The Topographic Organization of Repetitive DNA in the Human Nucleolus

Kaplan, Frederick S.; Murray, John I.; Sylvester, James E.; Gonzalez, Iris L.; O’Connor, J. P.; Doering, Jeffrey L.; Muenke, Maximilian; Emanuel, Beverly S.; Zasloff, Michael

doi:10.1006/geno.1993.1020

Cited by 49 publications

(32 citation statements)

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“…ASA are also the only HD breakpoints at which the identities of target genes may be readily inferred, as the rDNA repeats are the only genes located there. 62,63 Here, we show that rDNA is rearranged genomically in HDLM cells, as suggested by cytogenetic analysis, and amplified in both HDLM and KM-H2 cells. Like interstitial subtelomeres, rDNA/ASA rearrangements in HD cell lines might reflect a DNA processing defect occurring either passively, or as a means to facilitate gene rearrangement.…”

Section: Possible Roles For Rdna Changessupporting

confidence: 56%

Karyotypic dissection of Hodgkin's disease cell lines reveals ectopic subtelomeres and ribosomal DNA at sites of multiple jumping translocations and genomic amplification

MacLeod

Spitzer

Bar‐Am³

et al. 2000

Leukemia

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Although the neoplastic significance of the chromosome changes widespread in Hodgkin's disease (HD) remains obscure, a distinct cytogenetic picture has emerged combining aneuploidy with structural rearrangements clustered at certain breakpoints. Notably absent are the recurrent chromosome translocations which distinguish other hematopoietic neoplasms and serve as clues to underlying oncogene alterations. The paucity of neoplastic cells in HD biopsies hinders detailed chromosome analysis. As an alternative, we investigated a panel of well characterized cell lines by classical and molecular cytogenetics, using single-gene and subtelomeric probes, including three autologous HD examples (HDLM-1/2/3) analyzed by 'spectral karyotyping' -the first complete HD karyotype to be documented. Although complex, most rearrangements in HDLM cells arose in vivo and included few rare but many typical HD breakpoints, notably at the r(ibosomal)DNA regions. Two types of genomic rearrangement involving DNA repeats were conspicuous: insertion and genomic amplification/coamplification of rDNA -the first genomic rDNA rearrangements to be reported in a tumor cell, and the first example of multiple 'jumping translocations' (JT). Of four subtelomeric microsatellite repeats tested in HDLM cells, three exhibited interstitial sites at JT, of which two (at 5qter and 9pter) were respectively associated with deletion of the 5q31-32 myeloid region, and coamplification of a recently described HD-recurrent amplicon at 9p2 together with transcriptionally silent rDNA. Altogether, three out of four HD cell lines carried interstitial 9p subtelomeres and rDNA rearrangements. Taken together, these data suggest tumorigenic rearrangements may be facilitated by 'hitchhiking' along with mobile DNA repeat sequences which may target gene rearrangement at 9p in HD. Southern analysis of parallel rearrangements within rDNA intergenic spacers in HDLM cells highlighted several at, or near, retroposons. As well as validating HD cell lines as cytogenetic models, and resources for identifying genes rearranged in HD, our findings warrant further investigation of the roles of DNA repeat sequences, notably subtelomeric microsatellites, rDNA spacer sequences and retroposons as facilitators and markers of tumor-gene rearrangement.

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Section: Possible Roles For Rdna Changessupporting

confidence: 56%

Karyotypic dissection of Hodgkin's disease cell lines reveals ectopic subtelomeres and ribosomal DNA at sites of multiple jumping translocations and genomic amplification

MacLeod

Spitzer

Bar‐Am³

et al. 2000

Leukemia

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“…Although these elements are normally expressed only at very low levels, if at all, most have consensus TFIIIC-binding sites and cloned copies can be transcribed by RNA polymerase III in vitro. It is not currently known to what extent TFIIIC and other pol III components are bound to the elements in vivo, but imaging of SINE (human Alu element) positions in HeLa cells shows a punctate pattern (Kaplan et al 1993) that is consistent with local clustering. If pol III components and condensin associate with some subset of the SINEs, it is interesting to speculate that they might serve as symbiotic, rather than selfish DNA elements, in that they provide condensation signals for the relatively large metazoan genomes.…”

Section: Discussionmentioning

confidence: 99%

Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes

et al. 2008

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The 274 tRNA genes in Saccharomyces cerevisiae are scattered throughout the linear maps of the 16 chromosomes, but the genes are clustered at the nucleolus when compacted in the nucleus. This clustering is dependent on intact nucleolar organization and contributes to tRNA gene-mediated (tgm) silencing of RNA polymerase II transcription near tRNA genes. After examination of the localization mechanism, we find that the chromosome-condensing complex, condensin, is involved in the clustering of tRNA genes. Conditionally defective mutations in all five subunits of condensin, which we confirm is bound to active tRNA genes in the yeast genome, lead to loss of both pol II transcriptional silencing near tRNA genes and nucleolar clustering of the genes. Furthermore, we show that condensin physically associates with a subcomplex of RNA polymerase III transcription factors on the tRNA genes. Clustering of tRNA genes by condensin appears to be a separate mechanism from their nucleolar localization, as microtubule disruption releases tRNA gene clusters from the nucleolus, but does not disperse the clusters. These observations suggest a widespread role for condensin in gene organization and packaging of the interphase yeast nucleus.[Keywords: tRNA gene; condensin; microtubules; nuclear organization; nucleolus] Supplemental material is available at http://www.genesdev.org.

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“…According to Kaplan et al (1993), the association of these sequences might have a functional role in nuclear organization, whereas other researchers (Dover, 1986;Liu and Fredga, 1999) agree that this association is important for the maintenance of conserved and multiple arrays. On the other hand, specific association of 5S rRNA and histone H3 genes cannot be explained by an advantage in the cotranscription process, as these sequences are transcribed by different RNA polymerases, RNA polymerases III and II, respectively.…”

Section: Mapping Of Repetitive Dnas In D Geminatus Dc Cabral-de-mellmentioning

confidence: 99%

Chromosomal mapping of repetitive DNAs in the beetle Dichotomius geminatus provides the first evidence for an association of 5S rRNA and histone H3 genes in insects, and repetitive DNA similarity between the B chromosome and A complement

2009

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Chromosomal banding techniques and repetitive DNA mapping are useful tools in comparative analysis and in the elucidation of genome organization of several groups of eukaryotes. In this study, we contributed to the knowledge of Coleoptera genomes by reporting the chromosomal organization of repetitive DNA sequences, as well as the presence and characteristics of a B chromosome in two natural populations of Dichotomius geminatus (Coleoptera; Scarabaeidae) using classical, chromosomal banding and molecular cytogenetic techniques. As in other coleopteran species, the heterochromatin was mainly concentrated in pericentromeric regions and the B chromosome was composed almost entirely of heterochromatin. Physical mapping using double fluorescent in situ hybridization was performed for the first time in Coleoptera; using DNA probes for 5S and 18S ribosomal RNA (rRNA) and histone H3 genes, we showed that ribosomal 18S rDNAs are located in chromosomes 3 and 4, whereas 5S rRNA and histone H3 genes are colocalized in chromosomal pair 2 and show an apparently interspersed organization. Moreover, these genes are not present in the B chromosome, suggesting that the B chromosome did not originate from chromosomal pairs 2, 3 or 4. On the other hand, mapping of the C 0 t-1 DNA fraction showed that the B chromosome is enriched in repetitive DNA elements, also present in the standard complement, indicating an intraspecific origin of this element in D. geminatus. These results will contribute to our understanding of genome organization and evolution of repetitive elements in Coleoptera and other insects regarding both A and B chromosomes.

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The Topographic Organization of Repetitive DNA in the Human Nucleolus

Cited by 49 publications

References 0 publications

Karyotypic dissection of Hodgkin's disease cell lines reveals ectopic subtelomeres and ribosomal DNA at sites of multiple jumping translocations and genomic amplification

Karyotypic dissection of Hodgkin's disease cell lines reveals ectopic subtelomeres and ribosomal DNA at sites of multiple jumping translocations and genomic amplification

Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes

Chromosomal mapping of repetitive DNAs in the beetle Dichotomius geminatus provides the first evidence for an association of 5S rRNA and histone H3 genes in insects, and repetitive DNA similarity between the B chromosome and A complement

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