The human ribosomal RNA genes: structure and organization of the complete repeating unit

Sylvester, James E.; Whiteman, David A.H.; Podolsky, Robert S.; Pozsgay, Judith M.; Respess, James G.; Schmickel, Roy D.

doi:10.1007/bf00401226

Cited by 91 publications

(38 citation statements)

References 25 publications

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“…D21S190 (pVC1.21c), D21S5 (pPW235D), D21S187 (pVC10a), D21S1276 (pLSB77), D21S188 (pVC1.12c), and D21S191 (pVC1.23c) are subclones from phages derived from chromosome 21-specific phage libraries (Watkins et al 1985;Van Camp et al 1990;Stuyver et al 1991). Additionally, pA 2 and pC HB are clones of the 28S coding and spacer region of the rDNA gene cluster, respectively (Sylvester et al 1986). Finally, Xba21 contains an XbaI fragment of the chromosome 21 somatic cell hybrid 153E9A that was selected with an alphoid DNA probe (Thompson et al 1989).…”

Section: Methods Chromosome 21 Plasmid Clonesmentioning

confidence: 99%

A High-Resolution Physical Map of Human Chromosome 21p Using Yeast Artificial Chromosomes

et al. 1999

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The short arm of human chromosome 21 (21p) contains many different types of repetitive sequences and is highly homologous to the short arms of other acrocentric chromosomes. Owing to its repetitive nature and the lack of chromosome 21p-specific molecular markers, most physical maps of chromosome 21 exclude this region. We constructed a physical map of chromosome 21p using sequence tagged site (STS) content mapping of yeast artificial chromosomes (YACs). To this end, 39 STSs located on the short arm or near the centromere of chromosome 21 were constructed, including four polymorphic simple tandem repeats (STRs) and two expressed sequence tags (ESTs). Thirty YACs were selected from the St. Louis YAC library, the chromosome 21-enriched ICRF YAC library, and the CEPH YAC and megaYAC libraries. These were assembled in a YAC contig map ranging from the centromere to the rDNA gene cluster at 21p12. The total size of the region covered by YACs is estimated between 2.9 and 5 Mb. The integrity of the YAC contig was confirmed by restriction enzyme fingerprinting and fluorescence in situ hybridization (FISH). One gap with an estimated size of 400 kb remained near the telomeric end of the contig. This YAC contig map of the short arm of human chromosome 21 constitutes a basic framework for further structural and functional studies of chromosome 21p.

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Section: Methods Chromosome 21 Plasmid Clonesmentioning

confidence: 99%

A High-Resolution Physical Map of Human Chromosome 21p Using Yeast Artificial Chromosomes

et al. 1999

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“…The probe corresponding to human rRNA 5Ј external transcribed spacer (ETS) core sequences (ϩ693 to ϩ2921) was provided by Dr. J. Sylvester (Sylvester et al, 1986), or a shorter sequence (ϩ933 to ϩ1445) was provided by Dr. M. Olson (Dundr et al, 1998). The probe corresponding to human 28S rRNA (ϩ12,383 to ϩ12,969) was subcloned from p3ЈETS that spans the 3Ј end of 28S and the 5Ј end of the 3ЈETS sequence provided by Dr. M. Olson.…”

Section: In Situ Hybridizationmentioning

confidence: 99%

“…For double labeling with immunodetection of UBF, nucleolin, or fibrillarin, cells were incubated with primary and secondary antibodies and subsequently fixed again with 2% formaldehyde for 5 min. Cells were then rinsed in PBS two times for 15 min each and once with 2ϫ SSC followed by hybridization.The probe corresponding to human rRNA 5Ј external transcribed spacer (ETS) core sequences (ϩ693 to ϩ2921) was provided by Dr. J. Sylvester (Sylvester et al, 1986), or a shorter sequence (ϩ933 to ϩ1445) was provided by Dr. M. Olson (Dundr et al, 1998). The probe corresponding to human 28S rRNA (ϩ12,383 to ϩ12,969) was subcloned from p3ЈETS that spans the 3Ј end of 28S and the 5Ј end of the 3ЈETS sequence provided by Dr. M. Olson.…”

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confidence: 99%

Initiation of Nucleolar Assembly Is Independent of RNA Polymerase I Transcription

Dousset

Wang

Verheggen

et al. 2000

MBoC

124

122

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This report examines the distribution of an RNA polymerase I transcription factor (upstream binding factor; UBF), pre-rRNA processing factors (nucleolin and fibrillarin), and pre-rRNAs throughout mitosis and postmitotic nucleologenesis in HeLa cells. The results demonstrate that nucleolin, fibrillarin, and pre-rRNAs synthesized at G2/M phase of the previous cell cycle are directly recruited to UBF-associated nucleolar organizer regions (NORs) early in telophase before chromosome decondensation. Unlike the fusion of prenucleolar bodies to the nucleoli, this early recruitment of processing factors and pre-rRNAs is independent of RNA polymerase I transcription. In the absence of polymerase I transcription, the initial localization of nucleolin, fibrillarin, and pre-rRNAs to UBF-associated NORs generates segregated mininucleoli that are similar to the larger ones observed in interphase cells grown under the same conditions. Pre-rRNAs are juxtaposed to UBF-nucleolin-fibrillarin caps that may represent the segregated nucleoli observed by electron microscopy. These findings lead to a revised model of nucleologenesis. We propose that nucleolar formation at the end of mitosis results from direct recruitment of processing factors and pre-rRNAs to UBF-associated NORs before or at the onset of rDNA transcription. This is followed by fusion of prepackaged prenucleolar bodies into the nucleolus. Pre-ribosomal ribonucleoproteins synthesized in the previous cell cycle may contribute to postmitotic nucleologenesis. INTRODUCTIONThe nucleus is a complex structure within which various functions and components are spatially and temporally organized and interregulated (reviewed by Lamond and Earnshaw, 1998;Dreyfuss and Struhl, 1999). Nucleoli represent the most prominent example of this organization. The major function of the nucleolus is ribosome biogenesis (reviewed by Busch and Smetana, 1970). rRNAs are synthesized, processed, cleaved, and assembled with ribosomal proteins in the nucleolus before export to the cytoplasm. The nucleolus is composed of three structurally distinguishable constituents: fibrillar centers, dense fibrillar components, and granular components, as observed by electron microscopy (reviewed by Busch and Smetana, 1970;Hadjiolov, 1985). Although the spatial and temporal relationship between rRNA synthesis and the three structural constituents remains to be clarified, it is generally thought that transcription of rDNA takes place in a transient area between the fibrillar centers and the dense fibrillar components and that rRNA processing and preribosomal particle assembly progress from the dense fibrillar components to the surrounding granular components (reviewed by Spector et al., 1993;Shaw and Jordan, 1995;Scheer and Hock, 1999). More recent evidence (reviewed by Pederson, 1998;Garcia and Pillus, 1999) suggests that nucleoli have additional functions related to the cell cycle Visintin et al., 1999), cellular aging (Straight et al., 1999), signal recognition particle biosynthesis (Jacobson and Pederson, 1998),...

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“…19q13.1, D22S75 at 22q11, BCR at 22q11, D22S39 at 22q13 (Oncor); ALK at 2p23, chr. D5S23 at 5q15.2, CSF1R at 5q32 (Vysis); pBE15H3 at 1p36 (E Fleckenstein, DSMZ); pNB101 for MYCN at 2p23 (R Corvi, German Cancer Research Center (DKF2), Heidelberg, Germany); Cos B5-2 for BCL6/LAZ3 at 3q27 (T Miki, Tokyo Medical and Dental University, Tokyo, Japan); P1.164 for ETO at 8q22 and CO664 for AML1 at 21q22 (A Hagemeijer, Center for Human Genetics, Leuven, Belgium); Cos-6.31/6.7 for BCL1 at 11q13 (S Brookes, Imperial Cancer Research Fund (ICRF), London, UK); Cos 148B6 and 179A6 for ETV6 at 12p13 (P Marynen, Center for Human Genetics, Leuven, Belgium); NNX3 at 19q12 (F Van Leuven, Center for Human Genetics, Leuven, Belgium); Cos 50B11 and 40D2 for MN1 at 22q12 (E Zwarthoff, Erasmus University, Rotterdam, The Netherlands); and probes spanning both coding (pA, pB) and spacer (pCb2b3, pDes, pDsh) regions of RRN (26,27) as used for genomic analysis ( Figure 1). Single locus probes were labeled with digoxigenin-11-dUTP or biotin-14-dATP (Roche) by nick translation (Life Technologies, Karlsruhe, Germany), and 100-200 ng labeled probe dissolved in Hybrisol VI (Oncor) for hybridization (24 or 48 h) at 37°C in competition with a 50-…”

Section: Cytogeneticsmentioning

confidence: 99%

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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The human ribosomal RNA genes: structure and organization of the complete repeating unit

Cited by 91 publications

References 25 publications

A High-Resolution Physical Map of Human Chromosome 21p Using Yeast Artificial Chromosomes

A High-Resolution Physical Map of Human Chromosome 21p Using Yeast Artificial Chromosomes

Initiation of Nucleolar Assembly Is Independent of RNA Polymerase I Transcription

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

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