101
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Ström L, Lundgren M, Severinson E. Binding of Ikaros to germline Ig heavy chain gamma1 and epsilon promoters. Mol Immunol 2003; 39:771-82. [PMID: 12617992 DOI: 10.1016/s0161-5890(03)00004-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Immunoglobulin (Ig) class switching occurs in activated B cells and results in production of antigen-specific IgA, IgE or IgG. It involves a DNA recombination event and is partly regulated by germline (GL) immunoglobulin heavy chain promoters. Ikaros is an abundant nuclear protein expressed in hematopoietic cells. Many different functions have been ascribed to Ikaros, such as transcriptional activation or repression, cell cycle control and tumor suppression. A typical feature of Ikaros is its expression in large clusters in the nucleus of activated lymphocytes. We give evidence that Ikaros can bind to several sites in the germline gamma1 and epsilon immunoglobulin heavy chain promoters, in a cooperative manner. Using a promoter reporter assay, we found evidence that Ikaros can suppress germline gamma1 and epsilon promoter activity in a B cell line. When a mutated non-DNA-binding form of Ikaros was introduced into primary activated B cells by retrovirus transduction, the endogenous Ikaros clusters were disrupted. In spite of this, there was no effect on transcription or Ig class switching. The data are discussed in relation to the different hypotheses for the function of Ikaros.
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Affiliation(s)
- Lena Ström
- Department of Cell and Molecular Biology, Karolinska Institute, Box 285, SE-171 77 Stockholm, Sweden
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102
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Abstract
The C2H2 zinc finger is the most prevalent protein motif in the mammalian proteome. Two C2H2 fingers in Ikaros are dedicated to homotypic interactions between family members. We show here that these fingers comprise a bona fide dimerization domain. Dimerization is highly selective, however, as homologous domains from the TRPS-1 and Drosophila Hunchback proteins support homodimerization, but not heterodimerization with Ikaros. Ikaros-Hunchback selectivity is determined by 11 residues concentrated within the alpha-helical regions typically involved in base recognition. Preferential homodimerization of one chimeric protein predicts a parallel dimer interface and establishes the feasibility of creating novel dimer specificities. These results demonstrate that the C2H2 motif provides a versatile platform for both sequence-specific protein-nucleic acid interactions and highly specific dimerization.
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Affiliation(s)
- Aaron S McCarty
- Howard Hughes Medical Institute, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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103
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Harker N, Naito T, Cortes M, Hostert A, Hirschberg S, Tolaini M, Roderick K, Georgopoulos K, Kioussis D. The CD8alpha gene locus is regulated by the Ikaros family of proteins. Mol Cell 2002; 10:1403-15. [PMID: 12504015 DOI: 10.1016/s1097-2765(02)00711-6] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ikaros family members are important regulatory factors in lymphocyte development. Here we show that Ikaros may play an important role in CD4 versus CD8 lineage commitment decisions by demonstrating: (1) that it binds to regulatory elements in the endogenous CD8alpha locus in vivo using thymocyte chromatin immunoprecipitations, (2) that Ikaros suppresses position effect variegation of transgenes driven by CD8 regulatory elements, and (3) that mice with reduced levels of Ikaros and Aiolos show an apparent increase in CD4 populations with immature phenotype, i.e., cells that failed to activate the CD8alpha gene locus. We propose that Ikaros family members function as activators of the CD8alpha gene locus and that their associated activities are critical for appropriate chromatin remodeling transitions during thymocyte differentiation and lineage commitment.
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Affiliation(s)
- Nicola Harker
- Division of Molecular Immunology, National Institute for Medical Research, Medical Research Council, NW7 1AA, London, United Kingdom
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104
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Dovat S, Ronni T, Russell D, Ferrini R, Cobb BS, Smale ST. A common mechanism for mitotic inactivation of C2H2 zinc finger DNA-binding domains. Genes Dev 2002; 16:2985-90. [PMID: 12464629 PMCID: PMC187490 DOI: 10.1101/gad.1040502] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Many nuclear proteins are inactivated during mitotic entry, presumably as a prerequisite to chromatin condensation and cell division. C2H2 zinc fingers define the largest transcription factor family in the human proteome. The linker separating finger motifs is highly conserved and resembles TGEKP in more than 5000 occurrences. However, the reason for this conservation is not fully understood. We demonstrate that all three linkers in the DNA-binding domain of Ikaros are phosphorylated during mitosis. Phosphomimetic substitutions abolished DNA-binding and pericentromeric localization. A linker within Sp1 was also phosphorylated, suggesting that linker phosphorylation provides a global mechanism for inactivation of the C2H2 family.
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Affiliation(s)
- Sinisa Dovat
- Howard Hughes Medical Institute, Department of Microbiology, Immunology, and Molecular Genetics, California 90095, USA
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105
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Abstract
The ultimate goal of developmental immunology is to understand the normal processes that give rise to the immune system in order to diagnose and develop effective treatments for diseases that occur as a consequence of immune system defects. Central to achieving this goal is understanding the complex interplay between microenvironmental signals and transcription factors that direct human hematopoietic differentiation and lineage commitment. The ability to isolate highly purified populations of human hematopoietic cells at critical points in differentiation make it possible to answer very specific questions about the hematopoietic process and lineage restriction. This review describes the use of surface immunophenotypes to identify human hematopoietic cells at particular points in differentiation or with particular patterns of lineage restriction. Culture models are discussed in the context of the ability to detect, characterize and determine the lineage potential of human hematopoietic stem cells and progenitors. Variations in hematopoeises that correspond to ontogeny will be examined. Potential roles for the HOX and Ikaros proteins in human lineage commitment will be considered. Also included will be discussion of a number of factors that provide challenges to experimental design, to experimental interpretation, and to the development of a comprehensive model of human hematopoiesis.
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Affiliation(s)
- Kimberly J Payne
- Childrens Hospital Los Angeles, Division of Research Immunology/Bone Marrow Transplantation, Los Angeles, CA, USA.
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106
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Li S, Dobretsova A, Kokorina NA, Wight PA. Repression of myelin proteolipid protein gene expression is mediated through both general and cell type-specific negative regulatory elements in nonexpressing cells. J Neurochem 2002; 82:159-71. [PMID: 12091477 DOI: 10.1046/j.1471-4159.2002.00962.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The myelin proteolipid protein gene (Plp ) is expressed primarily in oligodendrocytes. Yet how the gene remains repressed in nonexpressing cells has not been defined, and potentially could cause adverse effects in an organism if the mechanism for repression was impaired. Previous studies suggest that the first intron contains element(s), which suppress expression in nonexpressing cells, although the identity of these elements within the 8 kb intron was not characterized. Here we report the localization of multiple negative regulatory elements that repress Plp gene expression in nonexpressing cells (+/+ Li). Two of these elements (regions) correspond to those used by Plp expressing cells (N20.1), whilst another acts in a cell type-specific manner (i.e. operational in +/+ Li liver cells, but not N20.1 cells). By gel-shift and DNase I footprinting analyses, the factor(s) that bind to the cell type-specific negative regulatory region appear to be far more abundant in +/+ Li cells than in N20.1 cells. Thus, Plp gene repression is mediated through the combinatorial action of both "general" and cell type-specific negative regulatory elements. Additionally, repression in +/+ Li cells cannot be overcome via an antisilencer/enhancer element, which previously has been shown to function in N20.1 cells.
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Affiliation(s)
- Shenyang Li
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, 4301 W. Markham Street, Little Rock, AR 72205, USA
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107
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Abstract
The development of the immune system and the host response to microbial infection rely on the activation and silencing of numerous, differentially expressed genes. Since the mid-1980s, a primary goal has been to identify transcription factors that regulate specific genes and specific immunological processes. More recently, there has been a growing appreciation of the role of chromatin structure in gene regulation. Before most activators of a gene access their binding sites, a transition from a condensed to a decondensed chromatin structure appears to take place. The activation of transcription is then accompanied by the remodeling of specific nucleosomes. Conversely, the acquisition of a more condensed chromatin structure is often associated with gene silencing. Chromatin structure is a particularly significant contributor to gene regulation because it is likely to be a major determinant of cell identity and cell memory. That is, the propagation of decondensed chromatin at specific loci through DNA replication and cell division helps a cell remember which genes are expressed constitutively in that cell type or are poised for expression upon exposure to a stimulus. Here we review recent progress toward understanding the role of chromatin in the immune system. The interleukin-4 gene serves as a primary model for exploring the events involved in the acquisition and heritable maintenance of a decondensed chromatin structure. Studies of the interleukin-12 p40 and interferon-beta genes are then reviewed for insight into the mechanisms by which the remodeling of specific nucleosomes in the vicinity of a promoter can contribute to rapid activation following cell stimulation. Finally, basic principles of gene silencing are discussed.
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Affiliation(s)
- Stephen T Smale
- Howard Hughes Medical Institute and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095-1662, USA.
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108
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Abstract
In general, transcriptionally active euchromatin replicates during the first half of S phase, whereas silent heterochromatin replicates during the second half. Moreover, changes in replication timing accompany key stages of development. Although there is not a strict correlation between replication timing and transcription per se, recent results reveal a strong relationship between heritably repressed chromatin and late replication that is conserved in all eukaryotes. A long-standing question is whether replication timing dictates the structure of chromatin or vice versa. Mounting evidence supports a model in which replication timing is both cause and consequence of chromatin structure by providing a means to inherit chromatin states that, in turn, regulate replication timing in the subsequent cell cycle. Moreover, new findings relating aberrations in replication timing to defects in centromere function, chromosome cohesion and genome instability suggest that the role of replication timing extends beyond its relationship to transcription. Novel systems in both yeasts and mammals are finally beginning to reveal some of the determinants that regulate replication timing, which should pave the way for a long-anticipated molecular dissection of this complex liaison.
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Affiliation(s)
- David M Gilbert
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA.
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109
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Abstract
The development of increasingly sophisticated tools to track chromosomes and proteins in living cells offers the possibility of visualising gene regulation in the nucleus with minimal distortion. This, in conjunction with powerful genetic approaches available in yeast, is beginning to allow functional definition of nuclear "compartments".
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Affiliation(s)
- Jonathan Baxter
- Lymphocyte Development Group, Medical Research Council, Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
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110
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Abstract
The past two decades have witnessed significant advances in our understanding of the cellular physiology and molecular regulation of hematopoiesis. At the heart of stem cell self-renewal and lineage commitment decisions lies the relative expression levels of lineage-specific transcription factors. The expression of these transcription factors in early stem cells may be promiscuous and fluctuate, but ultimately comes under the influence of extracellular regulatory signals in the form of hematopoietic cytokines. In this review, we first summarize our current understanding of the phenotypic characterization of hematopoietic stem cells. Next, we describe key known transcription factors which govern stem cell self-renewal and lineage commitment decisions. Finally, we review data concerning the role of specific cytokines in influencing these decisions. From this review, a picture emerges in which stem cell fate decisions are governed by the integrated effects of intrinsic transcription factors and external signaling pathways initiated by regulatory cytokines.
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Affiliation(s)
- Jiang Zhu
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, PA 19104, USA
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111
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Dillon N, Festenstein R. Unravelling heterochromatin: competition between positive and negative factors regulates accessibility. Trends Genet 2002; 18:252-8. [PMID: 12047950 DOI: 10.1016/s0168-9525(02)02648-3] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Heterochromatin mediates many diverse functions in the cell nucleus, including centromere function, gene silencing and nuclear organization. The condensed structure of pericentromeric heterochromatin is associated with the presence of a regular arrangement of nucleosomes, which might be due in part to the underlying sequence of the satellite repeats. Recent studies identified methylation of the histone H3 tail as an epigenetic mark that affects acetylation and phosphorylation of histone tail residues and also acts as a recognition signal for binding of heterochromatin protein 1 (HP1). The decision to silence or activate heterochromatic genes appears to be the result of a balance between negative factors that promote the formation of condensed higher-order chromatin structure, and positively acting transcription factors that bind to regulatory sequences and activate gene expression.
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Affiliation(s)
- Niall Dillon
- Gene Regulation and Chromatin Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Campus, Du Cane Road, London, UK W12 0NN.
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112
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Dorsam G, Goetzl EJ. Vasoactive intestinal peptide receptor-1 (VPAC-1) is a novel gene target of the hemolymphopoietic transcription factor Ikaros. J Biol Chem 2002; 277:13488-93. [PMID: 11812772 DOI: 10.1074/jbc.m107922200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vasoactive intestinal peptide and its G-protein-coupled receptors, VPAC-1 and VPAC-2, are highly expressed in the immune system and modulate diverse T cell functions. The human VPAC-1 5'-flanking region (1.4 kb) contains four high affinity Ikaros (IK) consensus sequences. Ikaros native protein from T cell nuclear extracts and IK-1 and IK-2 recombinant proteins recognized an IK high affinity binding motif in the VPAC-1 promoter in electrophoretic mobility shift assays by a sequence-specific mechanism, and anti-IK antibodies supershifted this complex. Stable NIH-3T3 clones overexpressing IK-1 or IK-2 isoforms were generated to investigate Ikaros regulation of endogenous VPAC-1 expression as assessed by quantifying VPAC-1 mRNA and protein. By traditional and fluorometric-based kinetic reverse transcription-PCR and (125)I-labeled vasoactive intestinal peptide binding, both IK-1 and IK-2 suppressed endogenous VPAC-1 expression in NIH-3T3 clones by a range of 50-93%. When a series of nested deletions of the VPAC-1 luciferase reporter construct were transiently transfected into IK-2 clones there was up to a 41% decrease in transcriptional activity compared with vector control. Two major IK-2 binding domains also were identified at -1076 to -623 bp and at -222 to -35 bp, respectively. As both Ikaros and its novel target VPAC-1 are highly expressed in T cells, this system may be a dominant determinant of the VPAC-1 expression in immune responses.
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MESH Headings
- 3T3 Cells
- Amino Acid Motifs
- Animals
- Cell Line
- DNA, Complementary/metabolism
- DNA-Binding Proteins
- Down-Regulation
- Genes, Dominant
- Genes, Reporter
- Humans
- Ikaros Transcription Factor
- Jurkat Cells
- Kinetics
- Luciferases/metabolism
- Mice
- Models, Genetic
- Peptides/chemistry
- Protein Binding
- Protein Isoforms
- Protein Structure, Tertiary
- RNA, Messenger/metabolism
- Rats
- Receptors, Vasoactive Intestinal Peptide/metabolism
- Receptors, Vasoactive Intestinal Polypeptide, Type I
- Recombinant Proteins/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Transcription Factors/metabolism
- Transcription, Genetic
- Transfection
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Affiliation(s)
- Glenn Dorsam
- Department of Medicine, University of California Medical Center, San Francisco, California 94143-0711, USA.
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113
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Koipally J, Heller EJ, Seavitt JR, Georgopoulos K. Unconventional potentiation of gene expression by Ikaros. J Biol Chem 2002; 277:13007-15. [PMID: 11799125 DOI: 10.1074/jbc.m111371200] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ikaros is essential for the normal development and regulated proliferation of lymphoid cells. In lymphocytes, Ikaros exists as an integral component of chromatin-remodeling complexes, including the Mi-2beta/nucleosome remodeling and deacetylation complex (NuRD) complex. It is expected that Ikaros, together with these associated activities effects repression, but here we show that they may also potentiate gene expression in cycling cells. Ikaros cannot activate transcription by itself; instead, it enhances the activity of both weak and strong activators. For this role in potentiation, Ikaros requires its DNA binding and dimerization domains. The DNA binding and dimerization properties of Ikaros are also responsible for its targeting to pericentromeric heterochromatin (PC-HC). Significantly, Ikaros mutants with altered specificity for DNA binding that are unable to localize to PC-HC are incapable of stimulating transcription from reporters bearing their cognate sites. Thus, potentiation of gene expression by Ikaros correlates strongly with its ability to localize to PC-HC in combination with the chromatin remodeler Mi-2beta.
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Affiliation(s)
- Joseph Koipally
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
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114
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Abstract
Although advances in molecular biology have allowed us to identify and describe many of the events associated with turning genes on, much less attention has generally been focussed on the related process of gene silencing. This is surprising as heritable gene inactivation plays an important role in determining cell lineage fates during development and defining their temporal order. Recent advances in the area of chromatin and chromosome organisation may have an impact on our understanding of cellular differentiation.
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Affiliation(s)
- Amanda G Fisher
- Lymphocyte Development Group, Medical Research Council, Clinical Sciences Centre, Faculty of Medicine, Imperial College of Science, Technology and Medicine, Hammersmith Campus, Du Cane Road, London W12 ONN, UK.
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115
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Abstract
The regulated production of several terminally differentiated cell types of the blood and immune systems (haematopoiesis) has been the focus of many studies on cell-fate determination. Chromatin and the control of its structure have been implicated in the regulation of cell-fate decisions and in the maintenance of the determined states. Here, I review advances in the field, emphasizing the potential role of chromatin in lineage commitment and differentiation. In this context, I discuss Ikaros, an essential regulator of lymphocyte development and an integral component of a functionally diverse chromatin remodelling network that operates from the early stages of haematopoiesis to the mature lymphocytes.
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116
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Wilson CB, Makar KW, Pérez-Melgosa M. Epigenetic regulation of T cell fate and function. J Infect Dis 2002; 185 Suppl 1:S37-45. [PMID: 11865438 DOI: 10.1086/338001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
During their development, T lymphocytes make sequential cell fate choices: T rather than B lymphocytes, then TCRalphabeta or TCRgammadelta, CD4 or CD8, and Th1 or Th2 lineage. These fate choices require the initiation of new programs of gene expression, and once initiated, these programs must be faithfully propagated in a heritable manner from parental cells to their progeny. With the exception of the T cell receptor, these changes in gene expression occur without a change in information encoded directly in the DNA sequence. Rather, these heritable programs of gene expression are imposed, at least in part, epigenetically through changes in chromatin structure and DNA methylation, allowing T cells to tune the threshold for expression of specific genes.
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Affiliation(s)
- Christopher B Wilson
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195, USA.
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117
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Ito T, Nomura S, Okada M, Katsumata Y, Kikkawa F, Rogi T, Tsujimoto M, Mizutani S. Ap-2 and Ikaros regulate transcription of human placental leucine aminopeptidase/oxytocinase gene. Biochem Biophys Res Commun 2002; 290:1048-53. [PMID: 11798181 DOI: 10.1006/bbrc.2001.6325] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
P-LAP is identical with cystine aminopeptidase as oxytocinase. We previously located on the placental leucine aminopeptidase (P-LAP) gene the footprint site with the high promoter activity (FP3: -214 to -183) and found a possible interaction between it and AP-2 in choriocarcinoma cells. Here, we investigated FP3 in detail and identified the elements responsible for the high basal rate of transcription. Electrophoretic mobility shift assays demonstrated that FP3 would interact with Ikaros as well as AP-2. Further analysis using antibody against Ikaros confirmed that Ikaros was indeed present and bound to FP3. In addition, AP-2alpha and AP-2gamma antibodies supershifted the second complex at FP3. Functionally, mutations that eliminate AP-2 binding reduced promoter activity significantly, while those that eliminate Ikaros binding reduced promoter activity insignificantly. Double mutations of AP-2 and Ikaros decreased promoter activity progressively. We conclude that AP-2 is the main activator and Ikaros functions cooperatively with it for maximal expression of the human P-LAP gene.
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Affiliation(s)
- Tomomi Ito
- Department of Obstetrics and Gynecology, Nagoya University School of Medicine, Nagoya, 466-8550, Japan
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118
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Tucker SN, Jessup HK, Fujii H, Wilson CB. Enforced expression of the Ikaros isoform IK5 decreases the numbers of extrathymic intraepithelial lymphocytes and natural killer 1.1+ T cells. Blood 2002; 99:513-9. [PMID: 11781232 DOI: 10.1182/blood.v99.2.513] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The zinc-finger protein Ikaros plays an important role in lymphoid homeostasis, and loss of Ikaros expression through germline disruption impairs lymphoid development. However, the role played by Ikaros after commitment to the T-cell lineage is unclear. To address this question, this study used the lck proximal promoter to drive the expression in T-cell progenitors of a naturally occurring short Ikaros isoform (IK5), which lacks the DNA-binding domain, reasoning that IK5 will form heterodimers with long isoforms and perturb their function. The IK5 transgene led to a selective and dramatic decrease in extrathymic intestinal intraepithelial lymphocytes (IELs) and natural killer 1.1+ T (NK T) cells with little effect on conventional alphabeta T cells, which resembles the T-cell phenotype of interleukin-15 receptor alpha chain (IL-15Ralpha) and IL-2/IL-15 receptor beta chain (IL-2Rbeta) knockout mice. The expression of IL-2Rbeta on double-negative T-cell progenitors of bi-5 was reduced, but enforced expression of IL-2Rbeta did not rescue IELs or NK T cells in bi-5 transgenic mice, suggesting that Ikaros or Ikaros family members regulate the expression of additional genes that are essential for the development of IELs and NK T cells. The study concludes that modest changes in the ratio of short to long Ikaros isoforms can substantially perturb T-cell development, and the development of IELs and NK T cells is particularly sensitive to such changes.
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Affiliation(s)
- Sean N Tucker
- Department of Immunology, University of Washington, Seattle 98195, USA
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