A cotranscriptional model for 3′-end processing of the <i>Saccharomyces cerevisiae</i> pre-ribosomal RNA precursor

Henras, Anthony K.; Bertrand, Édouard; Chanfreau, Guillaume

doi:10.1261/rna.7750804

Cited by 23 publications

(25 citation statements)

References 45 publications

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“…Two YCp50-based (URA3 CEN4 ARS1) yeast genomic libraries (45,75) were used for complementing the temperature-sensitive mutants. The plasmid overexpressing an artificial box C/D snoRNA (pG14-U14/MS2X2, 2) was obtained from Edouard Bertrand (91 (29). The MS2 probe used to detect an ectopically expressed artificial C/D snoRNA that serves as a nucleolar body marker was described previously (91).…”

Section: Methodsmentioning

confidence: 99%

Identification of Genes That Function in the Biogenesis and Localization of Small Nucleolar RNAs in Saccharomyces cerevisiae

Qiu

Eifert

Wacheul

et al. 2008

Molecular and Cellular Biology

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Small nucleolar RNAs (snoRNAs) orchestrate the modification and cleavage of pre-rRNA and are essential for ribosome biogenesis. Recent data suggest that after nucleoplasmic synthesis, snoRNAs transiently localize to the Cajal body (in plant and animal cells) or the homologous nucleolar body (in budding yeast) for maturation and assembly into snoRNPs prior to accumulation in their primary functional site, the nucleolus. However, little is known about the trans-acting factors important for the intranuclear trafficking and nucleolar localization of snoRNAs. Here, we describe a large-scale genetic screen to identify proteins important for snoRNA transport in Saccharomyces cerevisiae. We performed fluorescence in situ hybridization analysis to visualize U3 snoRNA localization in a collection of temperature-sensitive yeast mutants. We have identified Nop4, Prp21, Tao3, Sec14, and Htl1 as proteins important for the proper localization of U3 snoRNA. Mutations in genes encoding these proteins lead to specific defects in the targeting or retention of the snoRNA to either the nucleolar body or the nucleolus. Additional characterization of the mutants revealed impairment in specific steps of U3 snoRNA processing, demonstrating that snoRNA maturation and trafficking are linked processes.After synthesis in the nucleus, all RNA species undergo a series of maturation steps and transport from the site of synthesis to the site of action, and it is increasingly clear that RNA biogenesis and trafficking are closely linked (54). Whether they are destined to function in the cytoplasm (e.g., rRNA, tRNA, mRNA) or the nucleus (e.g., snRNAs or snoRNAs), all RNAs undergo intranuclear trafficking. It is well established that interactions between trans-acting factors and specific features of RNA substrates can govern which transport pathways will be utilized (38,59,73). However, little is known about the intranuclear trafficking factors and how they affect the molecular movement of RNAs within the nucleus.Small nucleolar RNAs (snoRNAs) provide excellent models to study intranuclear RNA transport. snoRNAs remain within the nucleus, where they undergo biogenesis including covalent alterations (e.g., 5Ј cap hypermethylation and 3Ј-end processing), as well as assembly with specific proteins into stable and functional RNP complexes (snoRNPs) (40,54,70,84). Ultimately, snoRNAs are targeted to nucleoli, where they function in rRNA maturation.The numerous snoRNA species fall into two structurally and functionally distinct classes called the box C/D and box H/ACA snoRNAs (40,54,70,84). Species of both RNA classes interact with pre-rRNA (via base pairing), mainly to guide site-specific nucleotide modification. The majority of box C/D snoRNAs orchestrate 2Ј-O-methylation (12,41,65,89), while the bulk of the box H/ACA RNA species guide pseudouridylation (21, 64). A few RNAs of both classes (e.g., box C/D snoRNA U3 and box H/ACA snoRNA U17 [vertebrates]/snR30 [yeast]) are critical for promoting specific endonucleolytic cleavages of pre-rRNA transcripts ...

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Section: Methodsmentioning

confidence: 99%

Identification of Genes That Function in the Biogenesis and Localization of Small Nucleolar RNAs in Saccharomyces cerevisiae

Qiu

Eifert

Wacheul

et al. 2008

Molecular and Cellular Biology

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“…The 39-end of the primary rRNA transcript is cleaved by the dsRNA-specific RNase III, Rnt1 (Elela et al 1996;Kufel et al 1999;Henras et al 2004). Inactivation of Rnt1 causes read-through at T1, indicating that, as with protein-coding genes, cotranscriptional cleavage is important for efficient termination Prescott et al 2004;Kawauchi et al 2008).…”

Section: Coupling Of Rrna Processing and Terminationmentioning

confidence: 99%

Transcription termination by nuclear RNA polymerases

Richard

Manley²

2009

Genes Dev.

291

326

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Gene transcription in the cell nucleus is a complex and highly regulated process. Transcription in eukaryotes requires three distinct RNA polymerases, each of which employs its own mechanisms for initiation, elongation, and termination. Termination mechanisms vary considerably, ranging from relatively simple to exceptionally complex. In this review, we describe the present state of knowledge on how each of the three RNA polymerases terminates and how mechanisms are conserved, or vary, from yeast to human.

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“…In contrast to Rat1, no ChIP signal above the background was detected for Rnt1-TAP (data not shown). The available data indicate that Rnt1 does bind to the pre-rRNA cotranscriptionally and is present at the site of transcription (Henras et al 2004), but its transient association with the nascent transcript apparently is not captured by cross-linking in ChIP analyses.…”

Section: Rat1 Associates With the 3ј-ets Region Of The Rdnamentioning

confidence: 99%

“…2A; Kufel et al 1999). Rnt1 was detected at the site of rRNA transcription (Henras et al 2004), and can interact physically with Pol I subunits including Rpa12 (Catala et al 2008). Moreover, loss of Pol I promoter.…”

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confidence: 99%

Efficient termination of transcription by RNA polymerase I requires the 5′ exonuclease Rat1 in yeast

Hage¹,

Koper²,

Kufel³

et al. 2008

Genes Dev.

110

128

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During transcription termination by RNA polymerase II on protein-coding genes, the nuclear 5 exonuclease Rat1/Xrn2 degrades the nascent transcript downstream from the polyadenylation site and "torpedoes" the polymerase. We report that the activity of Rat1 is also required for efficient termination by RNA polymerase I (Pol I) on the rDNA. In strains lacking catalytically active Rat1 or its cofactor Rai1, Pol I reads through the major, "Reb1-dependent" terminator (T1) but stops downstream at the "fail-safe" terminator (T2) and replication fork barrier (RFB). The absence of both Rat1 and the RFB-binding protein Fob1 increased Pol I read-through of T2 and the RFB. We propose that cotranscriptional cleavage of the pre-rRNA by the endonuclease Rnt1 generates a loading site for the Rat1/Rai1 complex, which then degrades the nascent transcript. When Rat1 catches Pol I, which is predicted to be paused at T1, transcription is terminated.[Keywords: Ribosome synthesis; rRNA synthesis; RNA polymerase I; exonuclease; transcription termination] Supplemental material is available at http://www.genesdev.org.

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A cotranscriptional model for 3′-end processing of the Saccharomyces cerevisiae pre-ribosomal RNA precursor

Cited by 23 publications

References 45 publications

Identification of Genes That Function in the Biogenesis and Localization of Small Nucleolar RNAs in Saccharomyces cerevisiae

Identification of Genes That Function in the Biogenesis and Localization of Small Nucleolar RNAs in Saccharomyces cerevisiae

Transcription termination by nuclear RNA polymerases

Efficient termination of transcription by RNA polymerase I requires the 5′ exonuclease Rat1 in yeast

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