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Kotlyarov S, Kotlyarova A. Participation of Krüppel-like Factors in Atherogenesis. Metabolites 2023; 13:metabo13030448. [PMID: 36984888 PMCID: PMC10052737 DOI: 10.3390/metabo13030448] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Atherosclerosis is an important problem in modern medicine, the keys to understanding many aspects of which are still not available to clinicians. Atherosclerosis develops as a result of a complex chain of events in which many cells of the vascular wall and peripheral blood flow are involved. Endothelial cells, which line the vascular wall in a monolayer, play an important role in vascular biology. A growing body of evidence strengthens the understanding of the multifaceted functions of endothelial cells, which not only organize the barrier between blood flow and tissues but also act as regulators of hemodynamics and play an important role in regulating the function of other cells in the vascular wall. Krüppel-like factors (KLFs) perform several biological functions in various cells of the vascular wall. The large family of KLFs in humans includes 18 members, among which KLF2 and KLF4 are at the crossroads between endothelial cell mechanobiology and immunometabolism, which play important roles in both the normal vascular wall and atherosclerosis.
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Affiliation(s)
- Stanislav Kotlyarov
- Department of Nursing, Ryazan State Medical University, 390026 Ryazan, Russia
| | - Anna Kotlyarova
- Department of Pharmacy Management and Economics, Ryazan State Medical University, 390026 Ryazan, Russia
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2
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Wieschaus E, Nüsslein-Volhard C. The Heidelberg Screen for Pattern Mutants of Drosophila: A Personal Account. Annu Rev Cell Dev Biol 2016; 32:1-46. [PMID: 27501451 DOI: 10.1146/annurev-cellbio-113015-023138] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In large-scale mutagenesis screens performed in 1979-1980 at the EMBL in Heidelberg, we isolated mutations affecting the pattern or structure of the larval cuticle in Drosophila. The 600 mutants we characterized could be assigned to 120 genes and represent the majority of such genes in the genome. These mutants subsequently provided a rich resource for understanding many fundamental developmental processes, such as the transcriptional hierarchies controlling segmentation, the establishment of cell states by signaling pathways, and the differentiation of epithelial cells. Most of the Heidelberg genes are now molecularly known, and many of them are conserved in other animals, including humans. Although the screens were initially driven entirely by curiosity, the mutants now serve as models for many human diseases. In this review, we describe the rationale of the screening procedures and provide a classification of the genes on the basis of their initial phenotypes and the subsequent molecular analyses.
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Affiliation(s)
- Eric Wieschaus
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544;
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3
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Kayukawa T, Nagamine K, Ito Y, Nishita Y, Ishikawa Y, Shinoda T. Krüppel Homolog 1 Inhibits Insect Metamorphosis via Direct Transcriptional Repression of Broad-Complex, a Pupal Specifier Gene. J Biol Chem 2015; 291:1751-1762. [PMID: 26518872 DOI: 10.1074/jbc.m115.686121] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Indexed: 01/13/2023] Open
Abstract
The Broad-Complex gene (BR-C) encodes transcription factors that dictate larval-pupal metamorphosis in insects. The expression of BR-C is induced by molting hormone (20-hydroxyecdysone (20E)), and this induction is repressed by juvenile hormone (JH), which exists during the premature larval stage. Krüppel homolog 1 gene (Kr-h1) has been known as a JH-early inducible gene responsible for repression of metamorphosis; however, the functional relationship between Kr-h1 and repression of BR-C has remained unclear. To elucidate this relationship, we analyzed cis- and trans elements involved in the repression of BR-C using a Bombyx mori cell line. In the cells, as observed in larvae, JH induced the expression of Kr-h1 and concurrently suppressed 20E-induced expression of BR-C. Forced expression of Kr-h1 repressed the 20E-dependent activation of the BR-C promoter in the absence of JH, and Kr-h1 RNAi inhibited the JH-mediated repression, suggesting that Kr-h1 controlled the repression of BR-C. A survey of the upstream sequence of BR-C gene revealed a Kr-h1 binding site (KBS) in the BR-C promoter. When KBS was deleted from the promoter, the repression of BR-C was abolished. Electrophoresis mobility shift demonstrated that two Kr-h1 molecules bound to KBS in the BR-C promoter. Based on these results, we conclude that Kr-h1 protein molecules directly bind to the KBS sequence in the BR-C promoter and thereby repress 20E-dependent activation of the pupal specifier, BR-C. This study has revealed a considerable portion of the picture of JH signaling pathways from the reception of JH to the repression of metamorphosis.
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Affiliation(s)
- Takumi Kayukawa
- From the Insect Growth Regulation Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan,.
| | - Keisuke Nagamine
- From the Insect Growth Regulation Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan,; Laboratory of Applied Entomology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo 113-8657, Japan, and
| | - Yuka Ito
- From the Insect Growth Regulation Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan
| | - Yoshinori Nishita
- Department of Biological Science and Center for Genome Dynamics, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yukio Ishikawa
- Laboratory of Applied Entomology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo 113-8657, Japan, and
| | - Tetsuro Shinoda
- From the Insect Growth Regulation Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan
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4
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Simon JM, Parker JS, Liu F, Rothbart SB, Ait-Si-Ali S, Strahl BD, Jin J, Davis IJ, Mosley AL, Pattenden SG. A Role for Widely Interspaced Zinc Finger (WIZ) in Retention of the G9a Methyltransferase on Chromatin. J Biol Chem 2015; 290:26088-102. [PMID: 26338712 PMCID: PMC4646261 DOI: 10.1074/jbc.m115.654459] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/23/2015] [Indexed: 11/06/2022] Open
Abstract
G9a and GLP lysine methyltransferases form a heterodimeric complex that is responsible for the majority of histone H3 lysine 9 mono- and di-methylation (H3K9me1/me2). Widely interspaced zinc finger (WIZ) associates with the G9a-GLP protein complex, but its role in mediating lysine methylation is poorly defined. Here, we show that WIZ regulates global H3K9me2 levels by facilitating the interaction of G9a with chromatin. Disrupting the association of G9a-GLP with chromatin by depleting WIZ resulted in altered gene expression and protein-protein interactions that were distinguishable from that of small molecule-based inhibition of G9a/GLP, supporting discrete functions of the G9a-GLP-WIZ chromatin complex in addition to H3K9me2 methylation.
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Affiliation(s)
- Jeremy M Simon
- From the Carolina Institute for Developmental Disabilities, Department of Cell Biology and Physiology, and the Department of Genetics, Curriculum in Bioinformatics and Computational Biology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Joel S Parker
- the Department of Genetics and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Feng Liu
- the Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599
| | - Scott B Rothbart
- the Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Slimane Ait-Si-Ali
- the Laboratoire Epigénétique et Destin Cellulaire, UMR7216, CNRS, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Brian D Strahl
- the Lineberger Comprehensive Cancer Center, the Curriculum in Genetics and Molecular Biology, and the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Jian Jin
- the Department of Structural and Chemical Biology, the Department of Oncological Sciences, and the Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Ian J Davis
- the Department of Genetics, the Lineberger Comprehensive Cancer Center, the Department of Pediatrics, and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and
| | - Amber L Mosley
- the Department of Biochemistry and Molecular Biology and the Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Samantha G Pattenden
- the Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599,
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5
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Presnell JS, Schnitzler CE, Browne WE. KLF/SP Transcription Factor Family Evolution: Expansion, Diversification, and Innovation in Eukaryotes. Genome Biol Evol 2015; 7:2289-309. [PMID: 26232396 PMCID: PMC4558859 DOI: 10.1093/gbe/evv141] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2015] [Indexed: 11/13/2022] Open
Abstract
The Krüppel-like factor and specificity protein (KLF/SP) genes play key roles in critical biological processes including stem cell maintenance, cell proliferation, embryonic development, tissue differentiation, and metabolism and their dysregulation has been implicated in a number of human diseases and cancers. Although many KLF/SP genes have been characterized in a handful of bilaterian lineages, little is known about the KLF/SP gene family in nonbilaterians and virtually nothing is known outside the metazoans. Here, we analyze and discuss the origins and evolutionary history of the KLF/SP transcription factor family and associated transactivation/repression domains. We have identified and characterized the complete KLF/SP gene complement from the genomes of 48 species spanning the Eukarya. We have also examined the phylogenetic distribution of transactivation/repression domains associated with this gene family. We report that the origin of the KLF/SP gene family predates the divergence of the Metazoa. Furthermore, the expansion of the KLF/SP gene family is paralleled by diversification of transactivation domains via both acquisitions of pre-existing ancient domains as well as by the appearance of novel domains exclusive to this gene family and is strongly associated with the expansion of cell type complexity.
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Affiliation(s)
| | - Christine E Schnitzler
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health
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6
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Yoshida T, Hayashi M. Role of Krüppel-like factor 4 and its binding proteins in vascular disease. J Atheroscler Thromb 2014; 21:402-13. [PMID: 24573018 DOI: 10.5551/jat.23044] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Krüppel-like factor 4(KLF4) is a zinc-finger transcription factor that plays a key role in cellular differentiation and proliferation during normal development and in various diseases, such as cancer. The results of recent studies have revealed that KLF4 is expressed in multiple vascular cell types, including phenotypically modulated smooth muscle cells(SMCs), endothelial cells and monocytes/macrophages and contributes to the progression of vascular diseases by activating or repressing the transcription of multiple genes via its associations with a variety of partner proteins. For example, KLF4 decreases the expression of markers of SMC differentiation by interacting with serum response factor, ELK1 and histone deacetylases. KLF4 also suppresses SMC proliferation by associating with p53. In addition, KLF4 enhances arterial medial calcification in concert with RUNX2. Furthermore, endothelial KLF4 represses arterial inflammation by binding to nuclear factor-κB. This article summarizes the role of KLF4 in vascular disease with a particular focus on in vivo studies and reviews recent progress in our understanding of the regulatory mechanisms involved in KLF4- mediated gene transcription.
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Affiliation(s)
- Tadashi Yoshida
- Apheresis and Dialysis Center, School of Medicine, Keio University
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7
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Lavore A, Esponda-Behrens N, Pagola L, Rivera-Pomar R. The gap gene Krüppel of Rhodnius prolixus is required for segmentation and for repression of the homeotic gene sex comb-reduced. Dev Biol 2014; 387:121-9. [PMID: 24406318 DOI: 10.1016/j.ydbio.2013.12.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 12/18/2013] [Accepted: 12/20/2013] [Indexed: 11/19/2022]
Abstract
The establishment of the anterior-posterior segmentation in insects requires the concerted action of a hierarchical gene network. Here, we study the orthologue of Krüppel gap gene in the hemipteran Rhodnius prolixus (Rp-Kr). We characterized its structure, expression pattern and function. The genomic sequence upstream of the Rp-Kr transcriptional unit shows a putative regulatory region conserved in the orthologue genes from Drosophila melanogaster and Tribolium castaneum. Rp-Kr expression is zygotic and it is expressed in the anterior half of the embryo (the posterior half of the egg) during the blastoderm stage and germ band formation; later, during germ band extension, it is expressed in a central domain, from T2 to A3. The Rp-Kr loss of function phenotypes shows disrupted thoracic and abdominal segmentation. Embryos with weak segmentation phenotypes show homeotic transformations, in which an ectopic tibial comb, typical of T1 leg, appears in T2, which correlates with the ectopic expression of Rp-sex-comb reduced in this leg.
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Affiliation(s)
- Andrés Lavore
- Laboratorio de Genética y Genómica Funcional, Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, Avenue Calchaqui Km 23.5, Florencio Varela, Buenos Aires, Argentina; Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de Buenos Aires, Pergamino, Argentina
| | - Natalia Esponda-Behrens
- Laboratorio de Genética y Genómica Funcional, Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, Avenue Calchaqui Km 23.5, Florencio Varela, Buenos Aires, Argentina
| | - Lucía Pagola
- Laboratorio de Genética y Genómica Funcional, Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, Avenue Calchaqui Km 23.5, Florencio Varela, Buenos Aires, Argentina
| | - Rolando Rivera-Pomar
- Laboratorio de Genética y Genómica Funcional, Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, Avenue Calchaqui Km 23.5, Florencio Varela, Buenos Aires, Argentina; Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de Buenos Aires, Pergamino, Argentina.
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8
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Blechert O, Douglas D, Baumgartner S. Conserved function of the Krüppel gap gene in the blowfly Lucilia sericata, despite anterior shift of expression. INSECT MOLECULAR BIOLOGY 2011; 20:257-265. [PMID: 21166911 DOI: 10.1111/j.1365-2583.2010.01063.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
To determine whether expression patterns of segmentation genes found in Drosophila melanogaster can be scaled to pattern larger insects, we studied the expression of the Krüppel (Kr) gene in the blowfly Lucilia sericata. Compared with Drosophila Kr, L. sericata Kr showed an unexpected 10% shift of expression towards the anterior pole. Furthermore, expression domains not found in D. melanogaster were present at the blastoderm stage of L. sericata. To compare Kr activity and function, we employed RNA interference-mediated gene silencing. We found Kr phenotypes in L. sericata comparable with those observed in D. melanogaster, demonstrating that L. sericata Kr functions as a gap gene as it does in Drosophila. Our results show that, despite an anterior shift in expression, Kr function has remained conserved during the evolution of the blowflies.
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Affiliation(s)
- O Blechert
- Lund University, Department of Experimental Medical Sciences, Lund, Sweden
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9
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Abstract
Gap genes are involved in segment determination during the early development of the fruit fly Drosophila melanogaster as well as in other insects. This review attempts to synthesize the current knowledge of the gap gene network through a comprehensive survey of the experimental literature. I focus on genetic and molecular evidence, which provides us with an almost-complete picture of the regulatory interactions responsible for trunk gap gene expression. I discuss the regulatory mechanisms involved, and highlight the remaining ambiguities and gaps in the evidence. This is followed by a brief discussion of molecular regulatory mechanisms for transcriptional regulation, as well as precision and size-regulation provided by the system. Finally, I discuss evidence on the evolution of gap gene expression from species other than Drosophila. My survey concludes that studies of the gap gene system continue to reveal interesting and important new insights into the role of gene regulatory networks in development and evolution.
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Affiliation(s)
- Johannes Jaeger
- Centre de Regulació Genòmica, Universtitat Pompeu Fabra, Barcelona, Spain.
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10
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Klug A. The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Annu Rev Biochem 2010; 79:213-31. [PMID: 20192761 DOI: 10.1146/annurev-biochem-010909-095056] [Citation(s) in RCA: 493] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An account is given of the discovery of the classical Cys(2)His(2) zinc finger, arising from the interpretation of biochemical studies on the interaction of the Xenopus protein transcription factor IIIA with 5S RNA, and of structural studies on its structure and its interaction with DNA. The finger is a self-contained domain stabilized by a zinc ion ligated to a pair of cysteines and a pair of histidines, and by an inner hydrophobic core. This discovery showed not only a new protein fold but also a novel principle of DNA recognition. Whereas other DNA binding proteins generally make use of the two-fold symmetry of the double helix, zinc fingers can be linked linearly in tandem to recognize nucleic acid sequences of varying lengths. This modular design offers a large number of combinatorial possibilities for the specific recognition of DNA (or RNA). It is therefore not surprising that the zinc finger is found widespread in nature, including 3% of the genes of the human genome. The zinc finger design is ideally suited for engineering proteins to target specific genes. In the first example of their application in 1994, a three-finger protein was constructed to block the expression of an oncogene transformed into a mouse cell line. In addition, a reporter gene was activated by targeting an inserted zinc finger promoter. Thus, by fusing zinc finger peptides to repression or activation domains, genes can be selectively switched off or on. It was also suggested that by combining zinc fingers with other effector domains, e.g., from nucleases or integrases, to form chimeric proteins, genomes could be manipulated or modified. Several applications of such engineered zinc finger proteins are described here, including some of therapeutic importance.
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Affiliation(s)
- Aaron Klug
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom.
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11
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The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation. Q Rev Biophys 2010; 43:1-21. [DOI: 10.1017/s0033583510000089] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AbstractA long-standing goal of molecular biologists has been to construct DNA-binding proteins for the control of gene expression. The classical Cys2His2 (C2H2) zinc finger design is ideally suited for such purposes. Discriminating between closely related DNA sequences both in vitro and in vivo, this naturally occurring design was adopted for engineering zinc finger proteins (ZFPs) to target genes specifically.Zinc fingers were discovered in 1985, arising from the interpretation of our biochemical studies on the interaction of the Xenopus protein transcription factor IIIA (TFIIIA) with 5S RNA. Subsequent structural studies revealed its three-dimensional structure and its interaction with DNA. Each finger constitutes a self-contained domain stabilized by a zinc (Zn) ion ligated to a pair of cysteines and a pair of histidines and also by an inner structural hydrophobic core. This discovery showed not only a new protein fold but also a novel principle of DNA recognition. Whereas other DNA-binding proteins generally make use of the 2-fold symmetry of the double helix, functioning as homo- or heterodimers, zinc fingers can be linked linearly in tandem to recognize nucleic acid sequences of varying lengths. This modular design offers a large number of combinatorial possibilities for the specific recognition of DNA (or RNA). It is therefore not surprising that the zinc finger is found widespread in nature, including 3% of the genes of the human genome.The zinc finger design can be used to construct DNA-binding proteins for specific intervention in gene expression. By fusing selected zinc finger peptides to repression or activation domains, genes can be selectively switched off or on by targeting the peptide to the desired gene target. It was also suggested that by combining an appropriate zinc finger peptide with other effector or functional domains, e.g. from nucleases or integrases to form chimaeric proteins, genomes could be modified or manipulated.The first example of the power of the method was published in 1994 when a three-finger protein was constructed to block the expression of a human oncogene transformed into a mouse cell line. The same paper also described how a reporter gene was activated by targeting an inserted 9-base pair (bp) sequence, which acts as the promoter. Thus, by fusing zinc finger peptides to repression or activation domains, genes can be selectively switched off or on. It was also suggested that, by combining zinc fingers with other effector or functional domains, e.g. from nucleases or integrases, to form chimaeric proteins, genomes could be manipulated or modified.Several applications of such engineered ZFPs are described here, including some of therapeutic importance, and also their adaptation for breeding improved crop plants.
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12
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Calestani C, Rogers DJ. Cis-regulatory analysis of the sea urchin pigment cell gene polyketide synthase. Dev Biol 2010; 340:249-55. [PMID: 20122918 DOI: 10.1016/j.ydbio.2010.01.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Revised: 01/21/2010] [Accepted: 01/22/2010] [Indexed: 11/19/2022]
Abstract
The Strongylocentrotus purpuratus polyketide synthase gene (SpPks) encodes an enzyme required for the biosynthesis of the larval pigment echinochrome. SpPks is expressed exclusively in pigment cells and their precursors starting at blastula stage. The 7th-9th cleavage Delta-Notch signaling, required for pigment cell development, positively regulates SpPks. In previous studies, the transcription factors glial cell missing (SpGcm), SpGatae and kruppel-like (SpKrl/z13) have been shown to positively regulate SpPks. To uncover the structure of the Gene Regulatory Network (GRN) regulating the specification and differentiation processes of pigment cells, we experimentally analyzed the putative SpPks cis-regulatory region. We established that the -1.5kb region is sufficient to recapitulate the correct spatial and temporal expression of SpPks. Predicted DNA-binding sites for SpGcm, SpGataE and SpKrl are located within this region. The mutagenesis of these DNA-binding sites indicated that SpGcm, SpGataE and SpKrl are direct positive regulators of SpPks. These results demonstrate that the sea urchin GRN for pigment cell development is quite shallow, which is typical of type I embryo development.
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Affiliation(s)
- Cristina Calestani
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA.
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13
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Rebilly JN, Gardner PW, Darling GR, Bacsa J, Rosseinsky MJ. Chiral II−VI Semiconductor Nanostructure Superlattices Based on an Amino Acid Ligand. Inorg Chem 2008; 47:9390-9. [DOI: 10.1021/ic801097w] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jean-Noël Rebilly
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K
| | - Paul W. Gardner
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K
| | - George R. Darling
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K
| | - John Bacsa
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K
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Okada G, Maruo K, Funada S, Nakamura M. Differential display analysis of gene expression in female-to-male sex-reversing gonads of the frog Rana rugosa. Gen Comp Endocrinol 2008; 155:623-34. [PMID: 17942098 DOI: 10.1016/j.ygcen.2007.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Revised: 08/07/2007] [Accepted: 08/13/2007] [Indexed: 11/25/2022]
Abstract
Sex steroids play pivotal roles in gonadal differentiation in many species of vertebrates. The sex can be reversed from female to male by testosterone in the Japanese wrinkled frog Rana rugosa, but it is still unclear what genes are up- or down-regulated during the XX sex-reversal in this species. To search the genes for the female-to-male sex-reversal, we employed differential display and 5'/3'-RACE. Consequently, we isolated from the gonads at day 8 after testosterone injection 24 different cDNA fragments showing a testosterone treatment-related change and then obtained three full-length cDNAs, which we termed Zfp64, Zfp112, and Rrp54. The former two cDNAs encoded different proteins with zinc-finger domains, whereas the latter cDNA encoded an unknown protein. Transcripts of the three genes were hardly detectable in the sex-reversing gonads at day 24 after the injection; at this time few growing oocytes were observed in the sex-reversing gonad. Besides, in situ hybridization analysis showed positive signals of the three genes in the cytoplasm of growing oocytes of an ovary when testosterone was injected into a tadpole. Thus, the decrease in expression of these three genes was probably due to the disappearance of growing oocytes and not to their direct involvement in the testis formation. To find the key-gene for testis formation, it will be necessary to analyze, by the differential display method, more genes showing a change in expression pattern during sex reversal.
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Affiliation(s)
- Goro Okada
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 1-6-1 Nishi-Waseda, Shinjuku-ku, Tokyo 169-8050, Japan
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15
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Abstract
Asymmetric cell divisions are a crucial mode of cell fate specification in multicellular organisms, but their relative contribution to early embryonic patterning varies among taxa. In the embryo of the mollusc Ilyanassa, most of the early cell divisions are overtly asymmetric. During Ilyanassa early cleavage, mRNAs for several conserved developmental patterning genes localize to interphase centrosomes, and then during division they move to a portion of the cortex that will be inherited by one daughter cell. Here we report an unbiased survey of RNA localization in the Ilyanassa embryo, and examine the overall patterns of centrosomal localization during early development. We find that 3-4% of RNAs are specifically localized to centrosomes during early development, and the remainder are either ubiquitously distributed throughout the cytoplasm or weakly enriched on centrosomes compared with levels in the cytoplasm. We observe centrosomal localization of RNAs in all cells from zygote through the fifth cleavage cycle, and asymmetric RNA segregation in all divisions after the four-cell stage. Remarkably, each specifically localized message is found on centrosomes in a unique subset of cells during early cleavages, and most are found in unique sets of cells at the 24-cell stage. Several specifically localized RNAs are homologous to developmental regulatory proteins in other embryos. These results demonstrate that the mechanisms of localization and segregation are extraordinarily intricate in this system, and suggest that these events are involved in cell fate specification across all lineages in the early Ilyanassa embryo. We propose that greater reliance on segregation of determinants in early cleavage increases constraint on cleavage patterns in molluscs and other spiralian groups.
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Affiliation(s)
- Evan P Kingsley
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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16
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Surkova S, Kosman D, Kozlov K, Manu, Myasnikova E, Samsonova AA, Spirov A, Vanario-Alonso CE, Samsonova M, Reinitz J. Characterization of the Drosophila segment determination morphome. Dev Biol 2008; 313:844-62. [PMID: 18067886 PMCID: PMC2254320 DOI: 10.1016/j.ydbio.2007.10.037] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 08/27/2007] [Accepted: 10/18/2007] [Indexed: 11/24/2022]
Abstract
Here we characterize the expression of the full system of genes which control the segmentation morphogenetic field of Drosophila at the protein level in one dimension. The data used for this characterization are quantitative with cellular resolution in space and about 6 min in time. We present the full quantitative profiles of all 14 segmentation genes which act before the onset of gastrulation. The expression patterns of these genes are first characterized in terms of their average or typical behavior. At this level, the expression of all of the genes has been integrated into a single atlas of gene expression in which the expression levels of all genes in each cell are specified. We show that expression domains do not arise synchronously, but rather each domain has its own specific dynamics of formation. Moreover, we show that the expression domains shift position in the direction of the cephalic furrow, such that domains in the anlage of the segmented germ band shift anteriorly while those in the presumptive head shift posteriorly. The expression atlas of integrated data is very close to the expression profiles of individual embryos during the latter part of the blastoderm stage. At earlier times gap gene domains show considerable variation in amplitude, and significant positional variability. Nevertheless, an average early gap domain is close to that of a median individual. In contrast, we show that there is a diversity of developmental trajectories among pair-rule genes at a variety of levels, including the order of domain formation and positional accuracy. We further show that this variation is dynamically reduced, or canalized, over time. As the first quantitatively characterized morphogenetic field, this system and its behavior constitute an extraordinarily rich set of materials for the study of canalization and embryonic regulation at the molecular level.
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Affiliation(s)
- Svetlana Surkova
- Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnical University, 29 Polytehnicheskaya Street, St. Petersburg, 195251, Russia
| | - David Kosman
- Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA
| | - Konstantin Kozlov
- Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnical University, 29 Polytehnicheskaya Street, St. Petersburg, 195251, Russia
| | - Manu
- Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-3600, USA
| | - Ekaterina Myasnikova
- Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnical University, 29 Polytehnicheskaya Street, St. Petersburg, 195251, Russia
| | - Anastasia A. Samsonova
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Alexander Spirov
- Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-3600, USA
| | - Carlos E. Vanario-Alonso
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Ave Brigadeiro Trompowsky, CCS BL-G, Rio de Janeiro, RJ 21949, Brazil
| | - Maria Samsonova
- Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnical University, 29 Polytehnicheskaya Street, St. Petersburg, 195251, Russia
| | - John Reinitz
- Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-3600, USA
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17
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Berg JM. Metal-Binding Domains in Nucleic Acid-Binding and Gene-Regulatory Proteins. PROGRESS IN INORGANIC CHEMISTRY 2007. [DOI: 10.1002/9780470166383.ch3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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18
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Mito T, Okamoto H, Shinahara W, Shinmyo Y, Miyawaki K, Ohuchi H, Noji S. Krüppel acts as a gap gene regulating expression of hunchback and even-skipped in the intermediate germ cricket Gryllus bimaculatus. Dev Biol 2006; 294:471-81. [PMID: 16616119 DOI: 10.1016/j.ydbio.2005.12.057] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Revised: 12/22/2005] [Accepted: 12/27/2005] [Indexed: 11/19/2022]
Abstract
In Drosophila, a long germ insect, segmentation occurs simultaneously across the entire body. In contrast, in short and intermediate germ insects, the anterior segments are specified during the blastoderm stage, while the remaining posterior segments are specified during later stages. In Drosophila embryos, the transcriptional factors coded by gap genes, such as Krüppel, diffuse in the syncytial environment and regulate the expression of other gap, pair-rule, and Hox genes. To understand the segmentation mechanisms in short and intermediate germ insects, we investigated the role of Kr ortholog (Gb'Kr) in the development of the intermediate germ insect Gryllus bimaculatus. We found that Gb'Kr is expressed in a gap pattern in the prospective thoracic region after cellularization of the embryo. To determine the function of Gb'Kr in segmentation, we analyzed knockdown phenotypes using RNA interference (RNAi). Gb'Kr RNAi depletion resulted in a gap phenotype in which the posterior of the first thoracic through seventh abdominal segments were deleted. Analysis of the expression patterns of Hox genes in Gb'Kr RNAi embryos indicated that regulatory relationships between Hox genes and Kr in Gryllus differ from those in Oncopeltus, another intermediate germ insect. Furthermore, we found that Gb'Kr regulates expression minimally of hunchback and even-skipped, directly or indirectly, in the prospective thoracic region. Our findings suggest that Gb'Kr is a gap gene that acts in the cellular environment and is required for segmentation in the thoracic and abdominal regions through the regulation of gap and pair-rule gene expression.
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Affiliation(s)
- Taro Mito
- Department of Biological Science and Technology, Faculty of Engineering, The University of Tokushima, 2-1 Minami-Jyosanjima-cho, Tokushima City 770-8506, Japan
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19
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Antoine K, Prosperi MT, Ferbus D, Boule C, Goubin G. A Kruppel zinc finger of ZNF 146 interacts with the SUMO-1 conjugating enzyme UBC9 and is sumoylated in vivo. Mol Cell Biochem 2005; 271:215-23. [PMID: 15881673 DOI: 10.1007/s11010-005-6417-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The OZF (ZNF146) protein is a 33 kDa Kruppel protein, composed solely of 10 zinc finger motifs. It is overexpressed in the majority of pancreatic cancers and in more than 80% of colorectal cancers. We have identified OZF interacting factors with a yeast two-hybrid screen. Half of the positive clones characterized encoded UBC9, the E2 enzyme involved in the covalent conjugation of the small ubiquitin-like modifier 1 (SUMO-1). SUMO-1 is a 17 kDa migrating protein that is conjugated to several proteins and has been reported to exhibit multiple effects, including modulation of protein stability, subcellular localization, and gene expression. In HeLa cells transfected with OZF and SUMO-1 expression vectors, immunoblot revealed a major band migrating at 50 kDa and a minor band at 67 kDa, corresponding to the attachment to OZF of one and two SUMO-1 proteins, respectively. The relative amount of the sumoylated proteins increased following transfection with a UBC9 expression vector. The presence of the sumoylated form in HeLa cells solely transfected by OZF indicates the physiological activity of the endogenous SUMO-1 conjugation pathway. Using deletion mutants, we showed that two SUMO-1 modification sites are located on the sixth zinc finger. Mutation of two lysine residues greatly reduced the amount of the sumoylated form of OZF though their surrounding sequences differ from the consensus sequence reported for most proteins modified by SUMO-1 conjugation. Despite the presence of the sixth zinc finger, an OZF mutant containing zinc fingers 1-6 was not modified by SUMO-1 and failed to interact with UBC9. Addition of zinc finger 7 restored SUMO-1 modification and UBC9 interaction and provides evidence that a region downstream of the target lysines is required for interaction with UBC9, in order to achieve SUMO-1 modification. This is the first report of in vivo conjugation of a SUMO-1 protein to a Kruppel zinc finger motif.
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Affiliation(s)
- Karène Antoine
- Laboratoire d'Oncogenèse, FRE 2584 CNRS, Institut Curie, 26 rue d'Ulm, 75248 Paris 05, France
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20
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Liu F, Zhu C, Xiao J, Wang Y, Tang W, Yuan W, Zhao Y, Li Y, Xiang Z, Wu X, Liu M. A novel human KRAB-containing zinc-finger gene ZNF446 inhibits transcriptional activities of SRE and AP-1. Biochem Biophys Res Commun 2005; 333:5-13. [PMID: 15936718 DOI: 10.1016/j.bbrc.2005.05.069] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Accepted: 05/05/2005] [Indexed: 11/29/2022]
Abstract
Kruppel-related zinc-finger proteins constitute the largest individual family of transcription factors in mammals [C. Looman, L. Hellman, M. Abrink, A novel Kruppel-associated box identified in a panel of mammalian zinc-finger proteins, Mammalian Genome 15 (1) (2004) 35-40.[1]]. Here we identified and characterized a novel zinc-finger gene named ZNF446. The predicted protein contains a KRAB and three C(2)H(2) zinc fingers. Northern blot analysis shows that ZNF446 is expressed in a variety of human adult tissues with the highest expression level in muscle. ZNF446 is a transcription repressor when fused to GAL4 DNA-binding domain and co-transfected with VP-16. Overexpression of ZNF446 in COS-7 cells inhibits the transcriptional activities of SRE and AP-1, in which the KRAB motif represents the basal transcriptional repressive activity, suggesting that the ZNF446 protein may act as a transcriptional repressor in mitogen-activated protein kinase (MAPK) signaling pathway to mediate cellular functions.
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Affiliation(s)
- Fang Liu
- The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China.
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21
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Mito T, Sarashina I, Zhang H, Iwahashi A, Okamoto H, Miyawaki K, Shinmyo Y, Ohuchi H, Noji S. Non-canonical functions of hunchback in segment patterning of the intermediate germ cricket Gryllus bimaculatus. Development 2005; 132:2069-79. [PMID: 15788457 DOI: 10.1242/dev.01784] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In short and intermediate germ insects, only the anterior segments are specified during the blastoderm stage, leaving the posterior segments to be specified later, during embryogenesis, which differs from the segmentation process in Drosophila, a long germ insect. To elucidate the segmentation mechanisms of short and intermediate germ insects, we have investigated the orthologs of the Drosophila segmentation genes in a phylogenetically basal, intermediate germ insect, Gryllus bimaculatus(Gb). Here, we have focused on its hunchback ortholog(Gb'hb), because Drosophila hb functions as a gap gene during anterior segmentation, referred as a canonical function. Gb'hb is expressed in a gap pattern during the early stages of embryogenesis, and later in the posterior growth zone. By means of embryonic and parental RNA interference for Gb'hb, we found the following: (1) Gb'hb regulates Hox gene expression to specify regional identity in the anterior region, as observed in Drosophila and Oncopeltus; (2) Gb'hb controls germband morphogenesis and segmentation of the anterior region, probably through the pair-rule gene, even-skipped at least; (3) Gb'hb may act as a gap gene in a limited region between the posterior of the prothoracic segment and the anterior of the mesothoracic segment; and (4) Gb'hb is involved in the formation of at least seven abdominal segments, probably through its expression in the posterior growth zone, which is not conserved in Drosophila. These findings suggest that Gb'hb functions in a non-canonical manner in segment patterning. A comparison of our results with the results for other derived species revealed that the canonical hbfunction may have evolved from the non-canonical hb functions during evolution.
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Affiliation(s)
- Taro Mito
- Department of Biological Science and Technology, Faculty of Engineering, The University of Tokushima, 2-1 Minami-Jyosanjima-cho, Tokushima City 770-8506, Japan
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22
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Kuzin A, Brody T, Moore AW, Odenwald WF. Nerfin-1 is required for early axon guidance decisions in the developing Drosophila CNS. Dev Biol 2005; 277:347-65. [PMID: 15617679 DOI: 10.1016/j.ydbio.2004.09.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Revised: 09/15/2004] [Accepted: 09/20/2004] [Indexed: 11/25/2022]
Abstract
Many studies have focused on the mechanisms of axon guidance; however, little is known about the transcriptional control of the navigational components that carryout these decisions. This report describes the functional analysis of Nerfin-1, a nuclear regulator of axon guidance required for a subset of early pathfinding events in the developing Drosophila CNS. Nerfin-1 belongs to a highly conserved subfamily of Zn-finger proteins with cognates identified in nematodes and man. We show that the neural precursor gene prospero is essential for nerfin-1 expression. Unlike nerfin-1 mRNA, which is expressed in many neural precursor cells, the encoded Nerfin-1 protein is only detected in the nuclei of neuronal precursors that will divide just once and then transiently in their nascent neurons. Although nerfin-1 null embryos have no discernible alterations in neural lineage development nor in neuronal or glial identities, CNS pioneering neurons require nerfin-1 function for early axon guidance decisions. Furthermore, nerfin-1 is required for the proper development of commissural and connective axon fascicles. Our studies also show that Nerfin-1 is essential for the proper expression of robo2, wnt5, derailed, G-oalpha47A, Lar, and futsch, genes whose encoded proteins participate in these early navigational events.
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Affiliation(s)
- Alexander Kuzin
- Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda MD 20892-4160, USA.
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23
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Liu PZ, Kaufman TC. Kruppel is a gap gene in the intermediate germband insect Oncopeltus fasciatus and is required for development of both blastoderm and germband-derived segments. Development 2004; 131:4567-79. [PMID: 15342481 DOI: 10.1242/dev.01311] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Segmentation in long germband insects such as Drosophila occurs essentially simultaneously across the entire body. A cascade of segmentation genes patterns the embryo along its anterior-posterior axis via subdivision of the blastoderm. This is in contrast to short and intermediate germband modes of segmentation where the anterior segments are formed during the blastoderm stage and the remaining posterior segments arise at later stages from a posterior growth zone. The biphasic character of segment generation in short and intermediate germ insects implies that different formative mechanisms may be operating in blastoderm-derived and germband-derived segments. In Drosophila, the gap gene Krüppel is required for proper formation of the central portion of the embryo. This domain of Krüppel activity in Drosophila corresponds to a region that in short and intermediate germband insects spans both blastoderm and germband-derived segments. We have cloned the Krüppel homolog from the milkweed bug, Oncopeltus fasciatus (Hemiptera, Lygaeidae), an intermediate germband insect. We find that Oncopeltus Krüppel is expressed in a gap-like domain in the thorax during the blastoderm and germband stages of embryogenesis. In order to investigate the function of Krüppel in Oncopeltus segmentation, we generated knockdown phenotypes using RNAi. Loss of Krüppel activity in Oncopeltus results in a large gap phenotype, with loss of the mesothoracic through fourth abdominal segments. Additionally, we find that Krüppel is required to suppress both anterior and posterior Hox gene expression in the central portion of the germband. Our results show that Krüppel is required for both blastoderm-derived and germband-derived segments and indicate that Krüppel function is largely conserved in Oncopeltus and Drosophila despite their divergent embryogenesis.
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Affiliation(s)
- Paul Z Liu
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington IN, 47405, USA
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24
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Huang C, Wang Y, Li D, Li Y, Luo J, Yuan W, Ou Y, Zhu C, Zhang Y, Wang Z, Liu M, Wu X. Inhibition of transcriptional activities of AP-1 and c-Jun by a new zinc finger protein ZNF394. Biochem Biophys Res Commun 2004; 320:1298-305. [PMID: 15249231 DOI: 10.1016/j.bbrc.2004.06.080] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2004] [Indexed: 12/01/2022]
Abstract
Zinc finger proteins play important roles in a variety of cellular functions, including cell growth, proliferation, apoptosis, and intracellular signal transduction, and the zinc finger-containing transcription factor has been implicated as a critical regulator of multiple cardiac-expressed genes as well as a regulator of inducible gene expression in response to hypertrophic stimulation. With the aim of identifying the genes involved in human heart development and diseases, we have isolated a novel LER-related zinc finger gene named ZNF394 from human heart cDNA library. ZNF394 gene has a predicted 561-amino acid open reading frame, encoding a 64kDa zinc finger protein. The N-terminus of ZNF394 protein has a leucine-rich region (LER or SCAN domain), followed by a well-conserved krüppel-associated box domain. The C-terminus of the protein contains 7 C2H2 zinc finger motifs in tandem arrays with the highly conserved space region of the H/C-link. ZNF394 gene is mapped to chromosome 7q11.21. Northern blot analysis indicates that a 2.18kb transcript specific for ZNF394 is specifically expressed in the heart, skeletal muscle, and brain in human adult tissues. ZNF394 protein is expressed in cell nucleus. Overexpression of ZNF394 in the cell inhibits the transcriptional activities of c-Jun and AP-1 reporters, suggesting that ZNF394 is a new transcriptional repressor in mitogen-activated protein kinase signaling pathways and may play an important role in cardiac development and/or cardiac function.
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Affiliation(s)
- Chunxia Huang
- The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
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25
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Hering TM, Kazmi NH, Huynh TD, Kollar J, Xu L, Hunyady AB, Johnstone B. Characterization and chondrocyte differentiation stage-specific expression of KRAB zinc-finger protein gene ZNF470. Exp Cell Res 2004; 299:137-47. [PMID: 15302581 DOI: 10.1016/j.yexcr.2004.05.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2003] [Revised: 05/17/2004] [Indexed: 11/15/2022]
Abstract
As part of a study to identify novel transcriptional regulators of chondrogenesis-related gene expression, we have cloned and characterized cDNA for zinc-finger protein 470 (ZNF470), the human ortholog of which encodes a 717 amino acid residue protein containing 17 Cys(2)His(2) zinc-finger domains, as well as KRAB-A and KRAB-B motifs. The cDNA library used to isolate the initial ZNF470 clone was prepared from human bone marrow-derived mesenchymal progenitor cells at an intermediate stage of chondrogenic differentiation. We have determined the intron-exon structure of the human ZNF470 gene, which has been mapped to a zinc-finger cluster in a known imprinted region of human chromosome 19q13.4. ZNF470 is expressed at high levels in human testis and is expressed at low or undetectible levels in other adult tissues. Human ZNF470 expressed in mammalian cells as an EGFP fusion protein localizes predominantly to the nucleus, consistent with a role in transcriptional regulation. ZNF470, analyzed by quantitative real time PCR, was transiently expressed before the maximal expression of COL2A1 during chondrogenic differentiation in vitro. We have also characterized the bovine ortholog of human ZNF470, which encodes a 508 amino acid residue protein having 10 zinc-finger domains. A bovine ZNF470 cDNA clone was used to examine expression of ZNF470 in bovine articular chondrocytes treated with retinoic acid to stimulate dedifferentiation. Bovine ZNF470 expression was undetectable in freshly isolated bovine articular chondrocytes, but was dramatically upregulated in dedifferentiated retinoic acid-treated chondrocytes. These results, in two model systems, suggest a possible role for ZNF470 in the regulation of chondrogenesis-specific gene expression.
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Affiliation(s)
- Thomas M Hering
- Department of Orthopaedics, Case Western Reserve University, Cleveland, OH 44106, USA.
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26
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Jauch R, Bourenkov GP, Chung HR, Urlaub H, Reidt U, Jäckle H, Wahl MC. The zinc finger-associated domain of the Drosophila transcription factor grauzone is a novel zinc-coordinating protein-protein interaction module. Structure 2004; 11:1393-402. [PMID: 14604529 DOI: 10.1016/j.str.2003.09.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
About one-third of the more than 300 C2H2 zinc finger proteins of Drosophila contain a conserved sequence motif, the zinc finger-associated domain (ZAD). Genes that encode ZAD proteins are specific for and expanded in the genomes of insects. Only three ZAD-encoding gene functions are established, and the role of ZAD is unknown. Here we present the crystal structure of the ZAD of Grauzone (ZAD(Grau)), a Drosophila transcription factor that specifically controls the maternal Cdc20-like APC subunit Cortex. ZAD forms an atypical treble-clef-like zinc-coordinating fold. Head-to-tail arrangement of two ZAD(Grau) molecules in the crystals suggests dimer formation, an observation supported by crosslinking and dynamic light scattering. The results indicate that ZAD provides a novel protein-protein interaction module that characterizes a large family of insect transcription factors.
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Affiliation(s)
- Ralf Jauch
- Max-Planck Institut für biophysikalische Chemie, Abteilung Molekulare Entwicklungsbiologie, Röntgenkristallographie, Am Fassberg 11, D-37077 Göttingen, Germany
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27
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Matyash A, Chung HR, Jäckle H. Genome-wide mapping of in vivo targets of the Drosophila transcription factor Kruppel. J Biol Chem 2004; 279:30689-96. [PMID: 15131112 DOI: 10.1074/jbc.m403345200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Krüppel (Kr), a member of the gap class of Drosophila segmentation genes, encodes a DNA binding zinc finger-type transcription factor. In addition to its segmentation function at the blastoderm stage, Krüppel also plays a critical role in organ formation during later stages of embryogenesis. To systematically identify in vivo target genes of Krüppel, we isolated DNA fragments from the Krüppel-associated portion of chromatin and used them to find and map Krüppel-dependent cis-acting regulatory sites in the Drosophila genome. We show that Krüppel binding sites are not enriched in Krüppel-associated chromatin and that the clustering of Krüppel binding sites, as found in the cis-acting elements of Krüppel-dependent segmentation genes used for in silico searches of Krüppel target genes, is not a prerequisite for the in vivo binding of Krüppel to its regulatory elements. Results obtained with the newly identified target gene ken and barbie (ken) indicate that Krüppel represses transcription and thereby restricts the spatial expression pattern of ken during blastoderm and gastrulation.
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Affiliation(s)
- Alexey Matyash
- Max-Planck-Institut für biophysikalische Chemie, Abteilung Molekulare Entwicklungsbiologie, D-37070 Göttingen, Germany
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28
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Weissig H, Narisawa S, Sikström C, Olsson PG, McCarrey JR, Tsonis PA, Del Rio-Tsonis K, Millán JL. Three novel spermatogenesis-specific zinc finger genes. FEBS Lett 2003; 547:61-8. [PMID: 12860387 DOI: 10.1016/s0014-5793(03)00669-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We have cloned and characterized the expression, during spermatogenesis, of three novel zinc finger genes (Zfp94, Zfp95, Zfp96). Analysis of the deduced protein sequences reveals that all three molecules belong to the LeR family (leucine-rich zinc fingers) and that ZFP95 contains a domain homologous to the Krüppel-associated box. All three genes were found expressed at high levels in testis among other tissues, but testis-specific transcripts were observed for Zfp95 and Zfp96. Northern blot analyses of the testis-specific transcripts of Zfp95 and Zfp96 were performed using whole testis RNA as well as RNA isolated from enriched populations of specific spermatogenic cell types. The testis-specific transcript of Zfp95 showed the highest expression in pachytene spermatocytes, while that of Zfp96 was highly expressed in pachytene spermatocytes, in round spermatids and residual bodies. Northern blot analysis of RNA from the testis of mice carrying the atrichosis mutation further validated these expression patterns. In particular, the testis-specific transcripts of Zfp95 and Zfp96 were greatly reduced in heterozygous, and completely absent in homozygous testis RNA from atrichosis mutant mice, further defining the germ cell specificity of these transcripts.
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29
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Ferbus D, Bovin C, Validire P, Goubin G. The zinc finger protein OZF (ZNF146) is overexpressed in colorectal cancer. J Pathol 2003; 200:177-82. [PMID: 12754738 DOI: 10.1002/path.1337] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Overexpression of the OZF gene has previously been demonstrated in the majority of pancreatic cancers. However, because the stages of tumour progression in this disease are poorly defined, no conclusion could be drawn concerning the relationship between OZF overexpression and the course of tumour progression. In contrast, initiation and progression steps are well defined in colorectal cancer. Most colon cancers are believed to arise from polypoid adenomas as a result of the gradual accumulation of genetic alterations, allowing the study of genetic events in the early stages of neoplasia. Accordingly, we wanted to assess the frequency of OZF overexpression in this tumour type and the relationship between overexpression and disease stage. Twenty-five colon carcinoma specimens from different sites and at various stages were analysed by immunoblotting using a highly specific mouse monoclonal antibody. Each sample was compared with adjacent normal colonic mucosa. Complementary immunohistochemical analysis was also carried out on a commercially available tissue array to identify cells expressing OZF. Of the 25 tumours analysed by immunoblotting, 20 expressed higher levels of OZF protein than their adjacent normal mucosa. Immunohistochemistry revealed OZF expression in tumour cells of 56/59 carcinomas and occasionally in infiltrating lymphocytes but at lower levels. Little or no staining was observed in cells taken from normal or inflammatory colon specimens. In both immunoblot and immunohistochemistry experiments, no correlation was found between OZF expression and clinical parameters such as TNM classification, stage, localization and age. Immunostaining was observed in low-grade adenomas, indicating that OZF expression occurs very early in the course of tumour progression. OZF expression, infrequent or absent in normal colonic mucosa, is present in more than 80% of colorectal cancers. Dysregulation of the OZF gene is an early event that may be implicated in the genesis of colonic carcinoma and may therefore provide a potential therapeutic target.
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Affiliation(s)
- Didier Ferbus
- Laboratoire d'Oncogenèse, Institut Curie, Paris, France
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30
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Ishizuka M, Ohshima H, Tamura N, Nakada T, Inoue A, Hirose S, Hagiwara H. Molecular cloning and characteristics of a novel zinc finger protein and its splice variant whose transcripts are expressed during spermatogenesis. Biochem Biophys Res Commun 2003; 301:1079-85. [PMID: 12589823 DOI: 10.1016/s0006-291x(03)00085-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Testicular zinc finger protein (TZF) has a zinc finger motif of the Cys2-His2 type and its transcript is expressed predominantly in mouse spermatogenic cells. Using the fragment of TZF as a probe, we isolated the alternative splice variant form (TZF-L) from mouse testis cDNA library. Analysis of the open reading frame of each cDNA indicated that TZF and TZF-L were polypeptides of 942 and 2025 amino acid residues, respectively, and the N-terminal 902 amino acids of TZF-L were identical to those of TZF. The C-terminal region of TZF-L had more a zinc finger motif of the Cys2-His2 type and poly-Glu and poly-Pro regions. The mouse TZF/TZF-L gene spanned >20 kb and consisted of 11 exons. RT-PCR analysis of the expression level of mRNAs for mouse TZF and TZF-L showed that both transcripts are highly expressed in testis and moderately in kidney and ovary. Elevated expression of both transcripts during testicular development in mice was restricted to spermatocytes at the pachytene stage of meiotic prophase. Fusion proteins with GFP also demonstrated the nuclear localization of TZF and TZF-L. These experiments suggest that TZF and TZF-L may act to control the gene activity during spermatogenesis.
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Affiliation(s)
- Masamichi Ishizuka
- Department of Biological Sciences, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, 226-8501, Yokohama, Japan
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31
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Chung HR, Schäfer U, Jäckle H, Böhm S. Genomic expansion and clustering of ZAD-containing C2H2 zinc-finger genes in Drosophila. EMBO Rep 2002; 3:1158-62. [PMID: 12446571 PMCID: PMC1308319 DOI: 10.1093/embo-reports/kvf243] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2002] [Revised: 09/27/2002] [Accepted: 10/18/2002] [Indexed: 11/14/2022] Open
Abstract
C2H2 zinc-finger proteins (ZFPs) constitute the largest family of nucleic acid binding factors in higher eukaryotes. In silico analysis identified a total of 326 putative ZFP genes in the Drosophila genome, corresponding to approximately 2.3% of the annotated genes. Approximately 29% of the Drosophila ZFPs are evolutionary conserved in humans and/or Caenorhabditis elegans. In addition, approximately 28% of the ZFPs contain an N-terminal zinc-finger-associated C4DM domain (ZAD) consisting of approximately 75 amino acid residues. The ZAD is restricted to ZFPs of dipteran and closely related insects. The evolutionary restriction, an expansion of ZAD-containing ZFP genes in the Drosophila genome and their clustering at few chromosomal sites are features reminiscent of vertebrate KRAB-ZFPs. ZADs are likely to represent protein-protein interaction domains. We propose that ZAD-containing ZFP genes participate in transcriptional regulation either directly or through site-specific modification and/or regulation of chromatin.
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Affiliation(s)
- Ho-Ryun Chung
- Abteilung Molekulare Entwicklungsbiologie, Max-Planck-Institut für biophysikalische Chemie, Am Fassberg, D-37077 Göttingen, Germany
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32
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Miyake N, Katoh O, Hirata S, Kimura S, Watanabe H, Yajin K. Expression of the Krüppel-type zinc finger gene, ZK7, in head and neck squamous cell carcinoma and normal mucosa. Cancer Lett 2002; 185:111-8. [PMID: 12142086 DOI: 10.1016/s0304-3835(02)00303-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
ZK7 is thought to be involved in the inhibitory effect of vascular endothelial growth factor on apoptotic cell death in human hematopoietic cells. In the present study, we examined the effects of ZK7 on human head and neck squamous cell carcinomas (HNSCC). The expression levels of messenger RNA for ZK7 in HNSCC clinical specimens exposed to platinum drugs and/or ionizing radiation were found to be higher than those in non-exposed specimens (P=0.0116). Cell lines examination showed that ZK7 over-expressing cells had low sensitivity to the chemotherapeutic agent cisplatin and ionizing radiation. These results suggest that ZK7 may inhibit apoptotic cell death in HNSCC.
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Affiliation(s)
- Nobuyuki Miyake
- Department of Otorhinolaryngology, Hiroshima University School of Medicine, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan.
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33
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Dupuy D, Dupérat VG, Arveiler B. SCAN domain-containing 2 gene (SCAND2) is a novel nuclear protein derived from the zinc finger family by exon shuffling. Gene 2002; 289:1-6. [PMID: 12036577 DOI: 10.1016/s0378-1119(02)00543-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The SCAN domain is a recently recognized protein domain that characterizes a subfamily of the Krüppel-like zinc finger proteins. We have previously described a novel SCAN domain-containing 2 gene (SCAND2) that does not belong to the zinc finger family. We report structural and sequence analyzes of all known members of the SCAN family and use these data to illustrate a model of gene family evolution. Most of the SCAN containing genes share common gene organization features that support the proposed origin for SCAND2 by disruption of an ancestral SCAN-zinc finger gene by a retroposition event and subsequent exon shuffling.
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Affiliation(s)
- Denis Dupuy
- Laboratoire de Pathologie Moléculaire et Thérapie Génique, Université Victor Segalen Bordeaux 2, 146 Rue Léo Saignat, 33076 Bordeaux Cedex, France
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34
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Nasiadka A, Dietrich BH, Krause HM. Anterior-posterior patterning in the Drosophila embryo. GENE EXPRESSION AT THE BEGINNING OF ANIMAL DEVELOPMENT 2002. [DOI: 10.1016/s1569-1799(02)12027-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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35
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Abrell S, Jäckle H. Axon guidance of Drosophila SNb motoneurons depends on the cooperative action of muscular Krüppel and neuronal capricious activities. Mech Dev 2001; 109:3-12. [PMID: 11677048 DOI: 10.1016/s0925-4773(01)00511-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The body wall musculature of the Drosophila larva consists of a stereotyped pattern of 30 muscles per abdominal hemisegment which are innervated by about 40 distinct motoneurons. Proper innervation by motoneurons is established during late embryogenesis. Guidance of motor axons to specific muscles requires appropriate pathfinding decisions as they follow their pathways within the central nervous system and on the surface of muscles. Once the appropriate targets are reached, stable synaptic contacts between motoneurons and muscles are formed. Recent studies revealed a number of molecular components required for proper motor axon pathfinding and demonstrated specific roles in fasciculation/defasciculation events, a key process in the formation of discrete motoneuron pathways. The gene capricious (caps), which encodes a cell-surface protein, functions as a recognition molecule in motor axon guidance, regulating the formation of the selective connections between the SNb-derived motoneuron RP5 and muscle 12. Here we show that Krüppel (Kr), best known as a segmentation gene of the gap class, functionally interacts with caps in establishing the proper axonal pathway of SNb including the RP5 axons. The results suggest that the transcription factor Krüppel participates in proper control of cell-surface molecules which are necessary for the SNb neurons to navigate in a caps-dependent manner within the array of the ventral longitudinal target muscles.
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Affiliation(s)
- S Abrell
- Max-Planck-Institut für biophysikalische Chemie, Abteilung Molekulare Entwicklungsbiologie, D-37070, Göttingen, Germany.
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36
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Yamashita R, Matsubara K, Kato K. A comprehensive collection of mouse zinc finger motifs compiled by molecular indexing. Gene 2001; 274:101-10. [PMID: 11675002 DOI: 10.1016/s0378-1119(01)00547-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The C(2)H(2) zinc finger motif found in many transcription factors is thought to be for nucleic acid binding and/or dimerization. Nearly 1% of eukaryote genes are estimated to encode this motif. We investigated the gene family encoding this motif in the Mus musculus mRNA by molecular indexing, a technique used to select a subpopulation of cDNA by ligation of adapters to cDNA fragments digested by a class IIS restriction enzyme(s). In place of oligo-dT primers in the original method, a polymerase chain reaction primer designed based on the conserved sequence of the C(2)H(2) zinc finger protein stranded cDNA was made from various mouse tissue mRNAs, digested with FokI and BsmAI, and joined with adapters. Amplification of the cDNA with an adapter primer and zinc finger-specific primer yielded products enriched in zinc finger protein genes. Fragments were separated by subsequent denaturing polyacrylamide gel electrophoresis, and characterized by DNA sequencing. Consequently, 259 C(2)H(2) zinc finger motif sequences were obtained, among which 166 were novel. Combined with the reported sequences, these mouse motif sequences were compared with those of other species such as Saccharomyces cerevisiae and Caenorhabditis elegans. Some of the amino acids in the motif sequence showed strong bias among species. Most of the novel sequences were supposed to be DNA-binding according to the surface potential of predicted tertiary structures.
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Affiliation(s)
- R Yamashita
- Taisho Laboratory of Functional Genomics, Nara Institutes of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0101, Japan
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37
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Shannon M, Kim J, Ashworth L, Branscomb E, Stubbs L. Tandem zinc-finger gene families in mammals: insights and unanswered questions. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 2001; 8:303-15. [PMID: 10993601 DOI: 10.3109/10425179809034075] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Evidence for the remarkable conservation of mammalian genomes, in both content and organization of resident genes, is rapidly emerging from comparative mapping studies. The frequent occurrence of familial gene clustering, presumably reflecting a history of tandem in situ duplications starting from a single ancestral gene, is also apparent from these analyses. Genes encoding Kruppel-type zinc-finger (ZNF) proteins, including those containing Kruppel-associated box (KRAB) motifs, are particularly prone to such clustered organization. Existing data suggest that genes in KRAB-ZNF gene clusters have diverged in sequence and expression patterns, possibly yielding families of proteins with distinct, yet related, functions. Comparative mapping studies indicate that at least some of the genes within these clusters in mammals were elaborated prior to the divergence of mammalian orders and, subsequently, have been conserved. These data suggest a possible role for these tandem KRAB-ZNF gene families in mammalian evolution.
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Affiliation(s)
- M Shannon
- Life Sciences Division, Oak Ridge National Laboratory, TN 37831-8077, USA.
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38
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Skapek SX, Jansen D, Wei TF, McDermott T, Huang W, Olson EN, Lee EY. Cloning and characterization of a novel Kruppel-associated box family transcriptional repressor that interacts with the retinoblastoma gene product, RB. J Biol Chem 2000; 275:7212-23. [PMID: 10702291 DOI: 10.1074/jbc.275.10.7212] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The retinoblastoma gene product, RB, seems to function as a key tumor suppressor by repressing the expression of genes activated by members of the E2F family of transcription factors. In order to accomplish this, RB has been proposed to interact with a transcriptional repressor. However, no genuine transcriptional repressors have been identified by virtue of interaction with RB. By using the yeast two-hybrid system, we have identified a novel member of a known family of transcriptional repressors that contain zinc fingers of the Kruppel type and a portable transcriptional repressor motif known as the Kruppel-associated box (KRAB). The mouse and human forms of the novel RB-associated KRAB protein (RBaK) are widely expressed. The amino acid motif that links the KRAB domain and zinc fingers appears to be required for interaction with RB in vitro. Human RBaK ectopically expressed in fibroblasts is an 80-kDa protein that is localized to the nucleus. The expression of either RB or RBaK in 10T1/2 fibroblasts represses the activation of an E2F-dependent promoter and decreases DNA synthesis to a similar degree. However, a mutant form of RBaK that cannot interact with RB in vitro is unable to prevent DNA synthesis. We present a model in which RB physically interacts with the novel transcriptional repressor RBaK to repress E2F-dependent genes and prevent DNA synthesis.
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Affiliation(s)
- S X Skapek
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas 78245, USA
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39
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La Rosée-Borggreve A, Häder T, Wainwright D, Sauer F, Jäckle H. hairy stripe 7 element mediates activation and repression in response to different domains and levels of Krüppel in the Drosophila embryo. Mech Dev 1999; 89:133-40. [PMID: 10559488 DOI: 10.1016/s0925-4773(99)00219-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Drosophila gap gene Krüppel (Kr) encodes a zinc finger-type transcription factor required for controlling the spatial expression of other segmentation genes during early blastoderm stage. Here we show that two independent and transferable repressor domains of Krüppel act to control expression of the pair-rule gene hairy, and that the minimal cis-acting element of hairy stripe7 (h7) mediates either Krüppel-dependent activation or repression in different regions of the blastoderm embryo. The C-terminal region of Krüppel which encompasses the predominant repressor domain is not essential for activation, but is required to fully suppress h7-mediated transcription in response to high levels of Krüppel activity. This domain contains an interaction motif for dCtBP, a homologue of the human co-repressor CtBP. dCtBP activity is, however, dispensable for Krüppel-mediated repression in the embryo since Krüppel-mediated repression functions in the absence of dCtBP. Possible modes of h7-mediated gene regulation in response to the different domains and levels of Krüppel are discussed.
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Affiliation(s)
- A La Rosée-Borggreve
- Abteilung Molekulare Entwicklungsbiologie, Max-Planck-Institut für biophysikalische Chemie, Am Fassberg, D-37077, Göttingen, Germany
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40
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Vorst OF, Voogt C, Borst-Vrensen TW, Takatsuji H. Developmental and wound-, cold-, desiccation-, ultraviolet-B-stress-induced modulations in the expression of the petunia zinc finger transcription factor gene ZPT2-2. PLANT PHYSIOLOGY 1999; 121:1153-62. [PMID: 10594102 PMCID: PMC59482 DOI: 10.1104/pp.121.4.1153] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/1999] [Accepted: 08/23/1999] [Indexed: 05/21/2023]
Abstract
The ZPT2-2 gene belongs to the EPF gene family in petunia (Petunia hybrida), which encodes proteins with TFIIIA-type zinc-finger DNA-binding motifs. To elucidate a possible function for ZPT2-2, we analyzed its pattern of expression in relation to different developmental and physiological stress signals. The activity of the ZPT2-2 promoter was analyzed using a firefly luciferase (LUC) reporter gene, allowing for continuous measurements of transgene activity in planta. We show that ZPT2-2::LUC is active in all plant tissues, but is strongly modulated in cotyledons upon germination, in leaves in response to desiccation, cold treatment, wounding, or ultraviolet-B light, and in petal tissue in response to pollination of the stigma. Analysis of mRNA levels indicated that the modulations in ZPT2-2::LUC expression reflect modulations in endogenous ZPT2-2 gene expression. The change in ZPT2-2::LUC activity by cold treatment, wounding, desiccation, and ultraviolet-B light suggest that the phytohormones ethylene and jasmonic acid are involved in regulating the expression of ZPT2-2. Although up-regulation of expression of ZPT2-2 can be blocked by inhibitors of ethylene perception, expression in plants is not induced by exogenously applied ethylene. The application of jasmonic acid does result in an up-regulation of gene activity and, thus, ZPT2-2 may play a role in the realization of the jasmonic acid hormonal responses in petunia.
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41
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Dreyer SD, Zheng Q, Zabel B, Winterpacht A, Lee B. Isolation, characterization, and mapping of a zinc finger gene, ZFP95, containing both a SCAN box and an alternatively spliced KRAB A domain. Genomics 1999; 62:119-22. [PMID: 10585779 DOI: 10.1006/geno.1999.5981] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A new zinc finger gene of the Krüppel family was identified by screening a human fetal cartilage cDNA library with degenerate oligonucleotides. Sequence analysis indicates that ZFP95 contains 12 highly conserved zinc finger motifs at the C-terminus and a SCAN box as well as a KRAB A domain at the N-terminus of the protein. ZFP95 represents a member of a new subclass of Krüppel zinc finger proteins containing both a SCAN box and a KRAB domain. Sequence comparison revealed that ZFP95 is the human ortholog of murine Zfp95, which is differentially expressed during spermatogenesis. We demonstrate that ZFP95 is ubiquitously expressed in adult and fetal tissues with the strongest expression in testis. Two transcripts, 4. 2 and 4.6 kb, were detected in all tissues tested. In testis, a third transcript of 3.8 kb was present. RT-PCR analysis confirmed alternative splicing for the KRAB A domain and an upstream exon leading to three transcripts of ZFP95 with and without this transcriptional repressor domain. Finally, we show that ZFP95 maps on human chromosome 7q22 between the markers D7S651 and WI-5853.
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Affiliation(s)
- S D Dreyer
- Children's Hospital, University of Mainz, Langenbeckstrasse 1, Mainz, D-55101, Germany
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42
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Prost JF, Nègre D, Cornet-Javaux F, Cortay JC, Cozzone AJ, Herbage D, Mallein-Gerin F. Isolation, cloning, and expression of a new murine zinc finger encoding gene. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1447:278-83. [PMID: 10542327 DOI: 10.1016/s0167-4781(99)00157-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the aim of identifying genes involved in cartilage differentiation, we have used a subtractive hybridization strategy with cDNAs from a chondrocytic cell line (MC615) and mRNAs from a mesenchymal precursor cell line (10T1/2). We have isolated a cDNA clone representing a novel mouse gene. The predicted 368-amino acid protein, designated ZF-12, contains four C(2)H(2)-type zinc finger motifs and one region homologous to the LeR domain, a finger-associated structural domain. ZF-12 mRNAs are expressed during embryonic development and in different organs in adult, including rib cartilage. These data suggest that ZF-12 might play an important role not only in cartilage differentiation, but also in basic cellular processes.
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Affiliation(s)
- J F Prost
- Institut de Biologie et Chimie des Protéines, CNRS UPR 412, 7 passage du Vercors 69367, Lyon, France
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43
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Ferbus D, Antoine K, Goubin G. Production and characterization of mouse monoclonal antibodies to human zinc finger OZF protein overexpressed in pancreatic carcinomas. Hybridoma (Larchmt) 1999; 18:431-6. [PMID: 10600030 DOI: 10.1089/hyb.1999.18.431] [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: 11/13/2022]
Abstract
Mouse monoclonal antibodies (MAbs) were raised against the human OZF protein, a zinc finger protein of the Krüppel family, consisting of 10 amino acids followed by 10 zinc finger motives. The OZF gene is amplified in 15-25% of pancreatic carcinomas and protein overexpression occurs in more than half of the tumors. Six MAbs effective in detecting the recombinant and the cellular protein by enzyme-linked immunoadsorbent assay (ELISA), Western immunoblotting, and immunofluorescence were purified and characterized. Five MAbs belong to the IgG1 subclass and one to the IgG3 subclass. In contrast to polyclonal antibodies, which detect many related proteins, they recognize an epitope unique to the human OZF protein. The sequence of the epitope, located at the junction between the first 10 amino acids and the zinc finger domain, is not present in other Krüppel proteins, including mouse and bovine OZF proteins. The MAbs are highly specific to the endogenous OZF protein in its denatured and native form. Therefore, they should be useful for OZF functional study and clinical diagnosis of tumors with aberrant OZF expression.
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Affiliation(s)
- D Ferbus
- Laboratoire d'Oncogenèse, UMR147 CNRS, Section de recherche, Institut Curie, Paris, France
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44
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Holmes DI, Wahab NA, Mason RM. Cloning and characterization of ZNF236, a glucose-regulated Kruppel-like zinc-finger gene mapping to human chromosome 18q22-q23. Genomics 1999; 60:105-9. [PMID: 10458916 DOI: 10.1006/geno.1999.5897] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report the cDNA cloning and characterization of ZNF236, a novel Kruppel-like zinc-finger gene initially identified by its glucose-regulated expression in human mesangial cells using mRNA differential display. Using the differential display fragment as a probe, we screened a human fetal kidney cDNA library and isolated several clones representing two differently spliced mRNA transcripts, designated ZNF236a and -b. Both transcripts were identical apart from the presence of an additional exon in ZNF236a that truncates the open reading frame. RT-PCR analysis confirmed the expression of both transcripts to be upregulated in human mesangial cells in response to elevated levels of d-glucose. ZNF236a and -b cDNAs encode polypeptides of 174 and 204 kDa, containing 25 and 30 C(2)H(2) zinc-finger motifs, respectively. Northern blot analysis showed that ZNF236 is ubiquitously expressed in all human tissues tested. Expression levels were highest in skeletal muscle and brain, intermediate in heart, pancreas, and placenta, and lowest in kidney, liver, and lung. Southern zoo blot analysis indicated that ZNF236 is conserved in the genomes of all mammalian species tested, but not in yeast. The mapping of ZNF236 to human chromosome 18q22-q23, close to the IDDM6 locus, coupled with the glucose-regulated expression of the gene in human mesangial cells, suggests that ZNF236 may be a candidate gene for diabetic nephropathy.
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MESH Headings
- Adult
- Alternative Splicing
- Amino Acid Sequence
- Animals
- Blotting, Northern
- Carrier Proteins/genetics
- Chromosome Mapping
- Chromosomes, Human, Pair 18/genetics
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- DNA-Binding Proteins/genetics
- Female
- Glucose/physiology
- Humans
- In Situ Hybridization, Fluorescence
- Kruppel-Like Transcription Factors
- Molecular Sequence Data
- Protein Isoforms/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Repressor Proteins
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Tissue Distribution
- Transcription Factors/genetics
- Zinc Fingers/genetics
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Affiliation(s)
- D I Holmes
- Division of Biomedical Sciences, Imperial College School of Medicine, BMS Building, South Kensington, London, SW7 2AZ, United Kingdom
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45
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Thomas JH, Horvitz HR. The C. elegans gene lin-36 acts cell autonomously in the lin-35 Rb pathway. Development 1999; 126:3449-59. [PMID: 10393123 DOI: 10.1242/dev.126.15.3449] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Caenorhabditis elegans gene lin-36 acts to antagonize Ras-mediated vulval induction in a pathway that includes genes with products similar to the mammalian retinoblastoma (Rb) protein and the Rb-binding protein p48. We report that lin-36 encodes a novel protein of 962 amino acids. We demonstrate that lin-36 functions in and is expressed in the vulval precursor cells, establishing that the lin-36 pathway is involved in intercellular signaling. We also report that the lin-36 pathway and/or another pathway that is functionally redundant with the lin-36 pathway antagonize a ligand-independent activity of the receptor tyrosine kinase/Ras vulval induction pathway.
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Affiliation(s)
- J H Thomas
- Howard Hughes Medical Institute, Department of Biology, Room 68-425, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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46
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Abstract
The development and function of T lymphocytes are regulated tightly by signal transduction pathways that include specific cell-surface receptors, intracellular signaling molecules, and nuclear transcription factors. Since 1988, several families of functionally important T cell transcription factors have been identified. These include the Ikaros, LKLF, and GATA3 zinc-finger proteins; the Ets, CREB/ATF, and NF-kappa B/Rel/NFAT transcription factors; the Stat proteins; and HMG box transcription factors such as LEF1, TCF1, and Sox4. In this review, we summarize our current understanding of the transcriptional regulation of T cell development and function with particular emphasis on the results of recent gene targeting and transgenic experiments. In addition to increasing our understanding of the molecular pathways that regulate T cell development and function, these results have suggested novel targets for genetic and pharmacological manipulation of T cell immunity.
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Affiliation(s)
- C T Kuo
- Department of Medicine, University of Chicago, Illinois 60637, USA
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47
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Mark C, Abrink M, Hellman L. Comparative analysis of KRAB zinc finger proteins in rodents and man: evidence for several evolutionarily distinct subfamilies of KRAB zinc finger genes. DNA Cell Biol 1999; 18:381-96. [PMID: 10360839 DOI: 10.1089/104454999315277] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although the KRAB zinc finger proteins probably constitute the single largest class of transcription factors within the human genome, almost nothing is known about their biological function. To increase our knowledge about this interesting and relatively unexplored family of potent transcriptional repressors, we here present the cloning, structural analysis, and expression study of three novel mouse KRAB zinc finger proteins. In addition, we present an extensive comparative analysis of various members of this gene family based on the structure of the common KRAB A motif. At least three larger subfamilies of KRAB zinc finger proteins are identified: one carrying the classical KRAB A motif only, another holding both a classical KRAB A and a classical KRAB B motif, and a third holding a classical KRAB A and a highly divergent KRAB B domain, named b. A large variation both in size and in primary amino acid sequence was observed in the linker region between the KRAB domain and the C-terminally located zinc finger repeats. This variability indicates that this region is of minor importance for the biological function of KRAB-containing zinc finger proteins. The fact that in many zinc finger genes, the entire or almost the entire linker region is composed of degenerate finger motifs substantiates this conclusion. The absence of identifiable KRAB A and B motifs in the genome of yeast, Saccharomyces cerevisiae, indicates a relatively late appearance of the KRAB domain in evolution and may suggest that the biological functions are restricted to multicellular organisms. In addition, we show that the expression of individual members of one subfamily of KRAB zinc finger genes is restricted to specific hematopoietic cell lineages. This finding suggests that KRAB zinc finger proteins may play a role in lineage commitment, possibly silencing leakage transcription from nonlineage-expressed genes.
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Affiliation(s)
- C Mark
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala, Sweden
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de la Serna I, Ng D, Tyler BM. Carbon regulation of ribosomal genes in Neurospora crassa occurs by a mechanism which does not require Cre-1, the homologue of the Aspergillus carbon catabolite repressor, CreA. Fungal Genet Biol 1999; 26:253-69. [PMID: 10361038 DOI: 10.1006/fgbi.1999.1121] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Transcription of the ribosomal protein and 40S rRNA genes is coordinately regulated during steady state growth and carbon shifts in Neurospora crassa. Recognition sequences for the Aspergillus nidulans carbon catabolite repressor, CreA, overlap transcriptional elements of a 40S rRNA gene and the crp-2 ribosomal protein gene. They also occur in similar locations in the promoters of several other ribosomal protein genes. Substitutions encompassing the -74 and -167 CreA consensus sequences in the crp-2 promoter result in a decrease in transcription. A cDNA encoding the N. crassa homologue of CreA was cloned and designated Cre-1. The Cre-1 protein is 45% identical to CreA from A. nidulans. Cre-1 protein produced in Escherichia coli binds to the CreA sites in the promoters of the 40S rRNA and crp-2 genes. An amino acid change from histidine (92) to threonine changed the Cre-1 binding specificity from (5'G/CC/TGGG/AG3') to (5'G/CC/TGGCG3'). Base substitutions in the Cre-1 binding sites of the crp-2 promoter disrupted binding of wildtype Cre-1 in vitro but had no effect on transcription during steady state growth or carbon shifts, indicating that regulation of ribosomal genes by carbon source is not mediated by Cre-1, but via different proteins binding the Cre-1 sites and the Dde boxes.
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Affiliation(s)
- I de la Serna
- Department of Plant Pathology, University of California, Davis, California, 95616, USA
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Dovat S, Gilbert KA, Petrovic-Dovat L, Rannels DE. Isolation, cloning, and characterization of a novel rat lung zinc finger gene, RLZF-Y. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1442:380-8. [PMID: 9804994 DOI: 10.1016/s0167-4781(98)00167-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Zinc-finger (ZF) proteins are widely distributed. The current study reports isolation, cloning and characterization of a novel ZF gene, RLZF-Y. Total RNA from rat lung was reverse transcribed. The 5' and 3' ends were isolated by rapid amplification of cDNA ends (RACE) using primers derived from a previously isolated partial clone. RACE products of 1.5 and 1.1 kb were cloned and sequenced. Identical overlapping sequence of 70 base pairs confirmed representation of the same cDNA approximately 2.5 kb in length. Probes derived from both 5' RACE and 3' RACE products independently hybridized to a 2.5 kb mRNA from rat lung. RLZF-Y mRNA is expressed in lung, brain, heart and kidney; expression is low in liver. Predicted amino acid sequence analysis defined three regions of similarity to known C2H2 ZF proteins: a region containing seven ZF structures characteristic of the Krüppel-like subfamily of ZF genes; a region with sequence similarity to the Krüppel-associated box A (KRAB-A) domain at the amino end; an amino-terminal leucine-rich region (LeR) adjacent to KRAB-A. The presence of KRAB-A and the adjacent LeR implies RLZF-Y protein may function as a transcriptional repressor.
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Affiliation(s)
- S Dovat
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, C4723, 500 University Drive, Hershey, PA 17033, USA
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Matsumoto K, Ishii N, Yoshida S, Shiosaka S, Wanaka A, Tohyama M. Molecular cloning and distinct developmental expression pattern of spliced forms of a novel zinc finger gene wiz in the mouse cerebellum. BRAIN RESEARCH. MOLECULAR BRAIN RESEARCH 1998; 61:179-89. [PMID: 9795207 DOI: 10.1016/s0169-328x(98)00216-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In the course of a study conducted to identify the mouse homologue of Drosophila eyes absent (eya), we isolated a novel mouse cDNA fragment which show little homology to eya but encodes a protein with Krüppel (C2H2)-type zinc finger motifs. By further screening using this cDNA fragment as a probe, we obtained the short and long forms of full-length cDNAs, which were apparently alternatively spliced products from one gene. Since both mRNAs encode proteins with widely-interspaced zinc finger motifs, we termed this gene wiz and refer to the short and long wiz transcripts as wizS and wizL, respectively. In situ hybridization studies using the probe against the region common to wizS and wizL showed that these mRNAs were expressed abundantly in the granule cell layers of the mouse cerebellum, the olfactory bulb, and the dentate gyrus, whereas the same technique using the probe against only wizL could not detect positive signals in the developing cerebellum, indicating that there is no expression of wizL mRNA there. Northern blot and in situ hybridization analyses demonstrated that the extracerebellar regions expressed both wizS and wizL mRNAs from the midgestational period to adulthood. The finding that two types of wiz transcripts (wizS and wizL) are expressed with different developmental patterns might indicate separate transcription functions in the cerebellar granule cells and the extracerebellar regions.
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Affiliation(s)
- K Matsumoto
- Division of Structural Cell Biology, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0101, Japan.
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