Human ribosomal RNA intergenic spacer sequence

Gonzalez, Iris L.; Wu, Shuang; Li, Wen-Mei; Kuo, Bruce A.; Sylvester, James E.

doi:10.1093/nar/20.21.5846

Cited by 18 publications

(13 citation statements)

References 5 publications

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“…The situation observed here contrasts with that seen in Drosophila where R elements are continually inserting into the rDNA [Zhang et al, 2008]. In the case of primates, multiple non-LTR Alu elements have become incorporated in the non-transcribed part of the IGS and have become fixed across all units [Brownell et al, 1983;Gonzalez et al, 1992Gonzalez et al, , 1993. The presence of fragmented and even several full-length Alu elements [Dickson et al, 1989;Gonzalez et al, 1993] demonstrates that homogenisation is able to act efficiently upon such inserted elements [Gonzalez et al, 1989[Gonzalez et al, , 1993.…”

Section: Evolution Of Class II Igs Sequencesmentioning

confidence: 87%

“…The only case reported for plants is a Gypsy LTR retrotransposon named monkey , of which most copies reside at unknown locations within the rDNA loci of some species of Musa [Balint-Kurti et al, 2000]. During the evolution of primates, multiple non-LTR Alu retrotransposons have inserted into the non-transcribed part of the IGS and become fixed across all rDNA units [Brownell et al, 1983;Gonzalez et al, 1992Gonzalez et al, , 1993. A DNA transposable element, Pokey , which targets the large rDNA subunit gene has been found in several Daphnia species [Sullender and Crease, 2001;Penton et al, 2002;Penton and Crease, 2004].…”

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confidence: 99%

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Single Integration and Spread of a Copia-Like Sequence Nested in rDNA Intergenic Spacers of Allium cernuum (Alliaceae)

Chester

Sýkorová²,

Fajkus³

et al. 2010

Cytogenet Genome Res

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The 35S ribosomal DNA (rDNA) intergenic spacer (IGS) of Allium cernuum is examined. Initial sequencing of IGS clones revealed that some rDNA units contain a truncated retrotransposon sequence most similar to members of the Copia superfamily. Fluorescence in situ hybridisation (FISH) to metaphase chromosomes indicates that this element is dispersed along both pairs of major rDNA arrays. Southern hybridisation confirmed the presence of this ‘relic’ Copia-like element in more than 10% of 35S rDNA units, in the same position within the IGS. To measure the intragenomic divergence of the relic retroelement and its flanking sequences amongst different rDNA units, a 1.1-kb region was amplified and cloned. These data collectively point to a single origin for units containing the putative retrotransposon fragment. It is likely that units containing the putative retroelement increased in copy number and dispersed via rDNA homogenisation mechanisms, rather than by multiple retrotransposition events.

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Section: Evolution Of Class II Igs Sequencesmentioning

confidence: 87%

mentioning

confidence: 99%

Single Integration and Spread of a Copia-Like Sequence Nested in rDNA Intergenic Spacers of Allium cernuum (Alliaceae)

Chester

Sýkorová²,

Fajkus³

et al. 2010

Cytogenet Genome Res

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“…Nuclear ribosomal ITS of some plants did not work well as plant DNA barcodes because of the problems of paralogy and other factors associated with the complex concerted evolution (22). A third limitation is that ITS primer pairs can simultaneously amplify the ITS of plants as well as of endophytic or contaminating fungi (4,23) and contaminating human secretions (24). This makes it difficult to obtain nucleotide sequences via the direct sequencing.…”

Section: Discussionmentioning

confidence: 99%

An Assessment of the Utility of Universal and Specific Genetic Markers for Opium Poppy Identification

Lee

Hwang

Kim

et al. 2010

Journal of Forensic Sciences

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The proper identification of illicit plants such as Papaver somniferum L (opium poppy) is important for law enforcement agencies. The identification of opium poppy was presently tested using 10 genetic markers that are universal for all plants or specific to a few poppy plants. The genetic distances of universal markers such as nuclear internal transcribed spacer (ITS), 18S rRNA, plastid rbcL, and trnL-trnF intergenic spacer (IGS) of 14 species included in the Papaveraceae and Fumariaceae family were acquired by sequence comparisons. Both the ITS region and trnL-trnF IGS showed high levels of interspecific divergence. Six Papaver genera-specific markers were developed from coding regions involved in morphine biosynthesis. Three markers (TYDC, NCS, and BBE) produced amplicons only in opium poppy, providing a presence/absence test for opium poppy, while three additional markers (CYP80B1, SAT, and COR) were genus specific. These 10 markers might be useful for the forensic DNA analysis of opium poppy.

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“…There are two reasons for thinking that this is unlikely to have accrued. First, the only highly repeated sequences known to be present in human rDNA are Alu repeats (17,23,37), and these appear to be concentrated in the region between probes 7 and 1, the region that yielded the highest strand abundance (Fig. 4 and 5).…”

Section: Experimental Rationale the Diagram Inmentioning

confidence: 99%

Mapping of Replication Initiation Sites in Human Ribosomal DNA by Nascent-Strand Abundance Analysis

Yoon

Sanchez

Brun

et al. 1995

Molecular and Cellular Biology

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New techniques for mapping mammalian DNA replication origins are needed. We have modified the existing nascent-strand size analysis technique (L. Vassilev and E. M. Johnson, Nucleic Acids Res. 17:7693-7705, 1989) to provide an independent means of studying replication initiation sites. We call the new method nascentstrand abundance analysis. We confirmed the validity of this method with replicating simian virus 40 DNA as a model. We then applied nascent-strand abundance and nascent-strand size analyses to mapping of initiation sites in human (HeLa) ribosomal DNA (rDNA), a region previously examined exclusively by two-dimensional gel electrophoresis methods (R. D. Little, T. H. K. Platt, and C. L. Schildkraut, Mol. Cell. Biol. 13:6600-6613, 1993). Our results partly confirm those obtained by two-dimensional gel electrophoresis techniques. Both studies suggest that replication initiates at relatively high frequency a few kilobase pairs upstream of the transcribed region and that many additional low-frequency initiation sites are distributed through most of the remainder of the ribosomal DNA repeat unit.Although DNA replication origins in the budding yeast Saccharomyces cerevisiae have been moderately well characterized (reviewed in references 14 and 20), those in mammalian cells are not yet well understood (reviewed in reference 10). Understanding mammalian replication origins will require identification of both the ''replicators'' (cis-acting sequences required for origin function [31]) and the ''initiation sites'' (sequences which serve as templates for the 5Ј ends of the first nascent strands) associated with each origin.Although it would be desirable to map initiation sites with single-nucleotide resolution, all of the current techniques-in vitro runoff (3, 32), determination of replication timing (15,22,35), two-dimensional (2D) gel electrophoresis of replicating restriction fragments (37, 47), measurement of leading-strand polarity (12, 24), measurement of lagging-strand polarity (11), and measurement of nascent-strand size (45)-offer precisions of several hundred nucleotides at best. Furthermore, the current techniques sometimes produce apparently contradictory observations. For example, the results obtained by most techniques are consistent with the presence of two discrete initiation sites downstream of the dihydrofolate reductase (DHFR) gene in Chinese hamster ovary (CHO) cells (11,24,35,46). In contrast, the results obtained by 2D gel electrophoresis methods argue in favor of a single broad (55-kbp) ''initiation zone'' downstream of the DHFR gene, within which replication initiates at so many locations that they cannot be resolved by the 2D gel electrophoresis techniques (18, 47). It should be noted that the 2D gel electrophoresis methods are capable of localizing the discrete initiation sites of S. cerevisiae with a precision of several hundred base pairs (7, 28).It is possible that these apparently contradictory observations represent different aspects of a potentially complex process of initiation at...

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Human ribosomal RNA intergenic spacer sequence

Cited by 18 publications

References 5 publications

Single Integration and Spread of a <i>Copia</i>-Like Sequence Nested in rDNA Intergenic Spacers of <i>Allium cernuum </i>(Alliaceae)

Single Integration and Spread of a <i>Copia</i>-Like Sequence Nested in rDNA Intergenic Spacers of <i>Allium cernuum </i>(Alliaceae)

An Assessment of the Utility of Universal and Specific Genetic Markers for Opium Poppy Identification

Mapping of Replication Initiation Sites in Human Ribosomal DNA by Nascent-Strand Abundance Analysis

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