Clones of human ribosomal DNA containing the complete 18 S-rRNA and 28 S-rRNA genes. Characterization, a detailed map of the human ribosomal transcription unit and diversity among clones

Maden, B.E.H.; Dent, Carolyn L.; Farrell, T.; Garde, Julie; McCallum, F S; Wakeman, Jane A.

doi:10.1042/bj2460519

Cited by 95 publications

(53 citation statements)

References 30 publications

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“…The plasmid pHrB was a gift from J. Sylvester (Wilson, 1982;Maden et al, 1987). The plasmid pHr-BES was a gift from L. Rothblum (Grummt et al, 1982;Miesfeld and Arnheim, 1982).…”

Section: Plasmidsmentioning

confidence: 99%

“…To test the possibility that longer pre-rRNA could recruit more pre-rRNA processing factors, we injected HeLa nuclei with plasmid pHrB that contains the same Pol I promoter, but also has an rDNA sequence that extends through the entire 3700-base pair 5Ј ETS and 1639 base pairs of the 18S rRNA (Wilson, 1982;Maden et al, 1987). As a result, pHrB includes the A 0 and A 1 processing sites ( Figures 4A and 7A).…”

Section: Recruitment Of Some Pre-rrna Processing Factors To Active Simentioning

confidence: 99%

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Pol I Transcription and Pre-rRNA Processing Are Coordinated in a Transcription-dependent Manner in Mammalian Cells

Kopp

Gasiorowski

Chen

et al. 2007

MBoC

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Pre-rRNA synthesis and processing are key steps in ribosome biogenesis. Although recent evidence in yeast suggests that these two processes are coupled, the nature of their association is unclear. In this report, we analyze the coordination between rDNA transcription and pre-rRNA processing in mammalian cells. We found that pol I transcription factor UBF interacts with pre-rRNA processing factors as analyzed by immunoprecipitations, and the association depends on active rRNA synthesis. In addition, injections of plasmids containing the human rDNA promoter and varying lengths of 18S rDNA into HeLa nuclei show that pol I transcription machinery can be recruited to rDNA promoters regardless of the product that is transcribed, whereas subgroups of pre-rRNA processing factors are recruited to plasmids only when specific pre-rRNA fragments are produced. Our observations suggest a model for sequential recruitment of pol I transcription factors and pre-rRNA processing factors to elongating pre-rRNA on an as-needed basis rather than corecruitment to sites of active transcription. INTRODUCTIONNucleoli contain hundreds of tandem rRNA genes and a large number of factors necessary for transcription of ribosomal DNA (rDNA), processing of pre-rRNA, and ribosome assembly. Electron microscopic imaging of nucleoli reveal three distinct subcompartments: the fibrillar centers (FC), dense fibrillar components (DFC), and granular components (GC;Huang, 2002). It is at the FC/DFC border that RNA polymerase I (pol I) and other pol I-specific transcription factors associate to form the pol I preinitiation complex (PIC) at rRNA promoters (Grummt, 2003;Grummt and Pikaard, 2003) for transcription of rDNA (Raska et al., 2004). In vivo activation of the human rRNA promoter requires proteinprotein interactions between the DNA-binding protein, upstream binding factor (UBF1), and SL1 for the targeting of pol I and stable PIC formation (Bell et al., 1988;Friedrich et al., 2005). In combination with several other evolutionarily conserved proteins, these and other pol I transcription factors confer pol I promoter specificity to produce a single polycistronic pre-rRNA transcript (45S pre-rRNA in humans; Grummt, 2003;Grummt and Pikaard, 2003).A large number of small nucleolar ribonucleoproteins (snoRNPs), composed of small nucleolar RNAs (snoRNAs) and their associated proteins, as well as more than 100 protein cofactors, are responsible for processing the 45S transcript (Fromont-Racine et al., 2003;Granneman and Baserga, 2005). The box C/D snoRNA U3 and its associated proteins are required for the initial cleavages of the 5Ј end of pre-rRNA at sites A 0 , A 1 , and A 2 and are thereby involved in the release of the 18S precursor (Fromont-Racine et al., 2003;Granneman and Baserga, 2005). Yeast U3 snoRNA exists in at least two types of complexes in vitro: a 12S monoparticle (Billy et al., 2000;Granneman et al., 2003) and a larger ϳ90S complex termed the small subunit (SSU) processome (Fabrizio et al., 1994;Dragon et al., 2002). The 12S monoparticle pre...

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“…The plasmid pHrB was a gift from J. Sylvester (Wilson, 1982;Maden et al, 1987). The plasmid pHr-BES was a gift from L. Rothblum (Grummt et al, 1982;Miesfeld and Arnheim, 1982).…”

Section: Plasmidsmentioning

confidence: 99%

Section: Recruitment Of Some Pre-rrna Processing Factors To Active Simentioning

confidence: 99%

Pol I Transcription and Pre-rRNA Processing Are Coordinated in a Transcription-dependent Manner in Mammalian Cells

Kopp

Gasiorowski

Chen

et al. 2007

MBoC

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“…rRNAs are transcribed from multigene families and heterogeneity arises from nucleotide substitutions and deletions among the individual rRNA genes. An analysis of human 28S rRNA genes revealed that 28S rRNA comprises a heterogeneous group of RNAs (7,69). These rRNAs were shown to be transcribed and to be present both in monosomes and in polysomes (70).…”

Section: Potential Effects Of Ribosome Heterogeneity On the Filtermentioning

confidence: 99%

“…In addition to the sequence variation that occurs in expansion segments, heterogeneity in the 28S rRNA genes has also been noted in regions that are conserved between species (70). Although 18S rRNA appears to be much less variable than 28S rRNA, some heterogeneity in 18S rRNA genes has also been described (69,74).…”

Section: Potential Effects Of Ribosome Heterogeneity On the Filtermentioning

confidence: 99%

The ribosome filter hypothesis

Mauro

Edelman²

2002

Proc. Natl. Acad. Sci. U.S.A.

230

199

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A variety of posttranscriptional mechanisms affects the processing, subcellular localization, and translation of messenger RNAs (mRNAs). Translational control appears to occur primarily at the initiation rather than the elongation stage. It has been suggested that translation is mediated largely by means of a cap-binding͞ scanning mechanism. On the basis of recent findings, we propose here that differential binding of particular mRNAs to eukaryotic 40S ribosomal subunits before translation may also selectively affect rates of polypeptide chain production. In this view, ribosomal subunits themselves are considered to be regulatory elements or filters that mediate interactions between particular mRNAs and components of the translation machinery. Differences in these interactions affect how efficiently individual mRNAs compete for ribosomal subunits. These competitive interactions would depend in part on the complementarity between sequences in mRNA and rRNA, as well as on structural differences among ribosomes in different cell types. By these means, translation may either be enhanced through increased recruitment of ribosomes or inhibited through strong interactions that sequester mRNAs. We propose that ribosomal filters may be important in cell differentiation and describe experimental tests for the filter hypothesis.

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“…The more prominent ones have been identified as expansion segments (7,46), divergent domains (27), or variable regions (17). The variability of some regions is such that closely related organisms such as mice and rats show many sequence differences (26), and sequence differences are even detected in different copies of the rRNA genes (rDNAs) from a single organism (25). These regions are absent in most eubacteria and archaebacteria and present in most eukaryotes (19,46), although exceptions to this rule have recently been found (4,10,43).…”

mentioning

confidence: 99%

An rRNA variable region has an evolutionarily conserved essential role despite sequence divergence.

1994

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Regions extremely variable in size and sequence occur at conserved locations in eukaryotic rRNAs. The functional importance of one such region was determined by gene reconstruction and replacement in Tetrahymena thermophila. Deletion of the D8 region of the large-subunit rRNA inactivates T. thermophila rRNA genes (rDNA): transformants containing only this type of rDNA are unable to grow. Replacement with an unrelated sequence of similar size or a variable region from a different position in the rRNA also inactivated the rDNA. Mutant rRNAs resulting from such constructs were present only in precursor forms, suggesting that these rRNAs are deficient in either processing or stabilization of the mature form. Replacement with D8 regions from three other organisms restored function, even though the sequences are very different. Thus, these D8 regions share an essential functional feature that is not reflected in their primary sequences. Similar tertiary structures may be the quality these sequences share that allows them to function interchangeably.Although much of the secondary structure of rRNA is evolutionarily conserved, these portions are interspersed with discrete variable regions at conserved positions within the structure (18). The more prominent ones have been identified as expansion segments (7,46), divergent domains (27), or variable regions (17). The variability of some regions is such that closely related organisms such as mice and rats show many sequence differences (26), and sequence differences are even detected in different copies of the rRNA genes (rDNAs) from a single organism (25). These regions are absent in most eubacteria and archaebacteria and present in most eukaryotes (19,46), although exceptions to this rule have recently been found (4, 10, 43). The functional role of variable regions has not been identified. While their absence from most eubacteria suggests that they are dispensable, their almost universal presence in eukaryotes implies that they may be important in these organisms.Two models for the evolution of rRNA both imply that variable regions initially had no functional role. Some rRNAs are fragmented (2,5,12,13,15,36,39,45,47) (44). Comparison of rRNA sequences from diverse phyla offers support for the secondary structure model of most of the LSU rRNA but is uninformative for variable regions because they are so divergent. Secondary structure models for variable regions have been proposed based on the assumption that, in addition to having a low free energy, a model must be structurally similar for all species (26). Comparing the sequences of closely related species has recently produced more-refined models (12,20).No functional role has been defined for any variable region. However, some pertinent evidence does exist. The D2 and D12 regions of the LSU rRNA in Tetrahymena thennophila tolerate insertion mutations with no apparent diminution of rRNA function in vivo, while insertions in the D8 region totally obliterate rRNA function (40a, 41). In Saccharomyces cerevisiae, rRNAs beari...

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Clones of human ribosomal DNA containing the complete 18 S-rRNA and 28 S-rRNA genes. Characterization, a detailed map of the human ribosomal transcription unit and diversity among clones

Cited by 95 publications

References 30 publications

Pol I Transcription and Pre-rRNA Processing Are Coordinated in a Transcription-dependent Manner in Mammalian Cells

Pol I Transcription and Pre-rRNA Processing Are Coordinated in a Transcription-dependent Manner in Mammalian Cells

The ribosome filter hypothesis

An rRNA variable region has an evolutionarily conserved essential role despite sequence divergence.

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