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K D Tartof

Publications and source records attributed to K D Tartof.

At least 19 recordsLinked to original sources
PubMed1995

Comprehensive allelotyping of human renal cell carcinomas using microsatellite DNA probes.

The von Hippel-Lindau locus on chromosome 3p is a tumor suppressor gene known to be involved in nonpapillary renal cell carcinoma. A previous loss of heterozygosity (LOH) study aimed at determining the allelotype of kidney tumors has indicated that in addition to 3p, chromosome arms 5q, 6q, 10q, 11q, 17p, and 19p may also harbor tumor suppressor genes. However, cytogenetic studies reveal that chromosomes 3p, 6q, 8p, 9pq, and 14q most frequently undergo karyotypic changes in renal tumors. To resolve these differences, a collection of microsatellite DNA probes has been used to scan for LOH so that 90% of individual tumor genomes were rendered informative for allele loss. The assay is capable of detecting quantitative genomic alterations in tumor cells as well. We find that LOH is most frequent for chromosome arm 3p. However, in no tumor is 3p exclusively affected. LOH for 6q, 8p, 9pq, and 14q is also distinctly elevated for both nonpapillary as well as papillary tumors and suggest that many of the tumor suppressor loci involved may be common to the etiology of both forms of kidney cancer.

Alleles↗
PubMed1994

Position effect variegation in yeast.

Classically, position effect variegation has been studied in Drosophila and results when a euchromatic gene is placed adjacent to either centromeric heterochromatin or to a telomeric domain. In such a circumstance expression of the locus variegates, being active in some cells and silent in others. Over the last few years a comparable phenomenon in yeast has been discovered. This system promises to tell us much about this curious behavior. Indeed, experiments reported recently(1) indicate that the variegation of a yeast telomeric gene is cell-cycle regulated. The results suggest the following model. During DNA replication there is a disassembly of chromatin that allows a competition between silencing factors and transactivators to take place. Thus, reassembly of the domain may result in either the repression or the expression of the affected gene and, hence, produce a variegating phenotype.

Animals↗
PubMed1994

Molecular analysis of cubitus interruptus (ci) mutations suggests an explanation for the unusual ci position effects.

The cubitus interruptus (ci) locus of Drosophila melanogaster is located proximally on chromosome 4. In ci mutants cubital wing veins are interrupted or absent. We have cloned this locus using a gypsy element associated with the ci1 mutation. Analysis of all extant ci mutations reveals that they contain conspicuous molecular alterations within a 13.7 kb region. Of the four homozygous viable mutations, three (ci1, ci361, ciw) have single insertions, while one (ci57g) has a small deletion, all located within a more restricted 1 kb region. The dominant mutations, ciD and Ce2 each contain two insertions within the 13.7 kb region. All these molecular alterations are located upstream of a transcript previously associated with the ciD mutation and thought to derive from a segment polarity gene. We induced revertants of the dominant ci phenotype (wing vein interruption) in ciD and found molecular alterations in this transcript (the ci+ transcript) in two revertant alleles, thereby demonstrating this transcript's involvement in the ci phenotype. The locations of the molecular alterations, together with the results of the ciD reversion experiment, provide a connection between the dominant and recessive ci mutations and argue that all are likely to be alleles of the same complex locus, ci, not two separate loci as previously proposed. The ci phenotype of dominant and recessive mutations can be explained by inappropriate expression of the ci+ transcript in the posterior wing compartment where the cubital vein is affected, while loss of ci+ function generates recessive lethality. Lack of repression of ci+ transcription, through a pairing-dependent, trans-acting silencer element, can explain the unusual position effects associated with ci (the Dubinin effect).

Animals↗
PubMed1992

A superfamily of Drosophila satellite related (SR) DNA repeats restricted to the X chromosome euchromatin.

The 1.688 g/cm3 class of Drosophila satellite DNA is predominantly localized to the centromeric heterochromatin of the X chromosome. We report here the existence of 1.688 satellite related (SR) DNA arrays present at numerous locations throughout the euchromatic portion of the X. Unlike their heterochromatic counterparts, euchromatic SRs consist of a small number of repeating units (usually 2-4), each of which is 63-81% identical to the 359-bp monomer of the 1.688 satellite. Although it appears that SR DNA arrays are not transcribed, in at least two cases, they are located adjacent to transcriptionally active genes. SR sequences also have significant similarity to a previously described Drosophila middle repeat found almost exclusively in the X euchromatin. It seems likely that these X linked sequences are required for sex chromosome specific functions.

Animals↗
PubMed1990

Mechanisms for the construction and developmental control of heterochromatin formation and imprinted chromosome domains.

The study of variegating position effects in Drosophila provides a model system to explore the mechanism and material basis for the construction and developmental control of heterochromatin domains and the imprinted genomic structures that they may create. The results of our experiments in this regard have implications for a diverse assortment of long-range chromosome phenomena related to gene and chromosome inactivation. Specifically, as a consequence of our studies on position effect variegation, we propose a simple mechanism of X-chromosome inactivation, suggest a purpose for genomic imprinting, and postulate a general means for regulating the time in development at which certain genes become heterochromatically repressed.

Animals↗
PubMed1989

Towards an understanding of position effect variegation.

Most variegating position effects are a consequence of placing a euchromatic gene adjacent to alpha-heterochromatin. In such rearrangements, the affected locus is inactivated in some cells, but not others, thereby giving rise to a mosaic tissue of mutant and wild-type cells. A detailed examination of the molecular structure of three variegating white mottled mutations of Drosophila melanogaster, all of which are inversions of the X chromosome, reveals that their euchromatic breakpoints are clustered and located approximately 25 kb downstream of the white promoter and that the heterochromatic sequences to which the white locus is adjoined are transposons. An analysis of three revertants of the wm4 mutation, created by relocating white to another euchromatic site, demonstrates that they also carry some heterochromatically derived sequences with them upon restoration of the wild-type phenotype. This suggests that variegation is not controlled from a heterochromatic sequence immediately adjacent to the variegating gene but rather from some site more internal to the heterochromatic domain itself. As a consequence of this observation we have proposed a boundary model for understanding how heterochromatic domains may be formed. It has been recognized for many years that the phenotype of variegating position effects may be altered by the presence of trans-acting dominant mutations that act to either enhance or suppress variegation. Using P-element mutagenesis, we have induced and examined 12 dominant enhancers of variegation that represent four loci on the second and third chromosomes. Most of these mutations are cytologically visible duplications or deficiencies. They exert their dominant effects through changes in the copy number of wild-type genes and can be divided into two reciprocally acting classes. Class I modifiers are genes that act as enhancers of variegation when duplicated and as suppressors when mutated or deficient. Conversely, class II modifiers are genes that enhance when mutated or deleted and suppress when duplicated. The available data indicate that, in Drosophila, there are 20-30 loci capable of dominantly modifying variegation. Of these, most appear to be of the class I type whereas only two class II modifiers have been identified so far.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1988

New cloning vectors and techniques for easy and rapid restriction mapping.

We have modified plasmid, phage lambda and cosmid cloning vectors to be of general use for easily and unambiguously determining restriction maps of recombinant DNA molecules. Each vector is constructed so that it contains the rarely found NotI restriction site joined to a short synthetic linker sequence that is followed by a multiple cloning site. DNA cloned into these vectors may be restriction-mapped by either of two methods. In one technique, the cloned DNA is completely digested with NotI, followed by partial digestion with any other restriction enzyme. After electrophoresis and transfer to a nylon membrane, the fragments are hybridized to a labeled probe complementary to the NotI linker. In the second technique, referred to as recession hybridization detection, cloned DNA is digested with NotI and then briefly treated with exonuclease III to recess the 3' ends. After hybridizing a labeled complementary oligodeoxynucleotide to the single-stranded 5' end containing the linker sequence, the DNA is partially digested with another restriction enzyme, electrophoresed and the gel is exposed to x-ray film. With either method the size of each labeled fragment corresponds directly to the distance that a restriction site is located from the NotI linker terminus. Methods for obtaining partial restriction enzyme digests have been devised so that as many as 20 different enzymes may be conveniently mapped on a single gel in little more than a day. The vectors and techniques described may also be adapted to automated or semi-automated devices that read fragment lengths and calculate the resulting restriction map.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteriophage lambda↗
PubMed1988

Dosage-dependent modifiers of position effect variegation in Drosophila and a mass action model that explains their effect.

Twelve dominant enhancers of position effect variegation, representing four loci on the second and third chromosomes of Drosophila melanogaster, have been induced by P-element mutagenesis. Instead of simple transposon insertions, seven of these mutations are cytologically visible duplications and three are deficiencies. The duplications define two distinct regions, each coinciding with a locus that also behaves as a dominant haplo-dependent suppressor of variegation. Conversely, two of the deficiencies overlap with a region that contains a haplo-dependent enhancer of variegation while duplications of this same region act to suppress variegation. The third deficiency defines another haplo-dependent enhancer. These data indicate that loci capable of modifying variegation do so in an antipodal fashion through changes in the wild-type gene copy number and may be divided into two reciprocally acting classes. Class I modifiers enhance variegation when duplicated or suppress variegation when deficient. Class II modifiers enhance when deficient but suppress when duplicated. From our data, and those of others, we propose that in Drosophila there are about 20 to 30 dominant loci that modify variegation. Most appear to be of the class I type whereas only two class II modifiers have been identified so far. From these observations we put forth a model, based on the law of mass action, for understanding how such suppressor-enhancer loci function. We propose that each class I modifier codes for a structural protein component of heterochromatin and their effects on variegation are a consequence of their dosage dependent influence on the extent of the assembly of heterochromatin at the chromosomal site of the position effect. It is further proposed that class II modifiers may inhibit the class I products directly, bind to hypothetical termination sites that define heterochromatin boundaries or promote euchromatin formation. Consistent with our mass action model we find that combining two enhancers together produce additive and not epistatic effects. Also, since different enhancers have different relative strengths on different variegating mutants, we suggest that heterochromatic domains are constructed by a combinatorial association of proteins. The mass action model proposed here is of general significance for any assembly driven reaction and has implications for understanding a wide variety of biological phenomena.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1985

A two-stage model for the control of rDNA magnification.

Males of the genotype bb/Ybb- have been shown to produce both magnified (bbm+) and, less frequently, reduced (bbrl) X chromosomes. An analysis of the progeny of single magnifying bb/Ybb- males reveals that bbm+ revertants may be recovered either as rare single events or, more frequently, in large clusters. To analyze the role of the bb phenotype in the induction of rDNA magnification we have constructed a series of bb and bb+ derivatives of Ybb-. Males carrying an X chromosomal bb allele and one of these derivatives (bb/bbYbb- or bb/bb+Ybb-) produce small numbers (one to two) of bbm+ progeny at a frequency similar to that observed for bb/Ybb- males but do not produce large clusters of bbm+ revertants. In addition, bb/bb+Ybb- males produce essentially equal numbers of magnified (bbm+) and reduced (bbrl) X chromosomes. These data, together with a consideration of the growth properties of the male germline in Drosophila, suggest that magnification/reduction may occur at two different times during development. Those events that give rise to large clusters, and, thus, necessarily arise early in germ cell development, appear to be dependent on the bb phenotype. However, those events that give rise to single bbm+ chromosomes arise late in spermatogenesis, probably at meiosis, and are independent of the bb phenotype.

Animals↗
PubMed1984

A structural basis for variegating position effects.

Variegating position effects in Drosophila result from chromosome rearrangements where normal genes, having been placed next to heterochromatin, are inactivated in some cells but not in others, thereby producing a variegated tissue. We have determined that the euchromatic breakpoints for three variegating white mutants are clustered and lie approximately 25 kb downstream of the white structural gene. In each case the white locus is adjoined in the heterochromatin to a mobile genetic element. Satellite sequences are not involved. We also demonstrate that revertants of the variegating mutant, wm4, are reinversions that leave the initial wm4-heterochromatic junction intact so that some heterochromatin-derived sequences remain joined to white at its new location. These results suggest a simple model for understanding the structure of heterochromatic domains and how variegating position effects may arise.

Animals↗
PubMed1983

The effect of mei-41 on rDNA redundancy in Drosophila melanogaster.

The recombination and repair defective mutant, mei-41, exhibits three rather striking effects on the genetic properties and chromosomal stability of rDNA in Drosophila. First, mei-41 inhibits rDNA magnification. However, mei-9, another recombination and repair defective mutation has no similar effect. This indicates that magnification requires some, but not all, of the gene products necessary for meiotic exchange. Second, under magnifying conditions, mei-41 induces interchanges between the X rDNA and either arm of the Ybb- chromosome. These interchanges occur at high frequency and are independent of rDNA orientation. Third, in mei-41 bb+/Ybb+ males, bobbed mutants in the X, but not the Y, also arise at high frequency. Evidence suggests that these events involve the rDNA type I insertion. The recombination and repair defective properties of mei-41 together with our results regarding its unusual and specific effects involving rDNA are explained in a simple model that has general implications for chromosome structure.

Animals↗
PubMed1982

Glutamate tRNA genes are adjacent to 5S RNA genes in Drosophila and reveal a conserved upstream sequence (the ACT-TA box).

In Drosophila melanogaster at least six transfer RNA genes are located adjacent to the 3' end of the 5S RNA gene cluster. Three of these have been sequenced and identified as coding for glutamate tRNA4. In the chromosome they are arranged as tandem repeats on the same DNA strand and transcribed in the same direction as is 5S DNA, towards the centromere. We have also identified a sequence, the ACT-TA box, that is highly conserved among the polymerase III transcribed genes. Usually the sequence is located at 37 +/- 8 base pairs upstream from the first nucleotide of the structural gene. A similar sequence is also observed upstream of yeast and silkworm tRNA genes and the mitochondrial tRNA genes of mouse and humans.

Animals↗
PubMed1980

Long spacers among ribosomal genes of Drosophila melanogaster.

The fruit fly, Drosophila melanogaster, has 200 tandemly arranged copies of the ribosomal RNA genes (rDNA) per haploid genome. One such cluster of rRNA genes occurs on the X and one on the Y chromosome. The basic repeating unit of the rRNA gene consists of a segment coding for 18S rRNA and 28S rRNA followed by a non-transcribed spacer (Fig.1). In the X chromosome, there are two major size classes (12 and 17 kilobases) and numerous minor size classes of rDNA repeats. Most of this length heterogeneity is generated by insertions at a specific site in the 28S gene. The frequency and size patterns of these insertions in the 28S gene differ in the X and Y chromosomes. Electron microscopic analysis of rDNA-rRNA hybrids has shown that there is also length heterogeneity in the rDNA non-transcribed spacer. This heterogeneity is due in part to internal sequence repetition. We have now examined further the length heterogeneity of the rDNA spacer and have observed a class of spacers that we shall refer to as 'long spacers'. The size and frequency of these long spacers are different in the X and Y rDNA.

Animals↗
PubMed1979

Evolution of transcribed and spacer sequences in the ribosomal RNA genes of Drosophila.

Examination of the ribosomal RNA (rRNA) gene of six sibling species that make up the D. melanogaster subgroup reveals that the nontranscribed spacer is highly conserved during evolution. Indeed, the spacer is at least as conserved as the transcribed rRNA sequence in four of the six species and only slightly less conserved in the others. These data support the hypothesis previously suggested (Tartof and Dawid, 1976) that selection has a significant role in maintaining the parallel evolution of genetically separate but homologous redundant gene clusters.

Animals↗