The association of transcribed genes with the nuclear matrix of<i>Drosophila</i>cells during heat shock

Small, Donald; Nelkin, Barry D.; Vogelstein, Bert

doi:10.1093/nar/13.7.2413

Cited by 114 publications

(50 citation statements)

References 57 publications

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“…These findings are in agreement with the hypothesis that replication from an upstream origin is a necessary but not sufficient condition for gene activity. However, an alternative possibility is suggested by reports that DNA replication initiates at the nuclear matrix (2,37), and that active (and potentially active) genes are anchored to the matrix (10,13,38) at specific DNA sequences (31,41); namely, that the correspondence of replication and transcription polarities is a coincidence resulting from DNA and RNA polymerases both using the nuclear matrix as a chromatin entry site. The similarity in the replication polarity of the alpha-globin domain in erythrocytes and lymphocytes could arise from the establishment early in the hematopoietic lineage of a common matrix binding site flanking these genes in these two cell types.…”

Section: Discussionmentioning

confidence: 99%

Polarity of DNA replication through the avian alpha-globin locus.

James

Leffak

1986

Mol. Cell. Biol.

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Toward understanding the controls affecting eucaryotic chromosome replication, we used a runoff replication assay to investigate whether the activity of a gene is related to its use of an upstream or downstream replication origin. When in vivo-initiated DNA polymerases are allowed to complete replication in vitro in the presence of bromodeoxyuridine triphosphate the density label is preferentially incorporated into origin-distal regions of DNA. Isopycnic centrifugation and blot hybridization analysis of the relative bromodeoxyuridine triphosphate incorporation into fragments spanning the chicken alpha-globin locus indicate that this region is replicated from an upstream origin both in chicken lymphocytes and in erythrocytes. Thus the replication polarity of these genes does not change as a function of transcriptional activity, consistent with earlier suggestions that DNA replication in the transcriptional direction may be a necessary but not sufficient condition for gene expression.The ordered nature of eucaryotic chromosome replication is evident in the replication of particular chromosome domains during discrete intervals of the S phase and in the synchronous initiation of replicon clusters whose size and number vary in a tissue-specific and developmentally regulated manner (reviewed in references 16, 21, and 47). These observations are consistent with recent data showing that DNA sequences complementary to probes for individual transcribed genes preferentially replicate early in the S phase and that chromosome position influences the timing of gene replication (6,11,17,20). In Saccharomyces cerevisiae, electron microscopic and biochemical data imply that DNA synthesis initiates at specific loci (5,7,18,46,50); the clearest evidence for the existence of discrete origins in higher eucaryotes comes from studies of the amplification of dihydrofolate reductase genes in CHO cells (22,23) and chorion genes in Drosophila follicle cells (36,44), where the extent -of amplification decreases bidirectionally from a central domain.The apparent nonrandom selection of sites for replication initiation and the asymmetry of chromatin replication at the level of DNA synthesis (16, 35) and protein deposition (28) have contributed to the proposal that replication origin selection may regulate gene activity (42, 49). As an initial step toward testing this hypothesis we have used a runoff replication assay to determine the direction of replication of the chicken alpha-globin genes in cells where these sequences are expressed (erythrocytes) or quiescent (lymphocytes). Following the logic used to locate the simian virus 40 origin of replication (12, 34), isolated nuclei were incubated in a replication cocktail containing bromodeoxyuridine (BrdU) triphosphate (BrdUTP) and allowed to complete the synthesis of DNA chains initiated in vivo. The direction of replication was deduced based on the relative incorporation of BrdU into DNA fragments encompassing the globin locus; those fragments farthest from the origin of replication incorpora...

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Section: Discussionmentioning

confidence: 99%

Polarity of DNA replication through the avian alpha-globin locus.

James

Leffak

1986

Mol. Cell. Biol.

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“…It has been shown that actively transcribed genes are located in the DNA loops at positions close to or at the nuclear matrix (Robinson et al, 1982;Ciejek et al, 1983). Both for multiple attachment of active genes to the matrix (Small et al, 1985) and for a unique attachment site (Mirkovitch et al, 1984) evidence has been presented. Interestingly, the sites are located upstream of the gene, possibly in regulatory sequences.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of DNA loop length in nontransformed and transformed hamster cells

Linskens

Eijsermans

Dijkwel

1987

Mutation Research/Fundamental and Molecular Mechanisms of Mutag

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“…The nuclear matrix, a meshwork of thick polymorphic fibers apparently underlayed by a meshwork of intermediate-sized core filaments (Jackson and Cook 1988;He et al 1990), probably consists of elements of this nucleoskeleton. Actively transcribed chromatin is associated with the matrix (Robinson et al 1982;Ross et al 1982;Ciejek et al 1983;Hentzen et al 1984;Small et al 1985;Thorburn et al 1988), and it appears to be the substratum upon which heterogenous nuclear RNA (hnRNA) processing occurs (Zeitlin et al 1987(Zeitlin et al , 1989. m R N A and pre-mRNA are tightly bound to structures within the eukaryotic nucleus (Zeitlin et al 1987(Zeitlin et al , 1989) and move along "tracks" from sites of synthesis in the nuclear interior to the periphery (Lawrence et al 1989;Huang and Spector 1991;Xing and Lawrence 1991), possibly in association with fibers of the nucleoskeleton.…”

Section: What Types Of Mutant Genes Might Be Identified Using the In mentioning

confidence: 99%

Isolation and characterization of RAT1: an essential gene of Saccharomyces cerevisiae required for the efficient nucleocytoplasmic trafficking of mRNA.

Amberg¹,

Goldstein²,

Cole³

1992

Genes Dev.

355

378

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We have combined techniques of genetics and histochemistry to identify genes required for the nucleocytoplasmic export of mRNA in the budding yeast Saccharomyces cerevisiae. We adapted in situ hybridization using a digoxigenin-labeled oligo(dT)s o probe to localize poly(A) + RNA in fixed yeast cells and used yeast strains carrying the rnal-1 mutation to develop an assay. The rnal-1 mutation is the only previously described mutation that causes defects in mRNA export. As visualized with this RNA localization assay, rnal-1 strains accumulated poly(A) + RNA at the nuclear periphery at the nonpermissive temperature. This was in contrast to the RNA localization pattern of wild-type cells or rnal-1 cells grown at permissive temperature. Wild-type cells showed bright uniform cytoplasmic staining with little detectable RNA in the nuclei. We used this RNA localization assay to screen a bank of temperature-sensitive yeast strains for mutants with inducible defects in mRNA trafficking. Strains identified in this manner are designated RAT mutants for ribonucleic acid trafficking. The ratl-1 allele conferred temperature-sensitive accumulation of poly(A) + RNA in one to several intranuclear spots that appear to lie at the nuclear periphery. RNA processing was unaffected in ratl-1 strains, except for an inducible defect in trimming the 5' end of the 5.8S rRNA. The wild-type RAT1 gene was cloned by complementation; it encodes an essential ll6-kD protein with regions of homology to the protein encoded by SEP1 (also known as DST2, XRN1, KEM1, and RARS). Seplp is a nucleic acid binding protein, a 5'---> 3' exonuclease, and catalyzes DNA strand transfer reactions in vitro. We discuss the possible significance of the Ratlp/Seplp homology for RNA trafficking. We also discuss the potential of this RNA localization assay to identify genes involved in nuclear structure and RNA metabolism.[Key Words: mRNA export; yeast; in situ hybridization; RAT1; RNA1; SEP1]

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The association of transcribed genes with the nuclear matrix ofDrosophilacells during heat shock

Cited by 114 publications

References 57 publications

Polarity of DNA replication through the avian alpha-globin locus.

Polarity of DNA replication through the avian alpha-globin locus.

Comparative analysis of DNA loop length in nontransformed and transformed hamster cells

Isolation and characterization of RAT1: an essential gene of Saccharomyces cerevisiae required for the efficient nucleocytoplasmic trafficking of mRNA.

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