101
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Galliano H, Müller AE, Lucht JM, Meyer P. The transformation booster sequence from Petunia hybrida is a retrotransposon derivative that binds to the nuclear scaffold. MOLECULAR & GENERAL GENETICS : MGG 1995; 247:614-22. [PMID: 7603441 DOI: 10.1007/bf00290353] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The transformation booster sequence (TBS) from Petunia hybrida enhances transformation frequencies in P. hybrida, Nicotiana tabacum and Zea mays. TBS also stimulates homologous inter- and intramolecular recombination in P. hybrida, the molecular basis for this stimulation is not known. We investigated whether TBS contains sequence elements that might contribute to the stimulation of recombination and whether its recombinogenic potential reflects a biological function of TBS. We identified a scaffold attachment region (SAR) within TBS and analysed its distribution in the genome and its homologies to other genomic sequences. A 516 bp subfragment of TBS binds to the nuclear scaffold. The sequence of the TBS-SAR fragment shows strong homologies to retroviral elements from plants, suggesting that TBS is an inactive derivative of a retrovirus that still promotes DNA recombination.
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Affiliation(s)
- H Galliano
- Max Delbrück Laboratorium, Köln, Germany
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102
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Hirano T, Mitchison TJ, Swedlow JR. The SMC family: from chromosome condensation to dosage compensation. Curr Opin Cell Biol 1995; 7:329-36. [PMID: 7662362 DOI: 10.1016/0955-0674(95)80087-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Recent genetic analyses in yeasts and biochemical studies in vertebrate cells have led to the discovery of a family of putative ATPases that play a fundamental role in chromosome condensation and segregation in mitosis. One of the members was also found to be involved in dosage compensation in Caenorhabditis elegans, providing a new link between global regulation of gene expression and chromosome structure. This unique family of proteins may control higher-order chromosome dynamics by regulated self-assembly or mechanochemical activity.
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Affiliation(s)
- T Hirano
- Department of Pharmacology, University of California, San Francisco 94143-0450, USA
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103
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Gunawardena S, Heddle E, Rykowski MC. ‘Chromosomal puffing’ in diploid nuclei of Drosophila melanogaster. J Cell Sci 1995; 108 ( Pt 5):1863-72. [PMID: 7657710 DOI: 10.1242/jcs.108.5.1863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In situ hybridization has become a powerful technique for dissecting nuclear structure. By localizing nucleic acids with high precision, it is possible to infer the native structure of chromosomes, replication factories and transcript processing complexes. To increase the value of this technique, we have established the limits of resolution of two-color in situ hybridization to chromosomal DNA in diploid chromosomes of Drosophila embryonic nuclei. Using high-resolution 3-dimensional optical microscopy and computational image analysis, we establish that we can distinguish the location of chromosomal sequences that lie 27–29 kb apart within a 40 kb transcription unit with an accuracy of about 100 nm. Contrary to observations made in mammalian tissue culture cells, we find that when the gene is expressed, it assumes an open configuration, and that the extent of decondensation is variable from chromosome to chromosome. Further experiments suggest that variation in gene structure results from asynchrony in transcriptional elongation. We suggest that the phenomenon we observe is the diploid analog to chromosomal puffing that occurs in the transcriptionally active regions of Drosophila polytene chromosomes.
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Affiliation(s)
- S Gunawardena
- Department of Cell Biology and Anatomy, College of Medicine, University of Arizona, Tucson 85724, USA
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104
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Ernst P, Smale ST. Combinatorial regulation of transcription II: The immunoglobulin mu heavy chain gene. Immunity 1995; 2:427-38. [PMID: 7749979 DOI: 10.1016/1074-7613(95)90024-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- P Ernst
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of California, Los Angeles School of Medicine 90095-1662, USA
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105
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Abstract
The mechanism by which eukaryotic chromosomes condense as cells enter mitosis has long been inaccessible to molecular biologists. An important clue has now been provided by a ubiquitous protein family, the SMCs.
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Affiliation(s)
- S M Gasser
- Swiss Institute for Experimental Cancer Research (ISREC), Epalinges
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106
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Ernst P, Smale ST. Combinatorial regulation of transcription. I: General aspects of transcriptional control. Immunity 1995; 2:311-9. [PMID: 7719936 DOI: 10.1016/1074-7613(95)90139-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- P Ernst
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of California, School of Medicine, Los Angeles 90095-1662, USA
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107
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Buhrmester H, von Kries JP, Strätling WH. Nuclear matrix protein ARBP recognizes a novel DNA sequence motif with high affinity. Biochemistry 1995; 34:4108-117. [PMID: 7696275 DOI: 10.1021/bi00012a029] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
ARBP is a nuclear protein that specifically binds to matrix/scaffold attachment regions (MARs/SARs). Here we characterize by DNase I footprinting, dimethyl sulfate protection, and mobility shift assays two binding sites for ARBP within a chicken lysozyme MAR fragment. Our results indicate that ARBP recognizes a novel DNA sequence motif containing the central sequence 5'-GGTGT-3' and flanking AT-rich sequences. Binding occurs through major groove contacts to two guanines of the central sequence. Collective and single-base substitutions in the 5'-GGTGT-3' core motif result in loss or significant reductions of ARBP binding, underscoring the importance of the GC-rich core sequence. Structural elements of the sequence motif are probably also recognized. The affinity of ARBP to both binding sites is surprisingly high [KD = (2-6) x 10(-10) M]. High-affinity recognition of the identified DNA motif in MARs/SARs by ARBP is likely an important feature in the domain organization of chromatin.
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Affiliation(s)
- H Buhrmester
- Institut für Physiologische Chemie, Universitäts-Krankenhaus Eppendorf, Hamburg, FR Germany
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108
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Murakami S, Yanagida M, Niwa O. A large circular minichromosome of Schizosaccharomyces pombe requires a high dose of type II DNA topoisomerase for its stabilization. MOLECULAR & GENERAL GENETICS : MGG 1995; 246:671-9. [PMID: 7898434 DOI: 10.1007/bf00290712] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have constructed circular minichromosomes, ranging in size from 36 to 110 kb, containing the centromeric repeats of Schizosaccharomyces pombe cen3. Comparison of their mitotic stability showed that the circular minichromosomes became more unstable with increasing in size, however, a linear cen3 minichromosome, which is almost the same size as the largest circular one tested, does not show such instability. High levels of expression of the top2+ (type II DNA topoisomerase; topo II) but not top1+ gene (type I DNA topoisomerase) suppressed the instability of the largest circular minichromosome, whereas partial inactivation of topo II dramatically destabilized the minichromosome. A mutant topo II, defective in nuclear localization but still retaining its in vitro relaxation activity, did not stabilize the circular minichromosome. These results indicate that endogenous type II DNA topoisomerase is insufficient for accurate segregation of the circular minichromosome. In addition, the replication of the minichromosomal DNA appears to proceed normally, because the presence of the unstable minichromosome did not cause G2 delay. A likely cause of the instability is intertwining of the minichromosome DNA possibly occurring after DNA replication. An interaction between topo II and the centromeric repeats is implied by the finding that multiple copies of the centromeric repeat, dg-dh, affect stability of the minichromosome similarly to top2+ gene dosage.
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Affiliation(s)
- S Murakami
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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109
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110
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Hirano T, Mitchison TJ. A heterodimeric coiled-coil protein required for mitotic chromosome condensation in vitro. Cell 1994; 79:449-58. [PMID: 7954811 DOI: 10.1016/0092-8674(94)90254-2] [Citation(s) in RCA: 389] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We report here a chromosomal protein that plays an essential role in mitotic chromosome condensation in Xenopus egg extracts. Two polypeptides, designated XCAP-C and XCAP-E, were found to associate with each other in the extracts, presumably forming a heterodimer. During chromosome assembly in mitotic extracts, XCAP-C/E was recruited to the chromatin and formed a discrete internal structure within assembled chromosomes. Antibody blocking experiments showed that XCAP-C function is required for both assembly and structural maintenance of mitotic chromosomes in vitro. Deduced amino acid sequences revealed that the two polypeptides share common structural motifs, consisting of an N-terminal NTP-binding domain, two central coiled-coil regions, and a C-terminal conserved domain. These motifs are highly conserved in a protein family, members of which have been identified recently in both prokaryotes and eukaryotes.
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Affiliation(s)
- T Hirano
- Department of Pharmacology, University of California, San Francisco 94143-0450
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111
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Oleinick NL, Balasubramaniam U, Xue L, Chiu S. Nuclear structure and the microdistribution of radiation damage in DNA. Int J Radiat Biol 1994; 66:523-9. [PMID: 7983440 DOI: 10.1080/09553009414551561] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Evidence for the roles of proteins and metal ions in the microheterogeneity of DNA damage is reviewed. Decondensation of chromatin in hypotonic buffers markedly sensitizes the DNA to radiation, while treatment of nuclei with hypertonic buffers strips the DNA of histones and other nuclear proteins and enhances the radiosensitivity of the DNA with respect to double-strand break (dsb) formation. Addition of the radical scavenger DMSO reduces the yield of strand breaks, but dehistonized chromatin remains approximately 2.5 times more sensitive to radiation than does native chromatin at 0.1 M DMSO. DNA-protein crosslink (DPC) formation is relatively unaffected by the removal of the majority of histones from chromatin. Most DPC form at or near the nuclear matrix, and matrix is stabilized and radiosensitized by Cu++. To elucidate the role of Cu++, the induction of dsb and DPC by gamma-radiation has been compared with that by hydroxyl radical from Fe(++)-EDTA, or Cu++ catalysed Fenton reactions. Data comparing the size of DNA fragments produced, the effect of expanding or dehistonizing chromatin, and the effects of radical scavengers suggest that gamma-radiation and Fe(++)-EDTA produce dsb at open chromatin sites, whereas Cu(++)-generated dsb are similar to radiation-induced DPC in their location at the nuclear matrix. Both metal ions appeared to produce damage by site-specific generation of hydroxyl radicals. The nuclear matrix, the proteinaceous skeleton which anchors chromosomal loops and provides sites for DNA replication and transcription, binds metal ions and matrix-attachment DNA regions (MARs) consisting of 300 + bp of AT-rich DNA. The interaction of cloned MARs with isolated nuclear matrices has been found to be hypersensitive to crosslinking upon gamma-irradiation, in comparison with associations formed by similarly sized DNA fragments lacking MAR sequences. Thus, the non-random distribution of radiation damage is partially explained by the protection of DNA afforded by histones and chromatin structure and partially by the hypersensitivity of DNA-nuclear matrix associations.
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Affiliation(s)
- N L Oleinick
- Department of Radiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4942
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112
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Abstract
Regulated gene expression within a complex chromosomal locus requires multiple nuclear processes. We have analyzed the transcriptional properties of the cloned chick beta-globin gene family when assembled into synthetic nuclei made by use of Xenopus egg extracts. Assembly in an erythroid protein environment correctly recapitulates tissue-specific chromatin structure and long-range promoter-enhancer interaction within the chromosomal locus, resulting in beta-globin gene activation. Nucleosome-repressed beta-globin templates can be transcriptionally activated by double-stranded DNA replication in the presence of staged erythroid proteins by remodeling of the chromatin structure within the promoter region and establishment of distal promoter-enhancer communication. The programmed transcriptional state of a gene, as encoded by its chromatin structure and long-range promoter-enhancer interactions, is stable to nuclear decondensation and DNA replication unless active remodeling occurs in the presence of specific DNA-binding proteins.
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Affiliation(s)
- M C Barton
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
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113
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Wada-Kiyama Y, Kiyama R. Periodicity of DNA bend sites in human epsilon-globin gene region. Possibility of sequence-directed nucleosome phasing. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)31782-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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114
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Markova D, Donev R, Patriotis C, Djondjurov L. Interphase chromosomes of Friend-S cells are attached to the matrix structures through the centromeric/telomeric regions. DNA Cell Biol 1994; 13:941-51. [PMID: 7522463 DOI: 10.1089/dna.1994.13.941] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
DNA of the attachment sites of Friend erythroleukemia cells, isolated according to the conventional procedure, represents short, nuclease-resistant fragments with sizes below 400 bp, belonging to the class of mouse satellite. A number of experiments have indicated that their unusual resistance is due to complexing with RNA. By various approaches, it was confirmed that similar fragments might be recovered from total DNA following extensive digestion with DNase I. In situ hybridizations revealed further that at mitosis the sequences of the attachment sites are located at the centromeric/telomeric regions of the chromosomes, while at interphase they are redistributed into 9-13 well-defined clusters spread throughout the entire nuclear area. Parallel biochemical and electronmicroscopic studies have clarified, moreover, that the all three compartments of the matrix harbor such sequences. Thus, it appears that the attachment sites described function only at interphase, anchoring the both ends of each interphase chromosome to the matrix structures.
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Affiliation(s)
- D Markova
- Department of Cell Proliferation, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia
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115
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Enomoto S, Longtine MS, Berman J. TEL+CEN antagonism on plasmids involves telomere repeat sequences tracts and gene products that interact with chromosomal telomeres. Chromosoma 1994; 103:237-50. [PMID: 7988285 DOI: 10.1007/bf00352248] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In Saccharomyces cerevisiae, circular plasmids that include either a centromere (CEN-plasmids) or a telomere sequence (TEL-plasmids) segregate more efficiently than circular ARS-plasmids. In contrast, circular plasmids that include both telomere and centromere sequences were unstable, a property we term TEL+CEN antagonism. TEL+CEN antagonism required a telomere repeat tract longer than 49 bp although the distance and relative orientation of the centromere and telomere sequences was not critical. TEL+CEN antagonism was alleviated in strains carrying different rap1 alleles including rap1ts, rap1s, and rap1t alleles. Mutations SIR2, SIR3, SIR4, NAT1 and ARD1, genes that influence transcriptional silencing at telomeres and at the silent mating type loci, abolished TEL+CEN antagonism Mutation of SIR1 also partially alleviated TEL-CEN antagonism. In some sir mutant strains short yeast artificial chromosomes (YACs), which are normally unstable, became more stable, suggesting that the same mechanism that caused TEL+CEN antagonism on circular plasmids may contribute to the instability of short linear plasmids.
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Affiliation(s)
- S Enomoto
- Department of Plant Biology, University of Minnesota, St. Paul 55108
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116
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Hampel KJ, Ashley C, Lee JS. Kilobase-range communication between polypurine.polypyrimidine tracts in linear plasmids mediated by triplex formation: a braided knot between two linear duplexes. Biochemistry 1994; 33:5674-81. [PMID: 8180192 DOI: 10.1021/bi00185a002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Linear plasmids were constructed containing two pyrimidine tracts that were 0.34 and 0.94 kilobases (kb) from either end and were separated by 2.8 kb. The tracts [d(TCCTTC)n and d(CTTCCT)n where n = 6 or 12] were designed so as to be able to form triplexes with each other but not with themselves. Upon lowering of the pH to 4 in the presence of spermine, these plasmids form intermolecular dimers and intramolecular loops of 2.8 kb, as judged from mobility changes on agarose gels. A tethered loop could also be formed in a linear plasmid containing two identical tracts by adding an homologous single-stranded oligopyrimidine, but not an oligopurine. In plasmids containing different tracts, the formation of both dimers and loops could be blocked by adding either homologous single-stranded oligopyrimidine but not an oligopurine. Together with the requirement of low pH, these results demonstrate that triplex formation is of the pyr.pur.pyr type. The extent of dimer and loop formation was dependent on the length of the pyrimidine tract: dimers could be detected in plasmids containing the 72 base pair (bp) inserts after incubation at pH 6, but in plasmids containing the 36 bp inserts, a pH of 5 was required. Hysteresis was also evident to a remarkable extent. Once formed at pH 4, loops and dimers remained stable indefinitely at pH 8, suggesting that the structures become topologically trapped. However, the structures were resolved into the component linear plasmids by incubation with nuclease P1. This is the first demonstration of a braided or hydrogen-bonded knot between two linear duplexes and may have implications for chromosomal loop formation.
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Affiliation(s)
- K J Hampel
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada
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117
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Breyne P, Van Montagu M, Gheysen G. The role of scaffold attachment regions in the structural and functional organization of plant chromatin. Transgenic Res 1994; 3:195-202. [PMID: 8025597 DOI: 10.1007/bf01973987] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Studies on nuclear scaffolds and scaffold attachment regions (SARs) have recently been extended to different plant species and indicate that SARs are involved in the structural and functional organization of the plant genome, as is the case for other eukaryotes. One type of SAR seems to delimit structural chromatin loops and may also border functional units of gene expression and DNA replication. Another group of SARs map close to regulatory elements and may be directly involved in gene expression. In this overview, we summarize the structural and functional properties of plant SARs in comparison with those of SARs from animals and yeast.
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Affiliation(s)
- P Breyne
- Laboratorium voor Genetica, Universiteit Gent, Belgium
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118
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Fackelmayer FO, Dahm K, Renz A, Ramsperger U, Richter A. Nucleic-acid-binding properties of hnRNP-U/SAF-A, a nuclear-matrix protein which binds DNA and RNA in vivo and in vitro. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 221:749-57. [PMID: 8174554 DOI: 10.1111/j.1432-1033.1994.tb18788.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We show that SAF-A, a nuclear protein which specifically binds vertebrate scaffold-attachment-region (SAR) elements with high affinity is identical with hnRNP-U, assumed to be involved in packaging of hnRNA in ribonucleoprotein particles. Ultraviolet cross-linking experiments show that the protein, referred to as hnRNP-U/SAF-A, is bound to chromosomal DNA in vivo. In vitro, the isolated protein binds to double-stranded and single-stranded DNA and forms higher ordered nucleic-acid-protein complexes. Filter-binding experiments performed with different types of natural and synthetic nucleic acids as substrates show that the protein binds DNA and RNA with different affinities and most likely at different binding sites. We conclude that hnRNP-U/SAF-A thus may have functions in the organisation of chromosomal DNA in addition to its suggested role in hnRNA metabolism.
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119
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von Kries JP, Rosorius O, Buhrmester H, Strätling WH. Biochemical properties of attachment region binding protein ARBP. FEBS Lett 1994; 342:185-8. [PMID: 8143875 DOI: 10.1016/0014-5793(94)80497-4] [Citation(s) in RCA: 5] [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
ARBP (attachment region binding protein) is an abundant nuclear protein that specifically binds to matrix/scaffold attachment regions (MARs/SARs). Here we show by gel filtration and gradient sedimentation that ARBP has an elongated shape. The sedimentation coefficient was determined as only 2.1 S. Furthermore, limited proteolysis of ARBP in situ (in isolated nuclei) with several proteases generated limiting resistant peptides from 14.5 to 18 kDa, that retained the ability to bind MARs specifically. This indicates that these peptides encompass the DNA binding domain of ARBP.
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Affiliation(s)
- J P von Kries
- Institut für Physiologische Chemie, Universitäts-Krankenhaus Eppendorf, Hamburg, Germany
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120
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Doenecke D, Albig W, Bouterfa H, Drabent B. Organization and expression of H1 histone and H1 replacement histone genes. J Cell Biochem 1994; 54:423-31. [PMID: 8014191 DOI: 10.1002/jcb.240540409] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The H1 family is the most divergent subgroup of the highly conserved class of histone proteins [Cole: Int J Pept Protein Res 30:433-449, 1987]. In several vertebrate species, the H1 complement comprises five or more subtypes, and tissue specific patterns of H1 histones have been described. The diversity of the H1 histone family raises questions about the functions of different H1 subtypes and about the differential control of expression of their genes. The expression of main type H1 genes is coordinated with DNA replication, whereas the regulation of synthesis of replacement H1 subtypes, such as H1 zero and H5, and the testis specific H1t appears to be more complex. The differential control of H1 gene expression is reflected in the chromosomal organization of the genes and in different promoter structures. This review concentrates on a comparison of the chromosomal organization of main type and replacement H1 histone genes and on the differential regulation of their expression. General structural and functional data, which apply to both H1 and core histone genes and which are covered by recent reviews, will not be discussed in detail.
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Affiliation(s)
- D Doenecke
- Georg August Universität Göttingen, Institut für Biochemie und Molekulare Zellbiologie, Germany
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121
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Romig H, Ruff J, Fackelmayer FO, Patil MS, Richter A. Characterisation of two intronic nuclear-matrix-attachment regions in the human DNA topoisomerase I gene. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 221:411-9. [PMID: 8168528 DOI: 10.1111/j.1432-1033.1994.tb18753.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We identify two high-affinity matrix-attachment regions (MAR elements) located in two introns of the human DNA topoisomerase I gene (TOP1). These intronic MAR elements, designated MI and MII, are specifically bound by the nuclear matrix and partition with scaffolds in vitro. One of these MAR elements, MII, is part of a genomic region which is hypersensitive for endogenous nucleases. We have sequenced both DNA elements and have characterized their mode of binding to the nuclear matrix. Experiments with the minor-groove-binding ligands distamycin and chromomycin indicate that the A+T-rich regions, most likely homopolymeric A tracts, are responsible for binding of these DNA elements to the nuclear matrix. MII contains an alu-like element and a segment of curved DNA. Analysis of subfragments of MII show that the curved DNA region itself shows only weak nuclear-matrix binding, and that the high-affinity binding sites are located on subfragments on the 5' side of the curved DNA. In addition, we found that the alu-like sequence does not contribute significantly to the binding of MII and of subfragments of MII to nuclear-matrix proteins. Comparing the distribution of repetitive sequences in the cloned parts of human DNA topoisomerase I gene with the location of high-affinity matrix-binding sites we find no evidence that repetitive DNA may be located close to MAR elements as has been previously suggested.
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Affiliation(s)
- H Romig
- Department of Biology, University of Konstanz, Germany
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122
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Leptomycin B targets a regulatory cascade of crm1, a fission yeast nuclear protein, involved in control of higher order chromosome structure and gene expression. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37374-x] [Citation(s) in RCA: 360] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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123
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Saitoh Y, Laemmli UK. Metaphase chromosome structure: bands arise from a differential folding path of the highly AT-rich scaffold. Cell 1994; 76:609-22. [PMID: 7510215 DOI: 10.1016/0092-8674(94)90502-9] [Citation(s) in RCA: 248] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Using the highly AT-specific fluorochrome daunomycin, a longitudinal optical signal called AT queue, thought to arise from a line-up of the highly AT-rich scaffold-associated regions (SARs) by the scaffolding, was identified in native chromosomes. Fluorescence banding is proposed to result from a differential folding path of the AT queue during its progression from telomere to telomere. The AT queue is tightly coiled or folded in a Q band, the resulting transverse striations across the chromatid, which also represent Giemsa subbands, generating a bright AT-rich signal over the Q region. The R bands, in contrast, contain a more central (unfolded) AT queue, yielding an AT-dull signal over the R regions. The AT queue is identified by immunofluorescence against topoisomerase II (topo II) and HMG-I/Y as the scaffold of native chromosomes; the fluorescence signal from both proteins is akin to a detailed Q-type banding pattern. Native chromosomes appear assembled according to the loop-scaffold model.
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Affiliation(s)
- Y Saitoh
- Department of Biochemistry, University of Geneva, Switzerland
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124
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Yu J, Bock JH, Slightom JL, Villeponteau B. A 5' beta-globin matrix-attachment region and the polyoma enhancer together confer position-independent transcription. Gene X 1994; 139:139-45. [PMID: 8112598 DOI: 10.1016/0378-1119(94)90747-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Insertions of reporter constructs into the genome of higher eukaryotes typically lead to variegated gene expression due to position effects at the sites of integration. The 20-kb human beta-globin (beta Glb) locus control region (LCR) has been found to dampen these position effects when included in an expression vector. Several studies have indicated that much of the activity of the beta Glb-LCR resides in hypersensitive site II, which contains a strong enhancer. In this study, we have focused on the matrix-attachment region (MAR) at the 5' boundary of the beta Glb-LCR. We find that the beta Glb-MAR, by itself, has little effect on transcription of a reporter gene in stable transformants. However, when the beta Glb-MAR is linked in cis with the polyoma virus enhancer, the MAR-enhancer construct confers high levels of copy-dependent transcription that is independent of the chromosomal site of integration. These results suggest that the beta Glb-MAR may work synergistically with particular enhancer elements to dampen chromosomal position effects and ensure high-level expression.
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Affiliation(s)
- J Yu
- Molecular Biology Research Unit, Geron Corporation, Menlo Park, CA 94025
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125
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Yasui LS, Fink TJ, Enrique AM. Nuclear scaffold organization in the X-ray sensitive Chinese hamster mutant cell line, xrs-5. Int J Radiat Biol 1994; 65:185-92. [PMID: 7907116 DOI: 10.1080/09553009414550221] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Nuclear organization was probed in the radiation-sensitive Chinese hamster ovary CHO) cell line, xrs-5, and compared with parental CHO K1 cells using the resinless section technique and DNase I digestions. The resinless section data showed no gross morphological differences in core filaments from the nuclear scaffolds of unirradiated CHO K1 and xrs-5 cells. However, the nuclear scaffolds of irradiated xrs-5 cells (1 Gy) had significantly increased ground substance. Irradiated and unirradiated CHO K1 cell nuclear scaffolds were morphologically identical. These data suggest that both CHO K1 and xrs-5 cell nuclear scaffolds had internal nuclear scaffolding networks that could provide DNA attachment sites. The rate of DNase I digestion of unirradiated CHO K1 and xrs-5 was not significantly different, but the extent of digestion was greater in unirradiated CHO K1 cells that in xrs-5 cells suggesting that less xrs-5 cell chromatin at DNA attachment points is accessible to the enzyme DNase I. The extents of digestion in irradiated (1 Gy) CHO K1 and xrs-5 cell nuclei also differed but the relationship was reversed. The irradiated xrs-5 cell samples were digested to a greater extent compared with CHO K1 cells. These chromatin digestion data suggest that the matrix attachment regions in xrs-5 cells are different from CHO K1 cells. The different DNA attachment organization in the xrs-5 cells may play a role in modulating radiation sensitivity.
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Affiliation(s)
- L S Yasui
- Northern Illinois University, Department of Biological Sciences, DeKalb 60115
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126
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Ferguson LR, Baguley BC. Topoisomerase II enzymes and mutagenicity. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 1994; 24:245-261. [PMID: 7851337 DOI: 10.1002/em.2850240402] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Topoisomerase II (topo II) enzymes maintain DNA structure by relieving torsional stress occurring in double-strand DNA during transcription and replication. Topo II causes transient breaks in both strands of DNA, allowing passage of one double helix through another, and probably acts as a structural protein in interphase cells, playing a role in the organisation of mitotic and meiotic chromosomes. A number of clinical anticancer drugs are thought to act on topo II enzymes to stabilise DNA-drug-topo II ternary complexes known as "cleavable complexes." These complexes may lead to illegitimate recombination events, as well as to the formation of other DNA lesions. Topo II-mediated genotoxicity is strongly dependent on the cell cycle status of the target cells. It is now apparent that some dietary components and environmental chemicals may act on topo II. Since the structural features of chemicals that lead to topo II interaction are not clear, it is currently not possible to predict such activity from chemical structure. For many years, the central dogma of chemical carcinogenesis has been that the most carcinogenic chemicals are those that can form a covalent bond with DNA, either directly or after metabolic activation. Topo II-directed drugs are not usually capable of forming covalent bonds with DNA and tend to have low mutagenicity in microbial assays. However, topo II-directed agents are potent cancerogens, inducing characteristic cytogenetic modifications. It is important to define the most sensitive tests to identify topo II-directed mutagens and to develop appropriate strategies for genotoxicity testing of such chemicals.
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Affiliation(s)
- L R Ferguson
- Cancer Research Laboratory, University of Auckland Medical School, New Zealand
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127
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Flickinger RA. Cell differentiation: an evolutionary perspective. INTERNATIONAL REVIEW OF CYTOLOGY 1994; 148:81-118. [PMID: 7509780 DOI: 10.1016/s0074-7696(08)62406-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- R A Flickinger
- Department of Biological Sciences, State University of New York at Buffalo 14260
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128
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Nahon E, Best-Belpomme M, Saucier JM. Analysis of the DNA topoisomerase-II-mediated cleavage of the long terminal repeat of Drosophila 1731 retrotransposon. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 218:95-102. [PMID: 8243480 DOI: 10.1111/j.1432-1033.1993.tb18355.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The interaction of DNA topoisomerase II with the long terminal repeat (LTR) of the Drosophila melanogaster 1731 retrotransposon was studied. The covalent binding of topoisomerase II to the LTR was strongly stimulated by different inhibitors of the enzyme 4'-demethylepipodophyllotoxin-9-(4,6-O-2-ethylidene-beta-D-glucopy ranoside (VP-16), 4'-(9-acridinylamino)methanesulfon-m-anisidine) (m-AMSA) and an ellipticine derivative. Enzyme-mediated DNA cleavage could be observed in the absence of inhibitors and was stimulated in their presence. Cleavage occurred predominantly at sites located within or at the boundary of alternating purine/pyrimidine tracts in agreement with previous observations [Spitzner, J. R., Chung, I. K. & Muller, M. T. (1990) Eukaryotic topoisomerase II preferentially cleaves alternating purine-pyrimidine repeats, Nucleic Acids Res. 18, 1-11]. In addition, all of the cleavage sites observed in the absence of inhibitor were located in the U3 region of the LTR. The site specificity of drug-induced cleavage was studied and the conformity of the cleavage sites with previously established consensus sequences was examined. Our results suggest that DNA topoisomerase II, through its ability to alter the degree of DNA supercoiling, might be involved in the control of different functions of the LTR.
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Affiliation(s)
- E Nahon
- URA Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, Paris, France
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129
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Paoletti C. The localization of topoisomerase II cleavage sites on DNA in the presence of antitumor drugs. Pharmacol Ther 1993; 60:381-7. [PMID: 8022867 DOI: 10.1016/0163-7258(93)90018-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Type II topoisomerase are enzymes that break and religate DNA phosphodiester bonds while crossing over DNA strands and altering DNA topology. They also are structural proteins that play a role in the spatial organization of chromatin and are involved in several crucial biological functions, such as DNA replication and transcription, chromosome segregation and recombination. Many drugs interfere with type II topoisomerases and can be assigned to two groups. Coumarin derivatives and synthetic quinolones act at the level of ATP binding or hydrolysis and are used for controlling bacterial infections. Drugs belonging to the second group produce DNA lesions by trapping a "cleavable complex" consisting of the normal transient topoisomerase II-DNA reaction intermediate in which the enzyme and the DNA are joined by two covalent bonds. There are four main categories of antitumour drugs that form cleavable complexes in eukaryotes: acridines, anthracyclines, ellipticines and epipodophyllotoxins. These drugs are cytotoxic and many--but not all--are endowed with antitumoral properties. The mechanisms of this pharmacological activity are not understood. Topoisomerase II-induced DNA breaks generated from cleavable complexes display different levels of cytotoxicity depending on their localization on DNA. The primary structure of DNA is not the only parameter that determines this localization. The spatial organization of the enzyme-DNA complex and both the topology and the structure of the underlying chromatin fiber constitute additional critical factors. It, therefore, may be unrealistic to expect that the actual pharmacological potency of antitumor drugs that act on type II topoisomerases can be accurately predicted solely on the basis of simple in vitro test tube experiments carried out using pure enzymes and naked DNA.
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Affiliation(s)
- C Paoletti
- Institut Gustave Roussy, Villejuif, France
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130
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Paul AL, Ferl RJ. Osmium tetroxide footprinting of a scaffold attachment region in the maize Adh1 promoter. PLANT MOLECULAR BIOLOGY 1993; 22:1145-1151. [PMID: 8400130 DOI: 10.1007/bf00028983] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Osmium tetroxide (OsO4) reacts with the thymine residues of double-stranded DNA, but thymines that are unpaired or under torsional stress are hyperreactive. Although OsO4 hyperreactivity has been primarily utilized to identify Z-DNA structures in supercoiled plasmids, OsO4 will also identify other torsional perturbations of DNA. In this study, OsO4 was used to footprint an AT-rich region (between -780 and -500) of the maize Adh1 promoter. Hyperreactive sites were identified both in vitro and in vivo in an area that coincides with AT motifs similar to those found in scaffold attachment regions. Further, the region of OsO4 hyperreactivity lies within a fragment of DNA that is associated with the nuclear scaffold in histone-depleted nuclei.
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Affiliation(s)
- A L Paul
- Department of Horticultural Science, University of Florida, Gainesville 32611
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131
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Chung JH, Whiteley M, Felsenfeld G. A 5' element of the chicken beta-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila. Cell 1993; 74:505-14. [PMID: 8348617 DOI: 10.1016/0092-8674(93)80052-g] [Citation(s) in RCA: 685] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We have characterized an element near the 5' boundary of the chicken beta-globin domain that insulates a reporter gene from the activating effects of a nearby beta-globin locus control region (5'HS2) when assayed in the human erythroid cell line K562. We show that the insulation mechanism is directional, that it operates at the level of transcription, and that it involves the alteration of chromatin structure over the promoter of the gene. The insulator has no significant stimulatory or inhibitory effects of its own. In transgenic Drosophila, the insulator protects the white minigene from position effects. The action of the insulator thus is not restricted to erythroid or mammalian cells, suggesting that such elements may serve an important and widely distributed function in the organization of chromatin structure.
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Affiliation(s)
- J H Chung
- Laboratory of Molecular Biology, National Institutes of Health, Bethesda, Maryland 20892
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132
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Mah DC, Dijkwel PA, Todd A, Klein V, Price GB, Zannis-Hadjopoulos M. ors12, a mammalian autonomously replicating DNA sequence, associates with the nuclear matrix in a cell cycle-dependent manner. J Cell Sci 1993; 105 ( Pt 3):807-18. [PMID: 8408306 DOI: 10.1242/jcs.105.3.807] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Origin enriched sequence ors8 and ors12, have been isolated previously by extrusion of nascent CV-1 cell DNA from replication bubbles at the onset of S-phase. Both have been shown to direct autonomous DNA replication in vivo and in vitro. Here, we have examined the association of genomic ors8 and ors12 with the nuclear matrix in asynchronous and synchronized CV-1 cells. In asynchronously growing cells, ors8 was found to be randomly distributed, while ors12 was found to be enriched on the nuclear matrix. Using an in vitro binding assay, we determined that ors12 contains two attachment sites, each located in AT-rich domains. Surprisingly, in early and mid-S-phase cells, ors12 homologous sequences were recovered mainly from the DNA loops, while in late-S the majority had shifted to positions on the nuclear matrix. In contrast, the distribution of ors8 over the matrix and loop DNA fractions did not change during the cell cycle. By bromodeoxyuridine substitution of replicating DNA, followed by immunoprecipitation with anti-bromodeoxyuridine antibodies and PCR amplification, we demonstrated that ors12 replicates almost exclusively on the matrix in early and mid-S-phase; replicating ors8 was also found to be enriched on the matrix in early S-phase. Chase experiments showed that the ors12 sequences labelled with bromodeoxyuridine in the first 2 hours of S-phase remain attached to the nuclear matrix, resulting in an accumulation of ors12 on the nuclear matrix at the end of the S period.
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Affiliation(s)
- D C Mah
- Department of Medicine, McGill University, Quebec, Canada
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133
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Abramova E, Vyguinnyi S, Mamaeva S. Increased frequency of acrocentric chromosome association during colcemid treatment. CANCER GENETICS AND CYTOGENETICS 1993; 68:52-9. [PMID: 8330283 DOI: 10.1016/0165-4608(93)90074-v] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The effect of Colcemid on satellite association frequencies was investigated in human cell lines U-937 GTB, SC-N-MC, HL-60, and Raji by silver staining method. Cell cultures were exposed to Colcemid at a concentration of 0.02 mg/ml for 15-60 minutes. As exposure time to Colcemid was increased, both the frequency of cells with satellite associations and the number of chromosomes involved in satellite associations increased significantly. Furthermore, the mean number of silver-stained chromosomes decreased with longer exposure time. Without Colcemid, we were able to obtain an adequate number of good-quality metaphase spreads. The data obtained may be of help in furthering research concerning satellite associations and in obtaining better quality chromosome preparations.
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Affiliation(s)
- E Abramova
- Institute of Cytology, Academy of Sciences, St. Petersburg, Russia
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134
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Wachsberger PR, Coss RA. Alterations in nuclear matrix ultrastructure of G1 mammalian cells following heat shock: resinless section electron microscopy, biochemical, and immunofluorescence studies. J Cell Physiol 1993; 155:615-34. [PMID: 7684045 DOI: 10.1002/jcp.1041550319] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Heat shock is known to inhibit vital nuclear functions associated with DNA and RNA metabolism. It has been proposed that the reported heat-induced excess protein accumulation in the nuclear matrix (NM) fraction may alter NM sites crucial for DNA and RNA processing. To test this hypothesis, we examined the fine structure of the NM in synchronous populations of G1 Chinese hamster ovary cells before and after heating by using the technique of resinless section electron microscopy. Heat did induce morphological alterations in the NM. The NM of control cells contained a honeycomb-like arrangement of fibers after chromatin removal. Following heat shock, NMs appeared as more highly anastomosing networks of polymorphic fibers and an overall increase in electron density was observed. Residual nucleoli from heated NMs underwent alterations in distributions of electron density both internally and at their peripheries. The increase in electron density observed in heated NMs was accompanied by an increase in protein mass and a relatively smaller increase in RNA mass as indicated by parallel sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) and isotopic labeling (protein/DNA and RNA) studies. Some excess protein accumulation could also be directly localized onto NM fibers by use of antibodies to heterogeneous ribonucleoprotein complex antigens. It is concluded that alterations of NM fine structure can reflect the heat-stressed state of the cell, may account for the heat-induced inhibition of nucleic acid metabolism, and may be useful as an indicator of physiological or pathological stress in general.
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Affiliation(s)
- P R Wachsberger
- Department of Radiation Oncology and Nuclear Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
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135
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Moore G, Gale MD, Kurata N, Flavell RB. Molecular Analysis of Small Grain Cereal Genomes: Current Status and Prospects. Nat Biotechnol 1993. [DOI: 10.1038/nbt0593-584] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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136
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Abstract
Although a formidable array of approaches fall under the broad umbrella of molecular genetics, the basic technology is elegant and conceptually simple (Watson et al. 1983, Roberts et al. 1992). It has enabled a reductionist approach to be applied to the study of genes and their sequences, as well as the transcripts that underlie organ development and function. Cardiovascular research has, in the past, utilized the systemic and integrative approaches that are inherent in the study of an organ system. Molecular genetics and recombinant DNA offer the cardiologist a complementary focus, as both normal and abnormal heart functions can be defined in terms of the underlying genetic complement and its regulation. One can approach heart function in terms of defining the basic components that participate in the developmental and functional processes of the heart at different developmental times. A future challenge will be to integrate the information regarding these different components with the heart's function in an intact biological system.
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Affiliation(s)
- J Robbins
- Department of Pharmacology and Cell Biophysics, University of Cincinnati College of Medicine, 231 Bethesda Avenue, Cincinnati, OH 45267-0575, USA
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137
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Schöffl F, Schröder G, Kliem M, Rieping M. An SAR sequence containing 395 bp DNA fragment mediates enhanced, gene-dosage-correlated expression of a chimaeric heat shock gene in transgenic tobacco plants. Transgenic Res 1993; 2:93-100. [PMID: 8513340 DOI: 10.1007/bf01969382] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A 395 bp fragment located downstream from the soybean heat shock gene Gmhsp 17.6-L exhibits several characteristics of scaffold attachment region (SAR) sequences. It contains matrix consensus elements, a topoisomerase II binding sequence and it associates with the isolated nuclear scaffold of soybean in vitro. Chimaeric genes containing the SARL fragment either at one side (5' or 3') or at both sides of a heat shock promoter-regulated beta-glucuronidase reporter gene were constructed. A five- to nine-fold increase of heat-inducible beta-glucuronidase activity was observed in transgenic tobacco plants containing constructs with SARL fragments either at both sides or with at least one SARL copy located upstream from the reporter gene. The gene copy number is positively correlated with the level of heat-inducible reporter gene activity in these plants but positional effects are not entirely eliminated. Thus, SAR sequences may potentially be used to increase gene expression, via as yet unknown mechanisms, and to reduce adverse effects on the expression of multiple gene copies in transgenic plants.
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Affiliation(s)
- F Schöffl
- Lehrstuhl für Allgemeine Genetik, Universität Tübingen, Germany
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138
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Eberharter A, Grabher A, Gstraunthaler G, Loidl P. Nuclear matrix of the lower eukaryote Physarum polycephalum and the mammalian epithelial LLC-PK1 cell line. A comprehensive investigation of different preparation procedures. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 212:573-80. [PMID: 7680312 DOI: 10.1111/j.1432-1033.1993.tb17695.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Agarose-encapsulated nuclear matrix preparations of the lower eukaryote Physarum polycephalum and the mammalian renal epithelial LLC-PK1 cell line were analyzed after various experimental protocols with respect to the protein composition. The effect of the mode of deproteinization (2 M NaCl, 0.25 M ammonium sulfate or 25 mM lithium diiodosalicylate), presence of 2-mercaptoethanol, Ca2+, Cu2+, chelating agents, the sequence of protein extraction and nuclease digestion, the use of RNase, the temperature at which the experimental manipulations were performed and the use of hypotonic or isotonic conditions was investigated. No significant differences in the final nuclear matrix composition could be observed, regardless of the experimental procedure applied. In Physarum, the major nuclear matrix proteins range over 12-70 kDa with prominent bands at 24, 31, 37 and 45 kDa; the proteins of the matrix in LLC-PK1 cells extend predominantly over 40-80 kDa. Furthermore, no essential differences in the protein composition could be observed when type I and type II nuclear matrices from the highly differentiated LLC-PK1 cell line were compared. The same was found for analogous matrix preparations of Physarum. Therefore, in both systems a distinction between type I/II matrix is questionable. Immunoblotting of the matrix preparations with a variety of antibodies against intermediate filament proteins and with antinuclear autoantibodies revealed the presence of intermediate filament proteins as components of the nuclear matrix. We conclude that the nuclear matrix represents a much more stable and reproducible structure than has been proposed so far, largely independent of changes in the preparation protocol.
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Affiliation(s)
- A Eberharter
- Department of Microbiology, University of Innsbruck, School of Medicine, Austria
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139
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Nocera A, Barocci S, Gorski J. Transcription analysis of non-HLA genes within or flanking the class II region in a B-cell line from an HLA-SCID patient. TISSUE ANTIGENS 1993; 41:94-6. [PMID: 8475494 DOI: 10.1111/j.1399-0039.1993.tb01985.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- A Nocera
- Molecular Genetics Laboratory, Immunogenetics Research Section, Blood Center of Southeastern Wisconsin, Milwaukee
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140
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Radiation-Induced Damage in Chromosomal DNA Molecules: Deduction of Chromosomal DNA Organization from the Hydrodynamic Data Used to Measure DNA Double-Strand Breaks and from Stereo Electron Microscopic Observations. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/b978-0-12-035417-7.50009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
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141
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Savage JR. Interchange and intra-nuclear architecture. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 1993; 22:234-244. [PMID: 8223504 DOI: 10.1002/em.2850220410] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
For chromatin lesions to interact to form exchanges of any sort, it is obvious that contact between them must be made. However, the probability of such interaction is conditioned by other factors like time, initial separation, metabolic activity, and, in the case of chemically induced lesions, scheduled DNA synthesis. The irradiated nucleus was, for a long time, regarded as a "bag of broken chromosomes" with the severed ends free to move around and find partners with which to form illegitimate reunions. Many of these would be seen at following metaphase as intra- and interchanges. Evidence is rapidly accumulating which indicates that this picture of the nucleus is false. We know now that chromosomes occupy highly localised domains with limited movement, and that there is no massive intermingling; that much of the chromatin is compacted and splinted with proteins and so precluded from exchange-type contact; that most of the chromatin is looped and "fixed" into an intra-nuclear protein scaffold or skeleton; that some chromatin is spun-out and associated with the nuclear envelope in the vicinity of the pore-complexes. Thus it would appear that movement, in the sense envisaged by early workers, is curtailed, and that only a proportion (probably a small proportion) of the chromatin is actually "at-risk" with respect to interchange formation. Where then does interchange take place? Are the "sites" pre-existent, or can proximity requirements be realised after radiation exposure? In what ways will the intra-nuclear architecture influence exchange? These are some of the questions which are considered in this paper.
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Affiliation(s)
- J R Savage
- MRC Radiobiology Unit, Chilton, Didcot, United Kingdom
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142
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Wevrick R, Willard VP, Willard HF. Structure of DNA near long tandem arrays of alpha satellite DNA at the centromere of human chromosome 7. Genomics 1992; 14:912-23. [PMID: 1478672 DOI: 10.1016/s0888-7543(05)80112-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The centromeric regions of human chromosomes contain long tracts of tandemly repeated DNA, of which the most extensively characterized is alpha satellite. In a screen for additional centromeric DNA sequences, four phage clones were obtained which contain alpha satellite as well as other sequences not usually found associated with tandemly repeated alpha satellite DNA, including L1 repetitive elements, an Alu element, and a novel AT-rich repeated sequence. The alpha satellite DNA contained within these clones does not demonstrate the higher-order repeat structure typical of tandemly repeated alpha satellite. Two of the clones contain inversions; instead of the usual head-to-tail arrangement of alpha satellite monomers, the direction of the monomers changes partway through each clone. The presence of both inversions was confirmed in human genomic DNA by polymerase chain reaction amplification of the inverted regions. One phage clone contains a junction between alpha satellite DNA and a novel low-copy repeated sequence. The junction between the two types of DNA is abrupt and the junction sequence is characterized by the presence of runs of A's and T's, yielding an overall base composition of 65% AT with local areas > 80% AT. The AT-rich sequence is found in multiple copies on chromosome 7 and homologous sequences are found in (peri)centromeric locations on other human chromosomes, including chromosomes 1, 2, and 16. As such, the AT-rich sequence adjacent to alpha satellite DNA provides a tool for the further study of the DNA from this region of the chromosome. The phage clones examined are located within the same 3.3-Mb SstII restriction fragment on chromosome 7 as the two previously described alpha satellite arrays, D7Z1 and D7Z2. These new clones demonstrate that centromeric repetitive DNA, at least on chromosome 7, may be more heterogeneous in composition and organization than had previously been thought.
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Affiliation(s)
- R Wevrick
- Department of Genetics, Stanford University, California 94305
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143
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Bradl J, Hausmann M, Ehemann V, Komitowski D, Cremer C. A tilting device for three-dimensional microscopy: application to in situ imaging of interphase cell nuclei. J Microsc 1992; 168:47-57. [PMID: 1447754 DOI: 10.1111/j.1365-2818.1992.tb03249.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The resolution of an optical microscope is considerably less in the direction of the optical axis (z) than in the focal plane (x-y plane). This is true of conventional as well as confocal microscopes. For quantitative microscopy, for instance studies of the three-dimensional (3-D) organization of chromosomes in human interphase cell nuclei, the 3-D image must be reconstructed by a point spread function or an optical transfer function with careful consideration of the properties of the imaging system. To alleviate the reconstruction problem, a tilting device was developed so that several data sets of the same cell nucleus under different views could be registered. The 3-D information was obtained from a series of optical sections with a Zeiss transmission light microscope Axiomat using a stage with a computer-controlled stepping motor for movement in the z-axis. The tilting device on the Axiomat stage could turn a cell nucleus through any desired angle and also provide movement in the x-y direction. The technique was applied to 3-D imaging of human lymphocyte cell nuclei, which were labelled by in situ hybridization with the DNA probe pUC 1.77 (mainly specific for chromosome 1). For each nucleus, 3-D data sets were registered at viewing angles of 0 degrees, 90 degrees and 180 degrees; the volumes and positions of the labelled regions (spots) were calculated. The results also confirm that, in principle, any angle of a 2 pi geometry can be fixed for data acquisition with a high reproducibility. This indicates the feasibility of axiotomographical microscopy of cell nuclei.
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Affiliation(s)
- J Bradl
- Institute of Applied Physics, University of Heidelberg, Germany
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144
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Bartjeliotou AJ, Dimitriadis GJ. The association of the human epsilon-globin gene with the nuclear matrix: a reconsideration. Mol Cell Biochem 1992; 115:105-15. [PMID: 1435759 DOI: 10.1007/bf00229102] [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: 12/27/2022]
Abstract
The association of the human epsilon-globin gene with the nuclear matrix was studied in erythroid and non-erythroid cell lines. Using a high salt method to prepare histone depleted nuclei we studied the association of variety of fragments covering a 7.8 kb region which contains the human epsilon-globin gene. We furthermore studied the association of a set of DNA fragments covering the 13 kb human G gamma/A gamma-globin gene domain, the 16 kb psi beta/delta-globin gene domain and the 10 kb beta-globin gene domain with the nuclear matrix of K562 and Raji cells. The results show that all fragments studied are easily released from the nuclear matrix, indicating no specific association. Summarizing our results we could say that a region starting 5.7 kb 5' to the human epsilon-globin gene and ending 4 kb 3' to the human beta-globin gene seems to contain no attachment sites with the nuclear matrix of both erythroid and non-erythroid cells.
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145
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Gudas JM, Fridovich-Keil JL, Datta MW, Bryan J, Pardee AB. Characterization of the murine thymidine kinase-encoding gene and analysis of transcription start point heterogeneity. Gene 1992; 118:205-16. [PMID: 1511894 DOI: 10.1016/0378-1119(92)90190-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have determined the molecular organization and transcription start points (tsp) for the murine gene (TK) encoding thymidine kinase. The exon/intron structure and sequences present at the splice junctions of the mammalian TK genes have been highly conserved; however, the promoter sequences of these genes have diverged widely. Both the human and Chinese hamster TK promoter regions contain CCAAT and TATA consensus motifs, whereas the mouse promoter has neither element. This difference between species is reflected in that, unlike the hamster and human TK genes, transcription initiates from numerous specific tsp within a 100-bp region in the mouse TK gene. The complex pattern of tsp seen in the endogenous gene was not maintained in transfected cell lines containing TK promoter::beta-globin (HBB) fusions. Transcription from the murine TK:HBB fusion genes initiated from a small number of tsp that were clustered downstream from the ATG in hybrids containing TK coding sequences, and in the HBB 5' UTR in hybrids that did not. Few or no specific tsp were detected from the upstream sites used in the endogenous mouse TK gene.
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Affiliation(s)
- J M Gudas
- Dana Farber Cancer Institute, Division of Cell Growth and Regulation, Boston, MA 02115
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146
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Abstract
A battery of monoclonal antibodies (mAbs) against brain cell nuclei has been generated by repeated immunizations. One of these, mAb A60, recognizes a vertebrate nervous system- and neuron-specific nuclear protein that we have named NeuN (Neuronal Nuclei). The expression of NeuN is observed in most neuronal cell types throughout the nervous system of adult mice. However, some major cell types appear devoid of immunoreactivity including cerebellar Purkinje cells, olfactory bulb mitral cells, and retinal photoreceptor cells. NeuN can also be detected in neurons in primary cerebellar cultures and in retinoic acid-stimulated P19 embryonal carcinoma cells. Immunohistochemically detectable NeuN protein first appears at developmental timepoints which correspond with the withdrawal of the neuron from the cell cycle and/or with the initiation of terminal differentiation of the neuron. NeuN is a soluble nuclear protein, appears as 3 bands (46-48 × 10(3) M(r)) on immunoblots, and binds to DNA in vitro. The mAb crossreacts immunohistochemically with nervous tissue from rats, chicks, humans, and salamanders. This mAb and the protein recognized by it serve as an excellent marker for neurons in the central and peripheral nervous systems in both the embryo and adult, and the protein may be important in the determination of neuronal phenotype.
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Affiliation(s)
- R J Mullen
- Department of Anatomy, University of Utah School of Medicine, Salt Lake City 84132
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147
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Marilley M, Pasero P, Got C. Molecular dissection of a specific nuclear domain: the chromatin region of the ribosomal gene cluster in Xenopus laevis. Exp Cell Res 1992; 202:87-97. [PMID: 1324846 DOI: 10.1016/0014-4827(92)90407-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Molecular dissection of the nuclear domain corresponding to the ribosomal chromatin cluster was investigated. The experimental scheme was based on the ability of restriction enzymes to digest the whole genome without affecting this region (several megabases in length). Such a strategy involved the judicious choice of restriction enzymes, which is possible in Xenopus laevis, where the rDNA sequence is known and the repeated units are organized into one unique cluster. SalI, XhoI, and EcoRV digestion produced frequent cutting of the genome leaving the ribosomal cluster intact. Isolation of the rDNA cluster was confirmed by separation of the digested DNA by pulsed-field electrophoresis. When applied to purified nuclei, this approach allowed the isolation of the ribosomal chromatin cluster under very mild conditions: no cleavages (either enzymatic or mechanical) were detectable. Since the purification scheme depends only on the DNA sequence outside of the rDNA cluster, it permits the obtention of this domain in different functional states. Electron microscopic analysis demonstrated that the domain organization is substantially preserved and maintains its looped organization (the size and the full number of loops were preserved). This purification scheme provides a powerful tool for studying the structure-function relationships within the ribosomal nuclear domain.
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Affiliation(s)
- M Marilley
- Laboratoire de Génétique, URA CNRS 1189, Université d'Aix-Marseille II, Faculté de Médecine, France
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148
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Ferraro A, Grandi P, Eufemi M, Altieri F, Turano C. Crosslinking of nuclear proteins to DNA by cis-diamminedichloroplatinum in intact cells. Involvement of nuclear matrix proteins. FEBS Lett 1992; 307:383-5. [PMID: 1644195 DOI: 10.1016/0014-5793(92)80718-v] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In order to detect the nuclear matrix proteins involved in DNA binding, avoiding possible artifacts derived from the disruption of nuclei, proteins were crosslinked to DNA by the action of cis-diamminedichloroplatinum on intact chicken liver cells and analyzed by two-dimensional gel electrophoresis. At least eleven species of crosslinked proteins were found to derive from the nuclear matrix prepared from the same cell type, and five of these were found also among the proteins crosslinked to DNA in intact liver cells from ox and pig. This subset of common proteins, conserved in different animal species, is likely to have a fundamental role for the anchorage of DNA to the nuclear matrix.
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Affiliation(s)
- A Ferraro
- Department of Biochemical Sciences, University La Sapienza, Rome, Italy
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149
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Gasser SM, Walter R, Dang Q, Cardenas ME. Topoisomerase II: its functions and phosphorylation. Antonie Van Leeuwenhoek 1992; 62:15-24. [PMID: 1332607 DOI: 10.1007/bf00584459] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The gene encoding topoisomerase II in yeast is unique and essential, required for both mitotic and meiotic proliferation. The use of temperature-sensitive mutants in topoisomerase II have demonstrated roles in the relaxation of tortional stress, reduction of recombination rates, and in the separation of sister chromatids after replication. In vertebrate cells, topoisomerase II was shown to be the most abundant component of the metaphase chromosomal scaffold, and has been shown to play a role in chromosome condensation in vitro. The cell cycle control of chromosome condensation may well require phosphorylation of topoisomerase II, since the enzyme is more highly phosphorylated in metaphase than in G1. Recent studies have identified casein kinase II as the major enzyme phosphorylating topoisomerase II in intact yeast cells. The target sites of CKII are exclusively in the C-terminal 400 amino acids of topoisomerase II, the region that is most divergent among the eukaryotic type II enzymes and which is absent in the bacterial gyrase homologues.
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Affiliation(s)
- S M Gasser
- Swiss Institute for Experimental Cancer Research (ISREC), Epalinges s/Lausanne
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150
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Roy C, Brown DL, Little JE, Valentine BK, Walker PR, Sikorska M, Leblanc J, Chaly N. The topoisomerase II inhibitor teniposide (VM-26) induces apoptosis in unstimulated mature murine lymphocytes. Exp Cell Res 1992; 200:416-24. [PMID: 1315287 DOI: 10.1016/0014-4827(92)90190-j] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This study shows that not only concanavalin A-stimulated proliferating lymphocytes but also unstimulated mouse splenic lymphocytes are sensitive to the topoisomerase II (topo II) inhibitor teniposide (VM-26). When unstimulated lymphocytes are pretreated with VM-26 for a 2-h period and are then incubated in drug-free medium, cell viability, as determined by trypan blue exclusion, decreases to 40% of the control by 6 h. The drug-treated cultures show two to three times the level of detergent soluble DNA than the control cultures and agarose gel electrophoresis of the soluble DNA shows the presence of oligonucleosomal-sized fragments, a feature considered to be a hallmark of apoptosis. Phase contrast microscopy, Hoechst staining for DNA, and immunofluorescence microscopy of various nuclear and cytoplasmic antigens (nucleolar fibrillarin, snRNP, ubiquitin, vimentin, tubulin) in the VM-26-treated cells characterize the morphological changes during apoptosis of these cells. The role of topo II as the mediator of the VM-26 effects is supported by pulsed field gel electrophoresis, which shows the typical topo II-induced cleavage of supercoiled DNA into loop-sized 300- and 50-kbp fragments. We conclude that the cancer chemotherapeutic agent VM-26 interacts with topo II and induces apoptosis in unstimulated lymphocytes.
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Affiliation(s)
- C Roy
- Department of Biology, University of Ottawa, Canada
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