysozyme F1/F2 element is abrogated by thyroid hormone Based on the occurrence of CTCF/TR composite elements and the functional interaction of CTCF and TR in regulation of transcription, we asked whether T3 has an effect on the enhancer blocking activity of CTCF. In order to functionally analyse the possible enhancer blocking activity of CTCF/TR composite elements, we used a colony assay, previously developed in K562 cells to analyze the insulator function of sequences from the chicken β-globin locus (Chung et al., 1993, 1997). This assay has been widely used for investigation of the enhancer blocking potential of DNA elements from diverse genes and species (Bell et al., 1999; Bell and Felsenfeld, 2000; Filippova et al., 2001; Chao et al., 2002). In this assay, any enhancer blocking element placed between an enhancer and the promoter of a neomycin resistance (Neor) gene reduces gene activity and thereby decreases the number of G418-resistant colonies. Since we were interested in the effect of T3 in this system, we first analysed whether K562 cells respond to induction by T3. Transient transfection of a reporter gene driven by a TRE-tk promoter showed a 10-fold T3-dependent induction (data not shown). In order to evaluate possible indirect hormone effects on colony numbers, we controlled whether the growth of the K562 cells is influenced by the presence of T3, but found no effect of the hormone on cell growth (data not shown). In the absence of an enhancer blocker, the Neor gene is fully active and therefore induces a large number of resistant colonies (Figure 2A). The number of colonies is substantially reduced by inserting the β-globin insulator between the enhancer and the Neor gene, whereas a multimerized F1/F2 unit in neither the sense nor antisense orientation had any effect on colony numbers when placed outside of the enhancer/Neor gene unit. Since the enhancer blocking activity of the β-globin insulator is also mediated by CTCF, these results confirm previous observations that CTCF-binding sites block enhancer activity when placed between the enhancer and the promoter (Bell et al., 1999). We therefore carried out the colony assay in the presence or absence of T3. Independent of the presence of an enhancer blocking element (Figure 2A), addition of T3 reduces somewhat the observed number of colonies, indicating a general inhibitory effect on colony formation. Importantly, there was no increase in colony number and therefore no loss of enhancer blocking by the β-globin insulator, a segment containing a CTCF site that is not associated with a TRE. No increase in colony numbers was observed after T3 addition when the F1/F2 element was placed in a position outside of the promoter/enhancer unit, demonstrating that the TR-bound F2 element was unable to regulate gene activity in this downstream position. These controls allowed testing of the F1/F2 composite elements in a position which should mediate enhancer blocking (Figure 2B). In the absence of T3, the duplicate β-globin insulator and the F1/F2 element as dimer or hexamer, in both the sense or antisense orientation, mediate enhancer blocking with similar strength. Addition of T3 again had no effect on enhancer blocking activity after transfection of the constructs that lack a TRE. In sharp contrast, for all constructs containing F1/F2 sequences in an enhancer blocking position and in both orientations, T3 addition led to loss of enhancer blocking activity. In order to test whether T3-mediated relief of enhancer blocking is dependent on the gene-specific F1/F2 sequences of the CTCF- and TR-binding sites, we also tested the myc upstream composite element myc-N/TRE. Although this element is similar to the F1/F2 element with respect to its ability to bind TR/RXR heterodimers and CTCF, it is different with respect to the spacing and orientation of individual sequences within the TRE (Figure 1). We placed this composite element as a monomeric site at the enhancer blocking position and compared the observed number of colonies with the hexameric F1/F2 element (Figure 3). The single composite element of the myc gene caused a similar degree of enhancer blocking as the F1/F2 hexamer, and addition of T3 almost fully relieved the enhancer blocking activity of the myc composite element. Importantly, no T3 effect was seen with a mutated sequence, which had two nucleotides exchanged within the CTCF-binding site of the myc composite element. This mutation caused a loss of in vitro CTCF binding (Filippova et al., submitted for publication), but had no effect on the TR-binding site. The weak enhancer blocking activity remaining could result from residual CTCF binding and/or possibly from a weak blocking activity mediated by TR itself. Figure 2.CTCF/TR-mediated enhancer blocking by the chicken lysozyme F1/F2 element is abrogated by thyroid hormone. K562 cells were transfected with the indicated DNA constructs and after neomycin selection in the absence (open bars) or presence of thyroid hormone (filled bars) the number of colonies was determined. (A) The F1/F2 sequences outside of the enhancer (E)/promoter unit in the sense (6xsF1/F2E) or antisense orientation (6xaF1/F2E) do not effect colony numbers. Addition of thyroid hormone causes a general reduction in colony numbers irrespective of the presence of a TR-binding site (F2). (B) Relative enhancer blocking activity (determined by dividing the colony numbers obtained with the control plasmid pNI-MCS by the colony number from the respective DNA constructs) for four constructs. F1/F2 elements placed between the enhancer and promoter in the sense (E6xsF1/F2) or antisense orientation (E6xaF1/F2) mediate enhancer blocking in the absence, but not in the presence of thyroid hormone. Download figure Download PowerPoint Figure 3.CTCF/TR-mediated enhancer blocking by the c-myc upstream composite element N and TRE(myc-N) is abrogated by thyroid hormone. Relative enhancer blocking activity in the absence (open bars) or presence of thyroid hormone (filled bars) was determined as in Figure 2. The composite element was tested between the enhancer and the promoter as a single wild-type sequence (Emyc-N/TRE) or as a single mutated sequence with a mutation in the CTCF-binding site (Emyc-Nmut/TRE). Download figure Download PowerPoint In summary, both the lysozyme F1/F2 and the myc-N/TRE composite CTCF/TR-binding sites mediate enhancer blocking. In contrast to previously analysed CTCF-binding sites, enhancer blocking by these composite elements is relieved by T3, thereby demonstrating a new feature of hormone regulated enhancer blocking. CTCF stays bound on the chromatin even after relief of enhancer blocking by thyroid hormone A simple explanation of the effects of T3 on CTCF insulation would be that CTCF binding to the composite elements is lost after hormone treatment. We therefore analysed the in vivo binding of CTCF on the F1/F2 element in chicken erythroblasts (HD37) and chicken monocytic cells (HD11), both of which show a DNase I hypersensitive site in the chromatin at the F1/F2 element at position −2.4 kb (Huber et al., 1995). HD37 cells are inactive for lysozyme expression whereas HD11 cells express the lysozyme gene, which can be further induced (Huber et al., 1995). Based on the DNase I responsiveness of the chromatin, a scenario was proposed in which the silencer (F1/F2) element at −2.4 kb is active in erythroblasts as well as in monocytes, whereas the enhancer at position −2.7 kb is only active in the monocytes (Huber et al., 1995). A further increase of lysozyme gene activity upon induction was envisaged as a loss of silencer function. In vivo DMS footprinting was therefore carried out using HD37 and HD11 cells in the absence or presence of thyroid hormone (Figure 4A and B). The large footprint typical of CTCF-binding sites covers ∼50 nucleotides in both HD37 and HD11 cells and is seen both in the presence as well as the absence of T3. Since in vivo footprints prove the occupation of specific sites but do not allow identification of the binding protein and do not allow quantitative analyses of changes in binding, we carried out chromatin immunoprecipitation (ChIP) assays. Formaldehyde cross-linked chromatin from both cell types, grown in the absence or presence of thyroid hormone, was sheared and precipitated with an antibody against CTCF. Different regions upstream of the lysozyme gene were detected by real-time PCR. Specifically, the region around the CTCF-binding site at −2.4 kb was tested and compared with CTCF negative controls at −3.9 kb, −4.8 kb and −6.1 kb. As seen in Figure 4C and D, the sequences enriched in the CTCF ChIP are those of the CTCF-binding site at −2.38 kb and the adjacent region at −2.54 kb, which although not harbouring a CTCF-binding site, is also precipitated since the sonicated chromatin fragments, average size ∼500 bp, represent an overlapping set of sequences. All of the other sequences tested showed a low ratio of precipitate to input chromatin. Furthermore, the presence or absence of thyroid hormone did not dramatically change the precipitation of the CTCF-binding site, in particular at position −2.38 kb. Therefore, it can be concluded from the in vivo footprinting and the ChIP experiments that loss of CTCF binding is not the cause of thyroid hormone-mediated relief of enhancer blocking by CTCF/TR composite elements. Figure 4.CTCF remains bound to the chromatin upstream of the chicken lysozyme gene even after thyroid hormone-induced relief of enhancer blocking. HD37 cells (non-expressing) and HD11 cells (lysozyme expressing) were grown in the absence or presence of thyroid hormone. (A) DMS in vivo footprinting shows protection over the CTCF-binding site under all conditions when compared with the G-ladder (G-DNA) prepared from purified DNA. (B) The scan of the autoradiograph shown in (A) demonstrates that the footprint is not changed upon incubation with T3. (C and D) Chromatin immunoprecipitation with antibodies against CTCF shows CTCF binding on the endogeneous F1 element (−2.38kb) in HD37 cells and HD11 cells. Absence (−T3) or presence of thyroid hormone (+T3) does not change CTCF binding on the −2.38kb sequence. Fold enrichment or fold depletion is plotted relative to non-specific precipitation at CTCF free sites (−3.9 kb, −4.8 kb and −6.1 kb; see Materials and methods). Download figure Download PowerPoint Relief of enhancer blocking by thyroid hormone is associated with enhanced acetylation of histone H4 in the enhancer blocking region as well as in the enhancer itself Previously, we showed that CTCF binds histone deacetylase activity from HeLa nuclear extracts (Lutz et al., 2000b). Since deacetylation of histones is often associated with transcriptional repression (Aranda and Pascual, 2001; Forsberg and Bresnick, 2001; Wade, 2001), we wondered whether such deacetylation is associated with the ability of CTCF to repress promoter activities (Lutz et al., 2000a) and, specifically, whether enhancer blocking is also associated with histone deacetylation. ChIP experiments with antibodies against acetylated histones H3 and H4 across the chicken β-globin locus have revealed that the CTCF-binding site in the locus control region is associated with a strong constitutive focus of hyperacetylation (Litt et al., 2001b). We therefore analysed acetylation of histone H4 in the lysozyme non-expressing and expressing cell lines, HD37 and HD11, respectively, in the presence or absence of T3. Since the CTCF-binding site within the enhancer blocking sequence at position −2.4 kb is in close proximity to the enhancer element at −2.7 kb, we analysed acetylation of mono-nucleosomes from this region. The positions of nucleosomes in this region have previously been established (Huber et al., 1996) and are summarized in Figure 5A. Chromatin fragments were generated from nuclei by micrococcal nuclease digestion and fractionation on sucrose gradients, only the mono-nucleosomal fraction being used for the ChIP assays. Input chromatin, as well as precipitated chromatin was analysed by real-time PCR using Taqman probes for the amplicons indicated in Figure 5A. Amplicon 4 is specific for the CTCF region, whereas amplicons 2 and 3 are specific for the adjacent enhancer. In addition, we analysed a region further upstream (amplicon 1), as well as one much further downstream (amplicon 5). A 6th amplicon monitored the promoter region adjacent to the start of transcription. The signals from the four input mono-nucleosomal fractions (HD37 and HD11 cells, in the presence or absence of thyroid hormone) show a similar level of sequence representation at all six amplicons (data not shown), indicating that there is no under-representation of nucleosomes at any of the points investigated, i.e. that none of the amplicons is devoid of nucleosomes. Furthermore, the level of representation of these six sequences (15–20% of genomic DNA) is that found typically for MNase-generated mono-nucleosomes derived from genic regions. The lysozyme non-expressing HD37 cell line shows only a very low level of acetylated H4 histone, both in thyroid hormone-treated as well as untreated cells (Figure 5B). In sharp contrast, lysozyme-expressing HD11 cells, in the absence of thyroid hormone, show a substantial level of histone H4 acetylation in all of the regions tested, including the CTCF site (Figure 5C). After addition of thyroid hormone, acetylation levels at all six amplicons were further increased. This was true for the enhancer blocking region (CTCF/TR sites) at −2.4 kb and for both the enhancer (E) and the promoter. Figure 5.H4 acetylation at the enhancer blocker, the enhancer and the promoter is present only in lysozyme-expressing cells and is further induced by T3 additon. (A) Nucleosomal structure in the upstream lysozyme chromatin (Huber et al., 1996) is indicated by the position of hypersensitive sites for micrococcal nuclease digestion (arrows). Enhancer factor binding sites for PU.1 and C/EBP (Faust et al., 1999) and binding sites for CTCF and TR on the F1/F2 element are indicated. Nucleotide positions for the amplicons 1 to 5 used for the ChIP assay in (B) and (C) are indicated. Amplicon 6 covers the promoter region (−182/−77; data not shown). Chromatin immunoprecipitation of acetylated histone H4 from HD37 cells and HD11 cells are given in (B) and (C), respectively. Fold enrichment or fold depletion is the ratio of the PCR signal from the Ab-precipitated chromatin relative to that from the input chromatin (see Materials and methods). The x-axis shows the amplicon positions relative to the lysozyme upstream region, as indicated at the bottom of the graph. Download figure Download PowerPoint There is thus no evidence for the involvement of unacetylated nucleosomes in CTCF-mediated enhancer blocking activity. Even in case of the HD37 cells, which show no significant H4 acetylation in the enhancer or the promoter regions, a small but significant acetylation over the CTCF site was observed. Lysozyme-expressing HD11 cells in the absenc" @default.
• W2088661602 created "2016-06-24" @default.
• W2088661602 creator A5047312369 @default.
• W2088661602 date "2003-04-01" @default.
• W2088661602 modified "2023-10-01" @default.
• W2088661602 title "Thyroid hormone-regulated enhancer blocking: cooperation of CTCF and thyroid hormone receptor" @default.
• W2088661602 cites W1523020113 @default.
• W2088661602 cites W1643500256 @default.
• W2088661602 cites W1669374546 @default.
• W2088661602 cites W1886928378 @default.
• W2088661602 cites W1919133853 @default.
• W2088661602 cites W1921479150 @default.
• W2088661602 cites W1968902673 @default.
• W2088661602 cites W1970385007 @default.
• W2088661602 cites W1970643613 @default.
• W2088661602 cites W1971723950 @default.
• W2088661602 cites W1972995961 @default.
• W2088661602 cites W1973075378 @default.
• W2088661602 cites W1974193054 @default.
• W2088661602 cites W1984203293 @default.
• W2088661602 cites W1990064913 @default.
• W2088661602 cites W1999874710 @default.
• W2088661602 cites W2002877822 @default.
• W2088661602 cites W2005001938 @default.
• W2088661602 cites W2018413423 @default.
• W2088661602 cites W2019937806 @default.
• W2088661602 cites W2023399658 @default.
• W2088661602 cites W2032129980 @default.
• W2088661602 cites W2035348062 @default.
• W2088661602 cites W2040029402 @default.
• W2088661602 cites W2049527237 @default.
• W2088661602 cites W2058151080 @default.
• W2088661602 cites W2059408460 @default.
• W2088661602 cites W2060694227 @default.
• W2088661602 cites W2064520673 @default.
• W2088661602 cites W2072245007 @default.
• W2088661602 cites W2074906225 @default.
• W2088661602 cites W2081945547 @default.
• W2088661602 cites W2081973434 @default.
• W2088661602 cites W2091664490 @default.
• W2088661602 cites W2091677482 @default.
• W2088661602 cites W2094595339 @default.
• W2088661602 cites W2109522025 @default.
• W2088661602 cites W2116599808 @default.
• W2088661602 cites W2120330695 @default.
• W2088661602 cites W2128878636 @default.
• W2088661602 cites W2131642720 @default.
• W2088661602 cites W2136932227 @default.
• W2088661602 cites W2138952587 @default.
• W2088661602 cites W2141567062 @default.
• W2088661602 cites W2142184151 @default.
• W2088661602 cites W2144050547 @default.
• W2088661602 cites W2155644156 @default.
• W2088661602 cites W2160166542 @default.
• W2088661602 cites W2166129344 @default.
• W2088661602 cites W2172174991 @default.
• W2088661602 cites W2407010899 @default.
• W2088661602 cites W2743254891 @default.
• W2088661602 cites W41831396 @default.
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