51
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Jonk LJ, de Jonge ME, Pals CE, Wissink S, Vervaart JM, Schoorlemmer J, Kruijer W. Cloning and expression during development of three murine members of the COUP family of nuclear orphan receptors. Mech Dev 1994; 47:81-97. [PMID: 7947324 DOI: 10.1016/0925-4773(94)90098-1] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have isolated the murine homologs of the members of the COUP-family of steroid hormone receptors, COUP-TF1, ARP-1 and EAR2. The proteins encoded by the murine genes appeared to be highly conserved when compared to their human counterparts. The expression of COUP-TF1 and ARP-1 was induced during differentiation of P19 embryonal carcinoma (EC) cells into derivatives of all three germ layers. Retinoic acid (RA) treatment rapidly induced expression of both genes, while other methods of differentiation were less effective. Undifferentiated P19 cells were found to express EAR2 mRNA and the expression level was only slightly elevated by RA-treatment. In addition, we analyzed the expression in P19 cells of three members of the retinoid X receptor (RXR) family, which have been shown to heterodimerize with members of the COUP-family. During RA mediated differentiation of P19 cells, RXR alpha expression was induced while RXR beta expression was not modulated and RXR gamma expression was down regulated. Gel shift analysis revealed that in P19 cells the members of the COUP-family comprise the major portion of proteins binding to a RA-responsive direct repeat of the consensus steroid hormone receptor binding half site (AGGTCA) spaced by one nucleotide (DR + 1). The members of the COUP-family appeared to down regulate RA-induced activation of RA-response element-containing reporter constructs in a promoter context-dependent manner. The expression patterns of COUP-TF1, ARP-1 and EAR2 during development were investigated by in situ hybridization. In agreement with the results obtained in vitro, the three genes appeared to be expressed in tissues derived from all three germ layers. However, COUP-TF1 and ARP-1 were found to be expressed predominantly in the developing central nervous system in mutually exclusive domains. Furthermore, strong ARP-1 expression was detected in lung and kidney. Our data strongly suggest an important role for the members of the COUP-family in the hormonal control of gene expression regulating embryogenesis.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- COUP Transcription Factor I
- COUP Transcription Factor II
- COUP Transcription Factors
- Carcinoma, Embryonal/chemistry
- Carcinoma, Embryonal/genetics
- Carcinoma, Embryonal/pathology
- Cloning, Molecular
- DNA, Neoplasm/analysis
- DNA, Neoplasm/genetics
- DNA-Binding Proteins/analysis
- DNA-Binding Proteins/genetics
- Gene Expression Regulation, Neoplastic
- In Situ Hybridization
- Mice
- Molecular Sequence Data
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- Receptors, Retinoic Acid/analysis
- Receptors, Retinoic Acid/genetics
- Receptors, Steroid/analysis
- Receptors, Steroid/genetics
- Retinoid X Receptors
- Transcription Factors/analysis
- Transcription Factors/genetics
- Tretinoin/pharmacology
- Tumor Cells, Cultured
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Affiliation(s)
- L J Jonk
- Hubrecht Laboratorium, Netherlands Institute for Developmental Biology, Utrecht
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52
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Botfield MC, Jancso A, Weiss MA. Mapping critical residues in eukaryotic DNA-binding proteins: a plasmid-based genetic selection strategy with application to the Oct-2 POU motif. Biochemistry 1994; 33:6177-85. [PMID: 8193131 DOI: 10.1021/bi00186a017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Discrimination between allowed and disallowed amino acid substitutions provides a powerful method for analysis of protein structure and function. Site-directed mutagenesis allows specific hypotheses to be tested, but its systematic application to entire structural motifs is inefficient. This limitation may be overcome by genetic selection, which allows rapid scoring of thousands of randomly (or pseudorandomly) generated mutants. To facilitate structural dissection of DNA-binding proteins, we have designed two generally applicable bacterial selection systems: pPLUS selects for the ability of a protein to bind to a user-defined DNA sequence, whereas pMINUS selects against such binding. Complementary positive and negative selections allow rapid mapping of critical residues. To test and calibrate the systems, we have investigated the bipartite POU domain of the human B-cell-specific transcription factor Oct-2. (i) An invariant residue (Asn347) in the DNA-recognition helix of the POU-specific homeodomain (POUHD) was substituted by each of the 19 other possible amino acids. The mutant proteins each exhibited decreased specific DNA binding as defined in vivo by genetic selection and in vitro by gel retardation; relative affinities correlate with phenotypes in the positive and negative selection systems. An essential role for Asn347 in wild-type POUHD-DNA recognition is consistent with homologous Asn-adenine interactions in cocrystal structures of canonical homeodomains. (ii) Extension of pPLUS/pMINUS selection to the POU-specific subdomain (POUs) is demonstrated by analysis of mutations in its putative helix-turn-helix (HTH) element.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M C Botfield
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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53
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Jancso A, Botfield MC, Sowers LC, Weiss MA. An altered-specificity mutation in a human POU domain demonstrates functional analogy between the POU-specific subdomain and phage lambda repressor. Proc Natl Acad Sci U S A 1994; 91:3887-91. [PMID: 8171007 PMCID: PMC43687 DOI: 10.1073/pnas.91.9.3887] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The POU motif, conserved among a family of eukaryotic transcription factors, contains two DNA-binding domains: an N-terminal POU-specific domain (POUS) and a C-terminal homeodomain (POUHD). Surprisingly, POUS is similar in structure to the helix-turn-helix domains of bacteriophage repressor and Cro proteins. Such similarity predicts a common mechanism of DNA recognition. To test this prediction, we have studied the DNA-binding properties of the human Oct-2 POU domain by combined application of chemical synthesis and site-directed mutagenesis. The POUS footprint of DNA contacts, identified by use of modified bases, is analogous to those of bacteriophage repressor-operator complexes. Moreover, a loss-of-contact substitution in the putative POUS recognition alpha-helix leads to relaxed specificity at one position in the DNA target site. The implied side chain-base contact is identical to that of bacteriophage repressor and Cro proteins. These results establish a functional analogy between the POUS and prokaryotic helix-turn-helix elements and suggest that their DNA specificities may be governed by a shared set of rules.
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Affiliation(s)
- A Jancso
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
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54
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Klemm JD, Rould MA, Aurora R, Herr W, Pabo CO. Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell 1994; 77:21-32. [PMID: 8156594 DOI: 10.1016/0092-8674(94)90231-3] [Citation(s) in RCA: 391] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The structure of an Oct-1 POU domain-octamer DNA complex has been solved at 3.0 A resolution. The POU-specific domain contacts the 5' half of this site (ATGCAAAT), and as predicted from nuclear magnetic resonance studies, the structure, docking, and contacts are remarkably similar to those of the lambda and 434 repressors. The POU homeodomain contacts the 3' half of this site (ATGCAAAT), and the docking is similar to that of the engrailed, MAT alpha 2, and Antennapedia homeodomains. The linker region is not visible and there are no protein-protein contacts between the domains, but overlapping phosphate contacts near the center of the octamer site may favor cooperative binding. This novel arrangement raises important questions about cooperativity in protein-DNA recognition.
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Affiliation(s)
- J D Klemm
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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55
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Wey E, Lyons GE, Schäfer BW. A human POU domain gene, mPOU, is expressed in developing brain and specific adult tissues. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 220:753-62. [PMID: 7908264 DOI: 10.1111/j.1432-1033.1994.tb18676.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
POU domain genes constitute a family of transcription factors that exhibit distinct temporal and spatial patterns of expression. To investigate the possible functions that POU proteins may have in muscle development we have isolated four novel POU-domain-encoding sequences from human muscle tissue. One of these sequences, referred to as mPOU, encodes a new member of subclass VI of the POU family. In the embryo, mPOU is expressed exclusively in the developing brain, whereas in the adult its expression is restricted to brain, heart, skeletal muscle and lung. In the brain, the highest expression levels were found in specific cell layers of the cortex, the olfactory bulb, the hippocampus and the cerebellum. mPOU is shown to bind to DNA sequences containing the octamer motif and other POU factor target sites. The distinct expression pattern and divergent DNA-binding characteristics indicate that mPOU may regulate a distinct set of genes.
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Affiliation(s)
- E Wey
- Department of Pediatrics, University of Zurich, Switzerland
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56
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Characterization of a negative retinoic acid response element in the murine Oct4 promoter. Mol Cell Biol 1994. [PMID: 8289793 DOI: 10.1128/mcb.14.2.1122] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression of Oct4 in embryonic stem cells is controlled by a distal upstream stem cell-specific enhancer that is deactivated during retinoic acid (RA)-induced differentiation by an indirect mechanism not involving binding of RA receptors (H. Okazawa, K. Okamoto, F. Ishino, T. Ishino-Kaneko, S. Takeda, Y. Toyoda, M. Muramatsu, and H. Hamada, EMBO J. 10:2997-3005, 1991). Here we report that in RA-treated P19 embryonal carcinoma cells the Oct4 promoter is also subject to negative regulation by RA. The minimal Oct4 promoter sequence mediating repression consists of a promoter-proximal sequence containing a GC-rich SP1 consensus-like sequence and several hormone response element half-sites that can be arranged into direct repeats with different spacing. The GC box binds a nuclear factor that is invariably present in undifferentiated and RA-treated differentiated P19 cells. By contrast, the hormone response element-containing sequence binds factors that are induced following RA treatment. Mutational analysis and competition experiments show that the functional entity binding the RA-induced factor is a direct repeat sequence with a spacing of one nucleotide, previously shown to be a binding site for COUP transcription factors (COUP-TFs). Cotransfected orphan receptors COUP-TF1, ARP-1, and EAR-2 were able to repress the activity of Oct4 promoter-driven reporters in P19 EC cells, albeit with different efficiencies. Furthermore, the negative transcriptional effect of COUP-TFs is dominant over the activating effect of the Oct4 embryonic stem cell-specific enhancer. These results show that negative regulation of Oct4 expression during RA-induced differentiation of embryonic stem cells is controlled by two different mechanisms, including deactivation of the embryonic stem cell-specific enhancer and promoter silencing by orphan nuclear hormone receptors.
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57
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Schoorlemmer J, van Puijenbroek A, van Den Eijnden M, Jonk L, Pals C, Kruijer W. Characterization of a negative retinoic acid response element in the murine Oct4 promoter. Mol Cell Biol 1994; 14:1122-36. [PMID: 8289793 PMCID: PMC358468 DOI: 10.1128/mcb.14.2.1122-1136.1994] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Expression of Oct4 in embryonic stem cells is controlled by a distal upstream stem cell-specific enhancer that is deactivated during retinoic acid (RA)-induced differentiation by an indirect mechanism not involving binding of RA receptors (H. Okazawa, K. Okamoto, F. Ishino, T. Ishino-Kaneko, S. Takeda, Y. Toyoda, M. Muramatsu, and H. Hamada, EMBO J. 10:2997-3005, 1991). Here we report that in RA-treated P19 embryonal carcinoma cells the Oct4 promoter is also subject to negative regulation by RA. The minimal Oct4 promoter sequence mediating repression consists of a promoter-proximal sequence containing a GC-rich SP1 consensus-like sequence and several hormone response element half-sites that can be arranged into direct repeats with different spacing. The GC box binds a nuclear factor that is invariably present in undifferentiated and RA-treated differentiated P19 cells. By contrast, the hormone response element-containing sequence binds factors that are induced following RA treatment. Mutational analysis and competition experiments show that the functional entity binding the RA-induced factor is a direct repeat sequence with a spacing of one nucleotide, previously shown to be a binding site for COUP transcription factors (COUP-TFs). Cotransfected orphan receptors COUP-TF1, ARP-1, and EAR-2 were able to repress the activity of Oct4 promoter-driven reporters in P19 EC cells, albeit with different efficiencies. Furthermore, the negative transcriptional effect of COUP-TFs is dominant over the activating effect of the Oct4 embryonic stem cell-specific enhancer. These results show that negative regulation of Oct4 expression during RA-induced differentiation of embryonic stem cells is controlled by two different mechanisms, including deactivation of the embryonic stem cell-specific enhancer and promoter silencing by orphan nuclear hormone receptors.
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Affiliation(s)
- J Schoorlemmer
- Hubrecht Laboratorium, Netherlands Institute for Developmental Biology, Utrecht
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58
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Abstract
We have suggested a random modification method for determining preferable binding sites of a DNA-binding protein and applied this method to the Oct-2B transcription factor. Our results indicate that the Oct-2B protein interacts with canonical oct sequence ATGC/TAAAT and degenerated sequences which contain TAAT motif in the binding site. We have determined nucleotides in the binding sites, involved in the DNA-protein interaction, and the equilibrium dissociation constants Kd for these sequences. These data show that a much greater number of potential targets for Oct proteins exist on DNA and changed our view on the gene expression regulation by this protein factor.
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Affiliation(s)
- A G Stepchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow
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59
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10 Comparative Aspects of Pituitary Development and Pit-1 Function. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/s1546-5098(08)60071-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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60
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Andrés V, Chiara MD, Mahdavi V. A new bipartite DNA-binding domain: cooperative interaction between the cut repeat and homeo domain of the cut homeo proteins. Genes Dev 1994; 8:245-57. [PMID: 7905452 DOI: 10.1101/gad.8.2.245] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The recently cloned Clox (Cut-like homeo box) and CDP (CCAAT displacement protein), two mammalian counterparts of the Drosophila Cut homeo protein, correspond to alternatively spliced products of the same gene (mClox, for mammalian Cut-like homeo box). Although these proteins reportedly bind to apparently unrelated DNA sequences, we show by in vitro selection of optimal binding sites that both Clox and CDP have the same preferred DNA-binding specificity. The palindromic consensus target sequence, 5'-(t/a)(a/t)tATCGATTAt(t/c)(t/g)(t/a)-3', contains a bona fide homeo domain binding motif (ATTA). In addition, 37% of the in vitro-selected sequences have a CCAAT box, the canonical target for members of the family of CCAAT-binding factors. A characteristic feature of the cut homeo proteins is the presence of three evolutionarily conserved 73-amino-acid repeats of unknown function, the so-called cut repeats. We present evidence that the cut repeat II binds to mClox consensus targets independently of the DNA-binding activity of the homeo domain. In vitro selection of binding sites shows that the optimal targets for the cut repeat II contain one or more CCAAT boxes and, like the homeo domain, an ATTA core. These results indicate that the DNA-binding activity of the second cut repeat can account for the suggested role of CDP mClox as CCAAT displacement protein, a putative repressor of gene expression. We also report that the mClox homeo domain and cut repeat II interact in vitro in the absence of DNA. This interaction, which greatly enhances the DNA-binding activity of the binary complex, is specific to the cut homeo proteins. No cooperativity was observed between the cut repeat II and the homeo domains of Oct-1 and Gtx. Furthermore, the Drosophila cut repeat II, which does not appear to bind to DNA, also enhances the DNA-binding activity of the mClox homeo domain. Thus, the bifunctional cut repeat II, which defines a new family of bipartite DNA-binding proteins, is likely to play an important role in the function of the cut homeo proteins.
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Affiliation(s)
- V Andrés
- Department of Cardiology, Children's Hospital, Boston, Massachusetts 02115
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61
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Andersen B, Pearse RV, Schlegel PN, Cichon Z, Schonemann MD, Bardin CW, Rosenfeld MG. Sperm 1: a POU-domain gene transiently expressed immediately before meiosis I in the male germ cell. Proc Natl Acad Sci U S A 1993; 90:11084-8. [PMID: 7902581 PMCID: PMC47926 DOI: 10.1073/pnas.90.23.11084] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Members of the POU-domain gene family encode for transcriptional regulatory molecules that are important for terminal differentiation of several organ systems, including anterior pituitary, sensory neurons, and B lymphocytes. We have identified a POU-domain factor, referred to as sperm 1 (Sprm-1). This factor is most related to the transactivator Oct-3/4, which is expressed in the early embryo, primordial germ cells, and the egg. However, in contrast with Oct-3/4, rat Sprm-1 is selectively expressed during a 36- to 48-hr period immediately preceding meiosis I in male germ cells. Although the POU-domain of Sprm-1 is divergent from the POU-domains of Oct-1 and Oct-2, random-site-selection assay reveals that Sprm-1 preferentially binds to a specific variant of the classic octamer DNA-response element in which the optimal sequence differs from that preferred by Oct-1 and Pit-1. These data suggest that the Sprm-1 gene encodes a DNA-binding protein that may exert a regulatory function in meiotic events that are required for terminal differentiation of the male germ cell.
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Affiliation(s)
- B Andersen
- Eukaryotic Regulatory Biology Program, University of California, San Diego, School of Medicine, La Jolla 92093-0648
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62
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Bendall AJ, Sturm RA, Danoy PA, Molloy PL. Broad binding-site specificity and affinity properties of octamer 1 and brain octamer-binding proteins. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 217:799-811. [PMID: 8223636 DOI: 10.1111/j.1432-1033.1993.tb18308.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The ubiquitous Pit-1-Oct-1-Unc-1 (POU)-domain protein octamer 1 (Oct-1) has been observed to bind specifically to a number of degenerate and dissimilar sequences. We have used antibodies directed against a C-terminal Oct-1 peptide to immunoselect binding sequences for HeLa cell Oct-1 from random-sequence oligonucleotides and we describe the isolation of binding sequences of considerable heterogeneity. Although our consensus alignment indicated a 9-bp TATGCAAAT motif with AT-rich flanking sequences, this binding motif is not immediately obvious in the population of sequences and no clone actually contained this sequence. Screening these Oct-1-binding sequences with a mouse whole-brain extract demonstrated that the neuronal octamer-binding proteins exhibit similar but distinct DNA sequence specificities. Unlike the reported selection of binding sequences for other transcription factors, the dependence of Oct-1-binding affinity upon sequence did not correspond tightly to the degree of conservation at particular positions of the consensus sequence. Our results suggest that either base-specific hydrogen bonding is not the only major determinant of binding affinity and specificity, or that Oct-1 binding to some sequences is mechanistically different from its binding to an octamer. These results exemplify the potential to overlook binding sites for some factors by searching gene sequences with a consensus nucleotide sequence.
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Affiliation(s)
- A J Bendall
- Commonwealth Scientific and Industrial Research Organisation, Division of Biomolecular Engineering, Sydney Laboratory, North Ryde, New South Wales, Australia
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63
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Andersen B, Schonemann M, Pearse RV, Jenne K, Sugarman J, Rosenfeld M. Brn-5 is a divergent POU domain factor highly expressed in layer IV of the neocortex. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)49475-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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64
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van de Wetering M, Oosterwegel M, van Norren K, Clevers H. Sox-4, an Sry-like HMG box protein, is a transcriptional activator in lymphocytes. EMBO J 1993; 12:3847-54. [PMID: 8404853 PMCID: PMC413668 DOI: 10.1002/j.1460-2075.1993.tb06063.x] [Citation(s) in RCA: 254] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Previous studies in lymphocytes have described two DNA-binding HMG box proteins, TCF-1 and LEF-1, with affinity for the A/TA/TCAAAG motif found in several T cell-specific enhancers. Evaluation of cotransfection experiments in non-T cells and the observed inactivity of an AACAAAG concatamer in the TCF-1/LEF-1-expressing T cell line BW5147, led us to conclude that these two proteins did not mediate the observed enhancer effect. We therefore searched for additional HMG box proteins. By a PCR-aided strategy, we cloned Sox-4, a gene with homology to the HMG box region of the sex determining gene SRY. Sox-4 was expressed in T and pre-B lymphocyte lines and in the murine thymus. Significantly, BW5147 T cells did not express Sox-4. Recombinant Sox-4 bound with high affinity (Kd 3 x 10(-11) M) to the minor groove of the AACAAAG motif, most likely contacting all seven base pairs. In contrast with observations on TCF-1 and LEF-1, cotransfection with Sox-4 unveiled a transactivating capacity, which mapped to its serine-rich C terminus. This region remained functional upon grafting onto a GAL4 DNA-binding domain. Sox-4 is thus the first 'classical' transcription factor in the Sox gene family with separable DNA-binding and transactivation domains. Our observations indicate that a detailed understanding of T cell-specific gene control must integrate the concerted activity of at least three tissue-specific HMG box genes.
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Affiliation(s)
- M van de Wetering
- Department of Immunology, University Hospital Utrecht, The Netherlands
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65
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Abstract
To determine the number of DNA binding proteins capable of binding a consensus Engrailed binding site, this consensus sequence was used to screen a library of Drosophila cDNA clones in a bacteriophage expression vector. We retrieved clones encoding 20 distinct DNA binding domains, 17 of which are homeodomains. Binding to a variety of oligonucleotides confirms the related sequence specificity of the retrieved binding domains. Nonetheless, the homeodomains have remarkably diverse amino acid sequences. We conclude that during the evolutionary divergence of homeodomains, the specificity of DNA binding has been much more highly conserved than the amino acid sequence.
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Affiliation(s)
- B Kalionis
- Department of Biochemistry and Biophysics, University of California at San Francisco 94143-0448
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66
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Abstract
SCIP is a POU domain transcription factor expressed by Schwann cells, the myelin-forming glial cells of the peripheral nervous system. In this study, we investigate SCIP regulation of the gene encoding P0, the major structural protein of peripheral myelin. We find that SCIP represses transcription of this gene through the joint action of the SCIP POU domain and an amino terminal domain that acts cell specifically. Maximal repression is DNA-binding-dependent, and analysis of the P0 promoter reveals the presence of multiple SCIP binding sites. Surprisingly, none of these sites in their native positions dramatically affect P0 promoter activity or its repression by SCIP, although they mediate repression when moved closer to the P0 transcription start site. We propose that repression occurs through a quenching mechanism mediated by the SCIP POU and amino terminal domains acting in concert with other nuclear proteins, including a Schwann cell-specific adapter.
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Affiliation(s)
- E S Monuki
- Molecular Neurobiology Laboratory, Salk Institute, La Jolla, CA 92037
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67
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Cox M, Dekker N, Boelens R, Verrijzer CP, van der Vliet PC, Kaptein R. NMR studies of the POU-specific DNA-binding domain of Oct-1: sequential 1H and 15N assignments and secondary structure. Biochemistry 1993; 32:6032-40. [PMID: 8507639 DOI: 10.1021/bi00074a014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The 1H and 15N resonances of the POU-specific DNA-binding domain of transcription factor Oct-1 have been assigned sequentially using two-dimensional homo- and heteronuclear NMR techniques, as well as three-dimensional heteronuclear NMR techniques, including TOCSY, 2D NOE, and NOESY-HMQC experiments. A number of typical short- and medium-range NOE contacts, as well as amide proton exchange data, gave evidence for the presence of four alpha-helices, in the peptide segments 1-19, 23-34, 40-49, and 54-71, which are connected by short loops of irregular structure. Interestingly, the second helix contains three glycine residues and the fourth helix a proline in the middle of the helix. Although the regular pattern of hydrogen bonds in the fourth helix is interrupted, due to the absence of an amide proton in proline, the helix is remarkably stable. All four helices are amphipathic, which suggests a packing of the apolar sides of the helices in the folded structure of the protein.
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Affiliation(s)
- M Cox
- Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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68
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Rigoni P, Xu L, Harshman K, Schaffner W, Arnosti DN. Conserved cysteine residues of Oct-2 POU domain confer sensitivity to oxidation but are dispensable for sequence-specific DNA binding. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1173:141-6. [PMID: 8504164 DOI: 10.1016/0167-4781(93)90174-c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The POU family of proteins, including the Oct-2 transcription factor, is characterized by a highly conserved bipartite DNA binding domain containing a 'POU homeodomain', distantly related to homeodomains of other DNA binding proteins, and a 'POU specific' domain unique to this class of factors. Prompted by the finding that in vitro DNA binding by Oct-2 is reversibly inhibited by oxidation of the protein, we investigated the role of the cysteine residues in the POU domain. All POU homeodomains identified contain a cysteine in the helix 3 region presumed to contact DNA directly; many (including Oct-2) also contain a less-well conserved cysteine residue(s) in the POU specific domain. Replacement of these cysteines with serine residues rendered the DNA binding domain resistant to oxidation but did not appreciably change the binding to a canonical octamer sequence, suggesting that the conserved cysteine residues are not required for sequence-specific DNA contacts, but may be important for another function.
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Affiliation(s)
- P Rigoni
- Institut für Molekularbiologie II, Universität Zürich, Switzerland
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69
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Pronk R, van der Vliet PC. The adenovirus terminal protein influences binding of replication proteins and changes the origin structure. Nucleic Acids Res 1993; 21:2293-300. [PMID: 8506126 PMCID: PMC309523 DOI: 10.1093/nar/21.10.2293] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The adenovirus terminal protein (TP) is covalently linked to the 5' ends of the adenovirus genome and enhances DNA replication in vitro by increasing template activity. To study the effect of TP in more detail we isolated short origin fragments containing functional TP using anion exchange chromatography. These fragments were highly active as templates for DNA replication in a reconstituted system. Employing band-shift assays we found that the affinity of the precursor terminal protein-DNA polymerase complex for the TP-containing origin was increased 2 to 3-fold. Binding affinities of two other replication stimulating proteins, NFI and Oct-1, were not influenced by the terminal protein. Upon DNaseI footprinting we observed, unexpectedly, that the breakdown pattern had changed at various positions in the origin, notably in the area 3-6 and 41-51 by the presence of TP. Some differences in the footprint pattern of NFI and Oct-1 were also found. Our results indicate that TP induces subtle changes in the origin structure that influence the interaction of other replication proteins.
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Affiliation(s)
- R Pronk
- Laboratory for Physiological Chemistry, University of Utrecht, The Netherlands
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70
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Dekker N, Cox M, Boelens R, Verrijzer CP, van der Vliet PC, Kaptein R. Solution structure of the POU-specific DNA-binding domain of Oct-1. Nature 1993; 362:852-5. [PMID: 8479524 DOI: 10.1038/362852a0] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The transcription factor Oct-1 belongs to a family containing a POU DNA-binding domain. This bipartite domain is composed of a POU-specific domain (POUs) and a POU-homeodomain (POUhd) connected by a flexible linker. The left half of the optimal POU binding site, the octamer ATGCAAAT, is recognized by POUs and the right half by POUhd. We have determined the solution structure of POUs by nuclear magnetic resonance. It consists of four alpha-helices connected by short loops. Helices I and IV are in a parallel coiled-coil arrangement. The folding topology appears to be similar to that of the bacteriophage lambda-repressor and 434 repressor. For the well defined parts of the protein (residues 1-71), the average root-mean square deviation for the backbone atoms is 0.9 A. Based on the observed selective exchange broadening in the (15N,1H)-HMQC (heteronuclear multiple quantum coherence) spectrum of the POUs-DNA complex we conclude that DNA-binding is mediated by helix III. We propose a model for the POU-DNA complex in which both recognition helices from the two subdomains have adjacent positions in the major groove.
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Affiliation(s)
- N Dekker
- Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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71
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Verrijzer CP, Van der Vliet PC. POU domain transcription factors. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1173:1-21. [PMID: 8485147 DOI: 10.1016/0167-4781(93)90237-8] [Citation(s) in RCA: 205] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- C P Verrijzer
- Laboratory for Physiological Chemistry, University of Utrecht, The Netherlands
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72
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Andersen B, Schonemann MD, Flynn SE, Pearse RV, Singh H, Rosenfeld MG. Skn-1a and Skn-1i: two functionally distinct Oct-2-related factors expressed in epidermis. Science 1993; 260:78-82. [PMID: 7682011 DOI: 10.1126/science.7682011] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Two forms of a member of the POU domain family of transcriptional regulators, highly related to Oct-2, are selectively expressed in terminally differentiating epidermis and hair follicles. One form, referred to as Skn-1i, contains an amino-terminal domain that inhibits DNA binding and can inhibit transactivation by Oct-1. A second form, Skn-1a, contains an alternative amino terminus and serves to activate cytokeratin 10 (K10) gene expression. The pattern of expression of the Skn-1a/i gene products and the effect of the alternative products on the expression of other genes suggest that these factors serve regulatory functions with respect to epidermal development.
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Affiliation(s)
- B Andersen
- Eukaryotic Regulatory Biology Program, Howard Hughes Medical Institute, University of California School of Medicine, San Diego, La Jolla 92093
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73
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Corcoran LM, Karvelas M, Nossal GJ, Ye ZS, Jacks T, Baltimore D. Oct-2, although not required for early B-cell development, is critical for later B-cell maturation and for postnatal survival. Genes Dev 1993; 7:570-82. [PMID: 8096198 DOI: 10.1101/gad.7.4.570] [Citation(s) in RCA: 225] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Oct-2, a POU homeo domain transcription factor, is believed to stimulate B-cell-restricted expression of immunoglobulin genes through binding sites in immunoglobulin gene promoters and enhancers. To determine whether Oct-2 is required for B-cell development or function, or has other developmental roles, the gene was disrupted by homologous recombination. Oct-2-l- mice develop normally but die within hours of birth for undetermined reasons. Mutants contain normal numbers of B-cell precursors but are somewhat deficient in IgM+ B cells. These B cells have a marked defect in their capacity to secrete immunoglobulin upon mitogenic stimulation in vitro. Thus, Oct-2 is not required for the generation of immunoglobulin-bearing B cells but is crucial for their maturation to immunoglobulin-secreting cells and for another undetermined organismal function.
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Affiliation(s)
- L M Corcoran
- Walter and Eliza Hall Institute of Medical Research, Royal Melbourne Hospital, Victoria, Australia
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74
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75
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Kristie T, Sharp P. Purification of the cellular C1 factor required for the stable recognition of the Oct-1 homeodomain by the herpes simplex virus alpha-trans-induction factor (VP16). J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53282-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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76
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Johansen T, Moens U, Holm T, Fjose A, Krauss S. Zebrafish pou[c]: a divergent POU family gene ubiquitously expressed during embryogenesis. Nucleic Acids Res 1993; 21:475-83. [PMID: 8441661 PMCID: PMC309142 DOI: 10.1093/nar/21.3.475] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We report the isolation and characterization of cDNA for a novel zebrafish (Brachyodanio rerio) POU domain gene, pou[c], which is ubiquitously expressed during embryonic development. This gene encodes a 610 amino acids long protein with a 149 amino acid POU domain ending only 8 residues before the C terminus. The 453 amino acids long region N-terminal to the POU domain contains several features typical of transcriptional activation domains such as an acidic region with a putative amphipathic alpha-helix, a glutamine-rich region, and short threonine- and/or serine-rich regions. Comparison of the POU domain of pou[c] to other known POU sequences clearly show that pou[c] has the most divergent POU domain sequence reported to date. Thus, we suggest that pou[c] should be placed as the presently sole member of a new, sixth class of POU proteins. DNA-binding studies revealed that pou[c] is not an octamer-binding transcription factor like the Oct proteins described from mammals, chicken and Xenopus. Rather, pou[c] binds with high affinity to the TAATGARAT motif found in the promoters of the herpes simplex virus immediate early genes and to degenerate octamer-TAATGA motifs. Circular permutation analyses also show that pou[c] induces DNA bending upon sequence-specific binding.
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Affiliation(s)
- T Johansen
- Department of Biochemistry, University of Tromsø, Norway
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77
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Hayes S, O'Hare P. Mapping of a major surface-exposed site in herpes simplex virus protein Vmw65 to a region of direct interaction in a transcription complex assembly. J Virol 1993; 67:852-62. [PMID: 8380468 PMCID: PMC237439 DOI: 10.1128/jvi.67.2.852-862.1993] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The cellular factor Oct-1 is selectively recruited, together with at least one other cellular protein (CFF), into a multicomponent transcription complex whose assembly is directed by the herpes simplex virus regulatory protein Vmw65 (VP16). The acidic carboxy terminus of Vmw65 is not involved in assembly of the complex but is absolutely required for subsequent transcriptional activation. Elucidation of the mechanism of action of Vmw65 is important for an understanding not only of combinatorial control of gene expression by POU- and homeodomain proteins but also of the interaction(s) between activation domains of regulatory proteins and components of the basal transcriptional apparatus. We used a combination of limited proteolysis with a number of site-specific proteases and immunological detection to demonstrate the presence of two main surface-exposed regions in Vmw65. We mapped these sites to within a few amino acids at positions 365-370 408/409. The site at 408/409 is indicative of a flexible exposed linker region between the acidic carboxy-terminal activation domain (residues 430-480) and an N-terminal domain involved in complex formation with the two cellular factors. The site around residues 365-370 is precisely within a region that results from this and other laboratories have shown to be critical for complex formation. Furthermore, we show that this site is selectively protected from proteolysis after complex assembly. Finally, using a series of overlapping peptide encompassing this region, we show that the eight amino acids, R-E-H-A-Y-S-R-A, from positions 360 through 367 are sufficient to inhibit complex formation by intact Vmw65. We propose that these residues contain sufficient information to selectively bind one of the cellular partners involved in complex assembly and that these residues are located in a physical surface-exposed domain of the protein.
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Affiliation(s)
- S Hayes
- Marie Curie Research Institute, Oxted, Surrey, United Kingdom
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78
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Kambe F, Tsukahara S, Kato T, Seo H. The POU-domain protein Oct-1 is widely expressed in adult rat organs. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1171:307-10. [PMID: 8424955 DOI: 10.1016/0167-4781(93)90071-k] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The cDNA encoding a rat Oct-1 POU-domain was cloned by the reverse transcription-polymerase chain reaction method and subsequently Oct-1 mRNA expression was investigated. Our results show that the POU-domain of Oct-1 has been highly conserved during vertebrate evolution and that Oct-1 mRNA is widely expressed in various organs of adult rat.
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Affiliation(s)
- F Kambe
- Department of Endocrinology and Metabolism, Nagoya University, Japan
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79
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Goldsborough AS, Healy LE, Copeland NG, Gilbert DJ, Jenkins NA, Willison KR, Ashworth A. Cloning, chromosomal localization and expression pattern of the POU domain gene Oct-11. Nucleic Acids Res 1993; 21:127-34. [PMID: 8441607 PMCID: PMC309074 DOI: 10.1093/nar/21.1.127] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
POU domain genes encode a family of highly conserved transacting factors that influence the transcriptional activity of several cell type-specific and ubiquitous genes. We have cloned and sequenced cDNAs encoding a novel mouse POU domain protein, Oct-11, that is closely related within the POU domain to the POU class II proteins, Oct-1 and Oct-2. Recombinant Oct-11 protein binds specifically to an octamer sequence in vitro. The Oct-11 gene is expressed during mouse embryogenesis and in the adult thymus and testis. In addition, it is abundant in the myeloma cell line P3/NS-1/1-Ag4.1. We describe the structure of Oct-11 and its chromosomal localization, and discuss the evidence that the POU class II gene family has evolved by duplication and divergence of a common ancestral gene.
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Affiliation(s)
- A S Goldsborough
- Chester Beatty Laboratories, Institute of Cancer Research, London, UK
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80
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Ciliberto G, Colantuoni V, De Francesco R, De Simone V, Monaci P, Nicosia A, Ramji DP, Toniatti C, Cortese R. Transcriptional Control of Gene Expression in Hepatic Cells. Gene Expr 1993. [DOI: 10.1007/978-1-4684-6811-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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81
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Abstract
An increasing number of transcription factors both from prokaryotic and eukaryotic sources are found to bend the DNA upon binding to their recognition site. Bending can easily be detected by the anomalous electrophoretic behaviour of the DNA-protein complex or by increased cyclization of DNA fragments containing the protein-induced bend. Induction of DNA bending by transcription factors could regulate transcription in various ways. Bending may bring distantly bound transcription factors closer together by facilitating DNA-looping or it could mediate the interaction between transcription factors and the general transcription machinery by formation of large nucleoprotein structures in which the DNA is wrapped around the protein complex. Alternatively, the energy stored in a protein-induced bend could be used to favour formation of an open transcription complex or to dissociate the RNA polymerase in the transition from initiation to elongation. Modification of the bend angles and bending centers, caused by homodimerization or heterodimerization of transcription factors, may well turn out to be an important way to enlarge the range of interactions required for regulation of gene expression.
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Affiliation(s)
- P C van der Vliet
- Laboratory for Physiological Chemistry, University of Utrecht, Vondellaan, The Netherlands
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82
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Theill LE. Transcriptional Control of Pituitary Gene Expression. Gene Expr 1993. [DOI: 10.1007/978-1-4684-6811-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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83
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Verrijzer CP, Strating M, Mul YM, van der Vliet PC. POU domain transcription factors from different subclasses stimulate adenovirus DNA replication. Nucleic Acids Res 1992; 20:6369-75. [PMID: 1475198 PMCID: PMC334529 DOI: 10.1093/nar/20.23.6369] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
POU domain proteins constitute a family of eukaryotic transcription factors that exert critical functions during development. They contain a conserved 160 amino acids DNA binding domain, the POU domain. Genetic data have demonstrated that some POU domain proteins are essential for the proliferation of specific cell types, suggesting a possible role in DNA replication. In addition, the ubiquitous POU transcription factor Oct-1 or its isolated POU domain enhances adenovirus DNA replication. Here we compared the DNA binding specificities of POU domain proteins from different subclasses. They exhibit overlapping, yet distinct binding site preferences. Furthermore, purified Pit-1, Oct-1, Oct-2, Oct-6, Oct-4 and zebrafish POU[C] could all stimulate adenovirus DNA replication in a reconstituted in vitro system. Thus, activation appears to depend on a property common to most POU domain proteins. Adenovirus DNA replication is also stimulated by the transcription factor NFI/CTF. In contrast to NFI, the POU domain did not enhance binding of precursor terminal protein-DNA polymerase to the origin nor did it stabilize the preinitiation complex. These results suggest that the POU domain acts on a rate limiting step after formation of the preinitiation complex.
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Affiliation(s)
- C P Verrijzer
- Laboratory for Physiological Chemistry, University of Utrecht, The Netherlands
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84
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Currie RA, Eckel RH. Characterization of a high affinity octamer transcription factor binding site in the human lipoprotein lipase promoter. Arch Biochem Biophys 1992; 298:630-9. [PMID: 1416992 DOI: 10.1016/0003-9861(92)90459-a] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A high affinity octamer transcription factor (OTF-1) binding site has been identified and characterized at position--46 base pairs (bp) in the proximal human lipoprotein lipase (LPL) promoter. The affinity of the LPL OTF-1 binding site was approximately 15-fold greater than a consensus octamer sequence, ATTTGCAT, present at position--66 bp in the mouse Vk T1 promoter, and approximately 5-fold greater than the OTF-1 site present at position--49 bp in the human histone H2B promoter. Diethylpyrocarbonate interference assays have identified both 5' and 3' adenine nucleotides, which flank the core LPL ATTTGCAT sequence and interfere with OTF-1 binding when chemically modified. Introduction of mutations in either 5' or 3' flanking AT-rich sequences lowered the affinity of OTF-1 binding below the level observed with the wild-type LPL octamer oligomer. A double mutation in both flanking AT regions, however, greatly reduced the affinity of this site to levels similar to that observed with the mouse Vk T1 OTF site. An additional nuclear transcription factor, NF-Y, has been shown to bind to a functional CCAAT box motif located at -65 bp in the LPL promoter using specific alpha-NF-Y antisera. The observation of high affinity OTF-1 and NF-Y binding sites in a region of the proximal LPL promoter which is necessary for high levels of LPL transcription suggests that these sites with their associated proteins play important functional roles in the transcriptional activation of the LPL promoter during adipocyte differentiation.
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Affiliation(s)
- R A Currie
- Department of Medicine, University of Colorado Health Sciences Center, Denver 80262
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85
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Jantzen HM, Chow AM, King DS, Tjian R. Multiple domains of the RNA polymerase I activator hUBF interact with the TATA-binding protein complex hSL1 to mediate transcription. Genes Dev 1992; 6:1950-63. [PMID: 1398072 DOI: 10.1101/gad.6.10.1950] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent evidence suggests that transcription initiation by all three eukaryotic RNA polymerases involves a complex of the TATA-binding protein (TBP) and multiple TBP-associated factors (TAFs). Here, we map the functional domains of the nucleolar HMG box protein hUBF, which binds to the human rRNA promoter and stimulates transcription by RNA polymerase I through cooperative interactions with a distinct TBP-TAF complex, hSL1. DNase I footprint analysis of mutant hUBF proteins and of a synthetic peptide of 84 amino acids reveals that HMG box 1 is necessary and sufficient for DNA sequence specificity, whereas other HMG boxes and the amino terminus modulate the binding efficiency. hUBF contains multiple activation domains that include the acidic carboxyl terminus and three HMG boxes. HMG boxes 3 and 4 and the acidic tail contribute significantly to an extended footprinting pattern in the presence of hSL1, suggestive of specific protein-protein interactions. Moreover, the inability of xUBF from Xenopus laevis to form an initiation complex with hSL1 can be overcome by hybrid proteins containing human HMG box 4 and the acidic carboxyl terminus. These results strongly suggest an important role of transcription activation domains of hUBF in mediating interactions with the TBP-TAF complex hSL1.
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Affiliation(s)
- H M Jantzen
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley 94720
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86
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Kües U, Casselton LA. Molecular and functional analysis of the A mating type genes of Coprinus cinereus. GENETIC ENGINEERING 1992; 14:251-68. [PMID: 1368279 DOI: 10.1007/978-1-4615-3424-2_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Affiliation(s)
- U Kües
- Department of Plant Sciences, University of Oxford, UK
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87
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Botfield MC, Jancso A, Weiss MA. Biochemical characterization of the Oct-2 POU domain with implications for bipartite DNA recognition. Biochemistry 1992; 31:5841-8. [PMID: 1610826 DOI: 10.1021/bi00140a020] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
B-cell specific regulation of immunoglobulin gene expression provides a model for the interaction of promoter and enhancer elements with eukaryotic sequence-specific DNA binding proteins. A critical element of this system, the octamer site (5'-ATGCAAAT-3'), is recognized by the B-cell transcription factor Oct-2. Octamer recognition is mediated by the POU domain, a conserved structural motif which--like the zinc finger and leucine zipper--defines a family of related transcription factors. Homologies among POU sequences suggest a bipartite structure, consisting of an N-terminal POU-specific subdomain and C-terminal variant homeodomain connected by a linker of variable length and sequence. As a first step toward a molecular understanding of the Oct-2 POU domain and its mechanism of DNA recognition, we have overexpressed in Escherichia coli the intact POU domain and subdomains as thrombin-cleavable fusion proteins and have purified these fragments to homogeneity following digestion with thrombin. Biochemical and biophysical characterization yields the following results. (i) The intact POU domain (166 residues) is monomeric and exhibits high-affinity octamer-specific DNA-binding activity. (ii) Limited proteolytic digestion demonstrates that the POU domain contains two proteolytically stable subdomains (the POU-specific subdomain and the variant homeodomain) connected by a proteolytically sensitive linker. (iii) The isolated subdomains are each monomeric and do not interact to form noncovalent heterodimers.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M C Botfield
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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88
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Zwartkruis F, Hoeijmakers T, Deschamps J, Meijlink F. The murine Hox-2.4 promoter contains a functional octamer motif. Nucleic Acids Res 1992; 20:1599-606. [PMID: 1349742 PMCID: PMC312244 DOI: 10.1093/nar/20.7.1599] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Like other HOX genes the murine Hox-2.4 gene is thought to be involved in regional specification along the antero-posterior axis. In addition it has been reported to have oncogenic potential. We studied expression Hox-2.4 in murine EC cells and determined the transcription start site. Studies of DNA-protein interactions in the promoter region showed that the Hox-2.4 promoter contains a CCAAT box and a perfect octamer motif, which is capable of binding Oct-factors. Cotransfection of Oct expression vectors influences the transcriptional activity of the promoter, suggesting that the Oct-gene family may be involved in regulating HOX genes.
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Affiliation(s)
- F Zwartkruis
- Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Utrecht
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89
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Meijer D, Graus A, Grosveld G. Mapping the transactivation domain of the Oct-6 POU transcription factor. Nucleic Acids Res 1992; 20:2241-7. [PMID: 1594443 PMCID: PMC312337 DOI: 10.1093/nar/20.9.2241] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The POU transcription factor Oct-6 is expressed in embryonic stem cells, glial progenitor cells and in a restricted set of neurons in the CNS. The protein has been shown to act as a transactivator as well as a repressor. Here we show that the Oct-6 protein activates transcription from three different promoters in HeLa cells. The ability to activate a minimal tk promoter via a multimerized IgH enhancer octamer motif relies on a domain within the aminoterminal third of the protein. Parts of this domain can be deleted without abolishing transactivation, suggesting that there is functional redundancy within this region. The transactivation domain of the Oct-6 protein is different from other described activation domains in that it is highly glycine and alanine rich.
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Affiliation(s)
- D Meijer
- MGC, Department of Cell Biology and Genetics, Erasmus University, Rotterdam, The Netherlands
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90
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Hara Y, Rovescalli AC, Kim Y, Nirenberg M. Structure and evolution of four POU domain genes expressed in mouse brain. Proc Natl Acad Sci U S A 1992; 89:3280-4. [PMID: 1565620 PMCID: PMC48850 DOI: 10.1073/pnas.89.8.3280] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Four mouse POU domain genomic DNA clones--Brain-1, Brain-2, Brain-4, and Scip--and Brain-2 cDNA, which are expressed in adult brain, were cloned and the coding and noncoding regions of the genes were sequenced. The amino acid sequences of the four POU domains are highly conserved; sequences in other regions of the proteins also are conserved but to a lesser extent. The absence of introns from the coding regions of the four POU domain genes and the similarity of amino acid sequences of the corresponding proteins suggest that the coding region of the ancestral class III POU domain gene lacked introns and therefore may have originated by reverse transcription of a molecule of POU domain mRNA followed by insertion of the cDNA into germ cell genomic DNA. Additional duplications of the ancestral class III POU domain gene (or mRNA) would create the Brain-1, Brain-2, Brain-4, and Scip genes.
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Affiliation(s)
- Y Hara
- Laboratory of Biochemical Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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91
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Annweiler A, Müller U, Wirth T. Functional analysis of defined mutations in the immunoglobulin heavy-chain enhancer in transgenic mice. Nucleic Acids Res 1992; 20:1503-9. [PMID: 1579442 PMCID: PMC312230 DOI: 10.1093/nar/20.7.1503] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We have analyzed the effect of defined mutations in the mouse immunoglobulin heavy-chain enhancer after introduction into the germline of transgenic mice. We have tested a mutation of the enhancer octamer motif, a double mutation of the octamer motif and the microB-site, and a triple mutation in the microE2, microE3 and microE4-sites. All constructs are expressed in the spleen of transgenic mice. Furthermore, expression is exclusively detectable in lymphoid organs and not in several nonlymphoid tissues. Whereas mutations in the microE-sites have a more pronounced effect on transgene activity in thymocytes as compared to bone marrow and spleen cells, the octamer/microB double mutation shows significantly reduced expression levels only in B-cells. Finally, our results demonstrate that the intronic heavy-chain enhancer element does not contribute to the increase steady state levels of heavy-chain mRNA after stimulation of spleen cells with LPS.
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Affiliation(s)
- A Annweiler
- Zentrum für Molekulare Biologie Heidelberg, Germany
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92
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Abstract
The POU domain is the conserved DNA binding domain of a family of gene regulatory proteins. It consists of a POU-specific domain and a POU homeodomain, connected by a variable linker region. Oct-1 is a ubiquitously expressed POU domain transcription factor. It binds to the canonical octamer sequence (ATGCAAAT) as a monomer. Here we show by chemical cross-linking and protein affinity chromatography that the Oct-1 POU domain monomers can interact in solution. This association requires both the POU homeodomain and the POU-specific domain. The interaction is transient in solution and can be stabilized by binding to the heptamer-octamer sequence in the immunoglobulin heavy-chain promoter. This correlates with cooperative DNA binding to this site. POU proteins from different subclasses, including Oct-1, Oct-2A, Oct-6, and a chimeric Oct-1 protein containing the Pit-1 POU domain, can bind cooperatively to a double binding site and form a heteromeric complex.
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93
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Verrijzer CP, van Oosterhout JA, van der Vliet PC. The Oct-1 POU domain mediates interactions between Oct-1 and other POU proteins. Mol Cell Biol 1992; 12:542-51. [PMID: 1346336 PMCID: PMC364225 DOI: 10.1128/mcb.12.2.542-551.1992] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The POU domain is the conserved DNA binding domain of a family of gene regulatory proteins. It consists of a POU-specific domain and a POU homeodomain, connected by a variable linker region. Oct-1 is a ubiquitously expressed POU domain transcription factor. It binds to the canonical octamer sequence (ATGCAAAT) as a monomer. Here we show by chemical cross-linking and protein affinity chromatography that the Oct-1 POU domain monomers can interact in solution. This association requires both the POU homeodomain and the POU-specific domain. The interaction is transient in solution and can be stabilized by binding to the heptamer-octamer sequence in the immunoglobulin heavy-chain promoter. This correlates with cooperative DNA binding to this site. POU proteins from different subclasses, including Oct-1, Oct-2A, Oct-6, and a chimeric Oct-1 protein containing the Pit-1 POU domain, can bind cooperatively to a double binding site and form a heteromeric complex.
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Affiliation(s)
- C P Verrijzer
- Laboratory for Physiological Chemistry, University of Utrecht, The Netherlands
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94
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Abstract
The ubiquitously expressed mammalian POU-domain protein Oct-1 specifically recognizes two classes of cis-acting regulatory elements that bear little sequence similarity, the octamer motif ATGCAAAT and the TAATGARAT motif. The related pituitary-specific POU protein Pit-1 also recognizes these two motifs but, unlike Oct-1, binds preferentially to the TAATGARAT motif. Yet in our assay, Pit-1 still binds octamer elements better than does the octamer motif-binding protein Oct-3. The POU domain is responsible for recognizing these diverse regulatory sequences through multiple DNA contacts that include the two POU subdomains, the POU-specific region, and the POU homeodomain. The DNA-binding properties of 10 chimeric POU domains, in which different POU-domain segments are derived from either Oct-1 or Pit-1, reveal a high degree of structural plasticity; these hybrid proteins all bind DNA well and frequently bind particular sites better than does either of the parental POU domains. In these chimeric POU domains, the POU-specific A and B boxes and the hypervariable POU linker can influence DNA-binding specificity. The surprising result is that the influence a particular segment has on DNA-binding specificity can be greatly affected by the origin of other segments of the POU domain and the sequence of the binding site. Thus, the broad but selective DNA-binding specificity of Oct-1 is conferred both by multiple DNA contacts and by dynamic interactions within the DNA-bound POU domain.
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95
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Abstract
The ubiquitously expressed mammalian POU-domain protein Oct-1 specifically recognizes two classes of cis-acting regulatory elements that bear little sequence similarity, the octamer motif ATGCAAAT and the TAATGARAT motif. The related pituitary-specific POU protein Pit-1 also recognizes these two motifs but, unlike Oct-1, binds preferentially to the TAATGARAT motif. Yet in our assay, Pit-1 still binds octamer elements better than does the octamer motif-binding protein Oct-3. The POU domain is responsible for recognizing these diverse regulatory sequences through multiple DNA contacts that include the two POU subdomains, the POU-specific region, and the POU homeodomain. The DNA-binding properties of 10 chimeric POU domains, in which different POU-domain segments are derived from either Oct-1 or Pit-1, reveal a high degree of structural plasticity; these hybrid proteins all bind DNA well and frequently bind particular sites better than does either of the parental POU domains. In these chimeric POU domains, the POU-specific A and B boxes and the hypervariable POU linker can influence DNA-binding specificity. The surprising result is that the influence a particular segment has on DNA-binding specificity can be greatly affected by the origin of other segments of the POU domain and the sequence of the binding site. Thus, the broad but selective DNA-binding specificity of Oct-1 is conferred both by multiple DNA contacts and by dynamic interactions within the DNA-bound POU domain.
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Affiliation(s)
- R Aurora
- Cold Spring Harbor Laboratory, New York 11724-2206
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96
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Nelsen B, Sen R. Regulation of immunoglobulin gene transcription. INTERNATIONAL REVIEW OF CYTOLOGY 1992; 133:121-49. [PMID: 1577586 DOI: 10.1016/s0074-7696(08)61859-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Analysis of the immunoglobulin gene suggests that their expression is controlled through the combinatorial action of tissue- and stage-specific factors (OTF-2, TF-microB, NF-kappa B), as well as more widely expressed E motif-binding factors such as E47/E12. Two basic issues cloud understanding of how these factors are involved in immunoglobulin gene regulation. First, cloning of these factors shows them to be members of families of proteins, all with similar DNA-binding specificities. OTF-2 is a member of the POU domain family, NF-kappa B is a related protein, and the microE5/kappa E2-binding factors are members of the bHLH family. Second, these binding sites and associated factors are involved in the regulation of many genes, not only the immunoglobulin genes, and in fact not only lymphoid-specific genes. These facts complicate understanding which member of a family is in fact responsible for interaction with, and activation of, a particular binding element in an enhancer/promoter. Recently, more detailed analysis of the interactions between such proteins and their related binding sites suggest that a certain level of specificity may in fact be encoded by the DNA element such that one family member of a protein is preferentially bound, or alternatively that the protein-DNA interactions that occur give subtle alterations in protein conformation that unmask an activation or protein-protein interactive domain. An additional level of regulation is imparted by combinatorial mechanisms such as adjacent DNA-binding elements and factors that may alter activity, as well as "cofactors" that, by forming a complex with the bound factor, affect its activation of a gene in a particular cell type. A third level of specificity may be obtained by factors such as NF-kappa B and the bHLH family due to their ability to create heterogeneous complexes, creating unique complexes in a tissue- or stage-specific manner. The multiple functions transcription factors such as NF-kappa B and OTF-2 play in the transcriptional regulation of multiple genes seems complex in contrast to a one factor, one gene regulation model. However, this type of organization may limit the number of factors lymphocytes would require if each lymphoid-specific gene were activated by a unique factor. Thus what appears to be complexity at the molecular level may reflect an economical organization at the cellular level. Investigation of the key factors controlling these genes suggests an ordered cascade of transcription factors becomes available in the cell during B cell differentiation.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- B Nelsen
- Rosenstiel Center, Department of Biology, Brandeis University, Waltham, Massachusetts 02254-9110
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97
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A human alpha-fetoprotein enhancer-binding protein, ATBF1, contains four homeodomains and seventeen zinc fingers. Mol Cell Biol 1991. [PMID: 1719379 DOI: 10.1128/mcb.11.12.6041] [Citation(s) in RCA: 103] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have isolated a full-length cDNA encoding a protein (ATBF1) that binds to an AT-rich motif in the human alpha-fetoprotein gene enhancer. The amino acid sequence deduced from the cDNA revealed that this is the largest DNA-binding protein (306 kDa) known to date, containing four homeodomains, 17 zinc finger motifs, and a number of segments potentially involved in transcriptional regulation. Although the exact function of this protein has not been determined, these structural features suggest that ATBF1 plays a transcriptional regulatory role.
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98
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Morinaga T, Yasuda H, Hashimoto T, Higashio K, Tamaoki T. A human alpha-fetoprotein enhancer-binding protein, ATBF1, contains four homeodomains and seventeen zinc fingers. Mol Cell Biol 1991; 11:6041-9. [PMID: 1719379 PMCID: PMC361769 DOI: 10.1128/mcb.11.12.6041-6049.1991] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have isolated a full-length cDNA encoding a protein (ATBF1) that binds to an AT-rich motif in the human alpha-fetoprotein gene enhancer. The amino acid sequence deduced from the cDNA revealed that this is the largest DNA-binding protein (306 kDa) known to date, containing four homeodomains, 17 zinc finger motifs, and a number of segments potentially involved in transcriptional regulation. Although the exact function of this protein has not been determined, these structural features suggest that ATBF1 plays a transcriptional regulatory role.
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Affiliation(s)
- T Morinaga
- Research Institute of Life Science, Snow Brand Milk Products Co., Ltd., Japan
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99
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Exocrine pancreas transcription factor 1 binds to a bipartite enhancer element and activates transcription of acinar genes. Mol Cell Biol 1991. [PMID: 1717824 DOI: 10.1128/mcb.11.10.4985] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Exocrine pancreas (XP) enhancers, which contain a conserved core sequence, are active only in XP cells. A core enhancer-binding activity also appears to be restricted to XP nuclei. Here we describe the properties of a factor, purified approximately 100,000-fold from pancreas nuclei, which displays core enhancer-binding activity. It is not identical to previously characterized factors and is termed exocrine pancreas transcription factor 1 (XPF-1). In the highly purified preparation, only a single major protein of 60 kDa was detected by silver staining on sodium dodecyl sulfate-gels and by UV cross-linking. XPF-1 binds to the core enhancer of all tested XP genes and not to a mutant sequence which is inactive in vivo. High-affinity binding sites are bipartite. The results of competition binding and UV-cross-linking assays suggest that XPF-1 interacts with both motifs. XPF-1 selectively stimulates transcription of core enhancer templates in an in vitro transcription system. We hypothesize that XPF-1 plays a role in activation of the transcription of XP-specific genes.
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100
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Abstract
Much effort has been directed towards the investigation of regulatory processes in the early mouse embryo. Several multigene families of developmental control genes have been identified. The POU family is a group of related transcription factors containing a particular type of bipartite DNA-binding domain. Members of this family show distinct expression patterns during embryonic development. Two members, Oct-4 and Oct-6, are expressed as early as in the preimplantation embryo and thus may regulate early events of murine development.
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Affiliation(s)
- H R Schöler
- Max-Planck Institute of Biophysical Chemistry, Department of Molecular Cell Biology, Göttingen, FRG
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