Human ribosomal RNA gene cluster: identification of the proximal end containing a novel tandem repeat sequence

Sakai, Kosuke; Ohta, Takayuki; Minoshima, Shinsei; Kudoh, Jun; Wang, Yimin; Jong, Pieter J. de; Shimizu, Nobuyoshi

doi:10.1016/0888-7543(95)80170-q

Cited by 66 publications

(43 citation statements)

References 22 publications

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“…Human NORs contain on average 3 Mb of rDNA (Sakai et al 1995). Although none of the XEn arrays described here are this large, we investigated the possibility that Chromatin immunoprecipitation demonstrates that UBF is bound to XEn arrays.…”

Section: Ubf Binding To Xen Arrays Induces Formation Of Novel Silver mentioning

confidence: 98%

UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machinery

Mais¹,

Wright²,

Prieto³

et al. 2004

Genes Dev.

163

191

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Human ribosomal genes (rDNA) are located in nucleolar organizer regions (NORs) on the short arms of acrocentric chromosomes. Metaphase NORs that were transcriptionally active in the previous cell cycle appear as prominent chromosomal features termed secondary constrictions that are achromatic in chromosome banding and positive in silver staining. The architectural RNA polymerase I (pol I) transcription factor UBF binds extensively across rDNA throughout the cell cycle. To determine if UBF binding underpins NOR structure, we integrated large arrays of heterologous UBF-binding sequences at ectopic sites on human chromosomes. These arrays efficiently recruit UBF even to sites outside the nucleolus and, during metaphase, form novel silver stainable secondary constrictions, termed pseudo-NORs, morphologically similar to NORs. We demonstrate for the first time that in addition to UBF the other components of the pol I machinery are found associated with sequences across the entire human rDNA repeat. Remarkably, a significant fraction of these same pol I factors are sequestered by pseudo-NORs independent of both transcription and nucleoli. Because of the heterologous nature of the sequence employed, we infer that sequestration is mediated primarily by protein-protein interactions with UBF. These results suggest that extensive binding of UBF is responsible for formation and maintenance of the secondary constriction at active NORs. Furthermore, we propose that UBF mediates recruitment of the pol I machinery to nucleoli independently of promoter elements.[Keywords: RNA polymerase I; ribosomal DNA; nucleolar organiser region; nucleolus; upstream-binding factor] Supplemental material is available at http://www.genesdev.org.

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Section: Ubf Binding To Xen Arrays Induces Formation Of Novel Silver mentioning

confidence: 98%

UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machinery

Mais¹,

Wright²,

Prieto³

et al. 2004

Genes Dev.

163

191

View full text Add to dashboard Cite

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“…As Pol I transcription is required for rDNA amplification, the transcription seems to bias the recombination towards increasing the copy number by selection of the replicated region (around rARS-1 in Fig. 2-c), as a recombination target, although E. coli 7 (Ellwood and Nomura, 1982) Saccharomyces cerevisiae 150 (Kobayashi et al, 1998) Drosophila melanogaster 240 (Tartof, 1979) Xenopus laevis 600 (Wallance and Birnstiel, 1966) Homo sapiens 350 (Sakai et al, 1995) Arabidopsis thaliana 570 (Pruitt and Meyerowitz, 1986) Pisum sativum (pea) 3,900 (Ingle et al, 1975) For review see Long and Dawid (1980) the mechanism is not elucidated yet. Analysis of cis-acting factors .…”

Section: Rdna Is a "Department Store" Of Genomic Elementsmentioning

confidence: 99%

Strategies to maintain the stability of the ribosomal RNA gene repeats -Collaboration of recombination, cohesion, and condensation-

Kobayashi

2006

Genes Genet. Syst.

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Ribosomal RNA gene repeats (rDNA) are one of the most characteristic regions in eukaryotic chromosomes. The repeats consist of more than 100 tandem units occupying large part of the chromosome in most of organisms. Cells are known to deal with this "unusual domain" in a unique manner. In this review, I will summarize work on rDNA repeat maintenance, focusing mainly on work done by our group, and show that the maintenance mechanism operates by a collaboration of recombination, sister-chromatid cohesion, and chromatin condensation.

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“…To obtain the sequences flanking the rDNA arrays, we made use of preexisting sequences adjacent to the rDNA on the proximal (centromeric; 493 bp) (Sakai et al 1995) and distal (telomeric; 8.3 kb) sides of the rDNA (Gonzalez and Sylvester 1997). Probes derived from these sequences were used to screen single-chromosome cosmid libraries, and several positive clones were sequenced.…”

Section: Identification Of Rdna Flanking Regionsmentioning

confidence: 99%

The shared genomic architecture of human nucleolar organizer regions

et al. 2013

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The short arms of the five acrocentric human chromosomes harbor sequences that direct the assembly and function of the nucleolus, one of the key functional domains of the nucleus, yet they are absent from the current human genome assembly. Here we describe the genomic architecture of these human nucleolar organizers. Sequences distal and proximal to ribosomal gene arrays are conserved among the acrocentric chromosomes, suggesting they are sites of frequent recombination. Although previously believed to be heterochromatic, characterization of these two flanking regions reveals that they share a complex genomic architecture similar to other euchromatic regions of the genome, but they have distinct genomic characteristics. Proximal sequences are almost entirely segmentally duplicated, similar to the regions bordering centromeres. In contrast, the distal sequence is predominantly unique to the acrocentric short arms and is dominated by a very large inverted repeat. We show that the distal element is localized to the periphery of the nucleolus, where it appears to anchor the ribosomal gene repeats. This, combined with its complex chromatin structure and transcriptional activity, suggests that this region is involved in nucleolar organization. Our results provide a platform for investigating the role of NORs in nucleolar formation and function, and open the door for determining the role of these regions in the well-known empirical association of nucleoli with pathology.

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Human ribosomal RNA gene cluster: identification of the proximal end containing a novel tandem repeat sequence

Cited by 66 publications

References 22 publications

UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machinery

UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machinery

Strategies to maintain the stability of the ribosomal RNA gene repeats -Collaboration of recombination, cohesion, and condensation-

The shared genomic architecture of human nucleolar organizer regions

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