Is Ribosome Synthesis Controlled by Pol I Transcription?

Chédin, Stéphane; Laferté, Arnaud; Hoang, Tran; Lafontaine, Denis L. J.; Riva, Michel; Carles, Christophe

doi:10.4161/cc.6.1.3649

Cited by 55 publications

(52 citation statements)

References 54 publications

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“…These observations also suggest a link to the production of ribosomal proteins, since the Pus7-catalyzed ⌿35 in U2 snRNA is important for the high-efficiency splicing of S. cerevisiae introns (79,80,111), which are preferentially located in ribosomal protein genes (32). Indeed, the interdependencies are consistent with the concept that the production of RNAP II and RNAP III transcripts is regulated in response to prerRNA synthesis via an extensive network of interactions (18,56,74,95,96).…”

supporting

confidence: 70%

“…Furthermore, the interaction of 5S rRNA and ribosomal protein L5 is critical for 5S rRNA stability and incorporation into the pre-60S ribosomal particle (22,23,73,77), and it has been proposed that the unstable nature of unbound 5S rRNA probably is connected to a lack of modification and that this is part of a network keeping pre-rRNA processing linked to RNA polymerase III activity (13). Interestingly, altered 5S rRNA stability also is observed when RNAP I activity is uncoupled genetically from attenuating its activity in response to stress (18,56). Our elucidation of Pus7 as the factor involved in the pseudouridylation of yeast 5S rRNA will facilitate the further examination of the possible link between 5S rRNA stability and modification.…”

mentioning

confidence: 99%

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Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs

Decatur

Schnare

2008

Molecular and Cellular Biology

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The selection of sites for pseudouridylation in eukaryotic cytoplasmic rRNA occurs by the base pairing of the rRNA with specific guide sequences within the RNA components of box H/ACA small nucleolar ribonucleoproteins (snoRNPs). Forty-four of the 46 pseudouridines (⌿s) in the cytoplasmic rRNA of Saccharomyces cerevisiae have been assigned to guide snoRNAs. Here, we examine the mechanism of ⌿ formation in 5S and 5.8S rRNA in which the unassigned ⌿s occur. We show that while the formation of the ⌿ in 5.8S rRNA is associated with snoRNP activity, the pseudouridylation of 5S rRNA is not. The position of the ⌿ in 5.8S rRNA is guided by snoRNA snR43 by using conserved sequence elements that also function to guide pseudouridylation elsewhere in the large-subunit rRNA; an internal stem-loop that is not part of typical yeast snoRNAs also is conserved in snR43. The multisubstrate synthase Pus7 catalyzes the formation of the ⌿ in 5S rRNA at a site that conforms to the 7-nucleotide consensus sequence present in other substrates of Pus7. The different mechanisms involved in 5S and 5.8S rRNA pseudouridylation, as well as the multiple specificities of the individual trans factors concerned, suggest possible roles in linking ribosome production to other processes, such as splicing and tRNA synthesis.RNA harbors a large array of structurally diverse, modified nucleosides (33, 93). Pseudouridine (5-ribosyluracil; ⌿) was the first discovered and is the most abundant (for a review, see reference 16). The isomerization of U to ⌿ involves the recognition of the specific U followed by the cleavage of the N-glycosidic bond, the rotation of the base, and the formation of a C-glycosidic bond (82). At the level of local RNA structure, ⌿ contributes to greater stability relative to that of U by providing an additional hydrogen-bonding capability that allows a water-mediated bridge to form between the base and the sugar-phosphate backbone as well as improved base stacking (for a review, see reference 16).In eukaryotes, ⌿ is found at specific sites in the rRNAs, tRNAs, and snRNAs. The cytoplasmic rRNA precursor (prerRNA) of eukaryotes is abundantly modified. As a result, in addition to about 54 ribose-methylated and 10 base-methylated nucleosides (61,89,108), 46 ⌿s are reported for the mature cytoplasmic rRNA of Saccharomyces cerevisiae (6,7,65,83,85). The pseudouridylation sites in eukaryotic, cytoplasmic rRNA are selected by the base pairing of the cytoplasmic rRNA with specific guide sequences present in the box H/ACA family of small nucleolar RNAs (snoRNAs) (for reviews, see references 10, 21, 54, and 114). These guide RNAs are associated with protein and function as ribonucleoprotein (RNP) particles, termed small nucleolar RNPs (snoRNPs).

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supporting

confidence: 70%

mentioning

confidence: 99%

Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs

Decatur

Schnare

2008

Molecular and Cellular Biology

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“…5A). COMPARE analysis of these data 3 indicates a unique mode of action for CX-3543, as the range of action profile, does not correlate with any compound in the current NCI database. Moreover, cancer cell lines overexpressing MDR1, MXR, or MRP1 drug resistance transporter genes retained sensitivity to CX-3543, indicating CX-3543 is not a substrate for these multidrug resistance pumps (Fig.…”

Section: Resultsmentioning

confidence: 99%

Anticancer Activity of CX-3543: A Direct Inhibitor of rRNA Biogenesis

Drygin¹,

Siddiqui‐Jain²,

O’Brien³

et al. 2009

Cancer Research

492

451

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“…Whereas the supply of ribosomal components needs the activities of three forms of nuclear RNA polymerase (pol I, pol II, and pol III) in eukaryotic cells, the control of pol I activity plays a central role in the regulation of ribosome biogenesis (Boulon et al, 2010;Chedin et al, 2007;Grewal et al, 2007). Pol I transcribes the eukaryotic ribosomal RNA genes (rDNA) to produce one precursor transcript, preribosomal RNA (pre-rRNA), in nucleoli.…”

Section: Introductionmentioning

confidence: 99%

CxxC-ZF Domain Is Needed for KDM2A to Demethylate Histone in rDNA Promoter in Response to Starvation

Tanaka

Umata

Okamoto

et al. 2014

Cell Struct. Funct.

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ABSTRACT. The transcription of ribosomal RNA genes (rDNA) is a rate-limiting step in ribosome biogenesis and changes profoundly in response to environmental conditions. Recently we reported that JmjC demethylase KDM2A reduces rDNA transcription on starvation, with accompanying demethylation of dimethylated Lys 36 of histone H3 (H3K36me2) in rDNA promoter. Here, we characterized the functions of two domains of KDM2A, JmjC and CxxC-ZF domains. After knockdown of endogenous KDM2A, KDM2A was exogenously expressed. The exogenous wild-type KDM2A demethylated H3K36me2 in the rDNA promoter on starvation and reduced rDNA transcription as endogenous KDM2A. The exogenous KDM2A with a mutation in the JmjC domain lost the demethylase activity and did not reduce rDNA transcription on starvation, showing that the demethylase activity of KDM2A itself is required for the control of rDNA transcription. The exogenous KDM2A with a mutation in the CxxC-ZF domain retained the demethylase activity but did not reduce rDNA transcription on starvation. It was found that the CxxC-ZF domain of KDM2A bound to the rDNA promoter with unmethylated CpG dinucleotides in vitro and in vivo. The exogenous KDM2A with the mutation in the CxxC-ZF domain failed to reduce H3K36me2 in the rDNA promoter on starvation. Further, it was suggested that KDM2A that bound to the rDNA promoter was activated on starvation. Our results demonstrate that KDM2A binds to the rDNA promoter with unmethylated CpG sequences via the CxxC-ZF domain, demethylates H3K36me2 in the rDNA promoter in response to starvation in a JmjC domain-dependent manner, and reduces rDNA transcription.

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Is Ribosome Synthesis Controlled by Pol I Transcription?

Cited by 55 publications

References 54 publications

Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs

Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs

Anticancer Activity of CX-3543: A Direct Inhibitor of rRNA Biogenesis

CxxC-ZF Domain Is Needed for KDM2A to Demethylate Histone in rDNA Promoter in Response to Starvation

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