Functional importance of individual rRNA 2′-<i>O</i>-ribose methylations revealed by high-resolution phenotyping

Esguerra, Jonathan L.S.; Warringer, Jonas

doi:10.1261/rna.845808

Cited by 60 publications

(62 citation statements)

References 36 publications

(34 reference statements)

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“…Even the best test for functional significance, gene inactivation in knockout model systems, does not always provide immediate and simple answers. In yeast, very few knockouts of snoRNAs showed a clear phenotype as was the case for U14 (Li et al 1990), but not, for example, snR189 (Thompson et al 1988), or only over time or under certain conditions with respect to other snoRNAs (Badis et al 2003;King et al 2003;Esguerra et al 2008). Bacterial genomes like those of Escherichia coli do not have much space to waste and everything without a selective advantage would not remain in the genome for long.…”

Section: The (Nucleic) Acid Test For Functionmentioning

confidence: 97%

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

Brosius

2014

Cold Spring Harbor Perspectives in Biology

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Section: The (Nucleic) Acid Test For Functionmentioning

confidence: 97%

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

Brosius

2014

Cold Spring Harbor Perspectives in Biology

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“…Post-transcriptional modifications in spliceosomal small nuclear RNAs (snRNAs) and ribosomal RNAs (rRNAs) are essential for spliceosome assembly and splicing competency (Yu et al 1998;Donmez et al 2004;Yu 2004, 2007;Yang et al 2005;Karijolich and Yu 2010) as well as for the assembly of functional ribosomal subunits and the efficiency and fidelity of translation (Lapeyre 2005;Liang et al 2007Liang et al , 2009Esguerra et al 2008;Jack et al 2011). Two common alterations in these RNAs, namely, pseudouridylation and 2 ′ -O-methylation, are usually mediated by the so-called modification guide RNAs, the box H/ACA and box C/D RNAs, respectively.…”

Section: Introductionmentioning

confidence: 99%

Novel small Cajal-body-specific RNAs identified in Drosophila: probing guide RNA function

Deryusheva

Gall

2013

RNA

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The spliceosomal small nuclear RNAs (snRNAs) are modified post-transcriptionally by introduction of pseudouridines and 2 ′ -Omethyl modifications, which are mediated by box H/ACA and box C/D guide RNAs, respectively. Because of their concentration in the nuclear Cajal body (CB), these guide RNAs are known as small CB-specific (sca) RNAs. In the cell, scaRNAs are associated with the WD-repeat protein WDR79. We used coimmunoprecipitation with WDR79 to recover seven new scaRNAs from Drosophila cell lysates. We demonstrated concentration of these new scaRNAs in the CB by in situ hybridization, and we verified experimentally that they can modify their putative target RNAs. Surprisingly, one of the new scaRNAs targets U6 snRNA, whose modification is generally assumed to occur in the nucleolus, not in the CB. Two other scaRNAs have dual guide functions, one for an snRNA and one for 28S rRNA. Again, the modification of 28S rRNA is assumed to take place in the nucleolus. These findings suggest that canonical scaRNAs may have functions in addition to their established role in modifying U1, U2, U4, and U5 snRNAs. We discuss the likelihood that processing by scaRNAs is not limited to the CB.

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“…The majority of snoRNAs act as guides for posttranscriptional nucleotide modifications in rRNA (2Ј-O-ribose methylation or pseudouridylation) that fine-tune ribosome performance (13,30,39). However, several snoRNAs, including U3, U14, and U17/snR30, are required for cleavages within pre-rRNA and therefore are essential for ribosome production and cell viability (2,24,28,37,42).…”

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confidence: 99%

Mammalian DEAD Box Protein Ddx51 Acts in 3′ End Maturation of 28S rRNA by Promoting the Release of U8 snoRNA

Srivastava

Lapik

Wang

et al. 2010

Molecular and Cellular Biology

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Biogenesis of eukaryotic ribosomes requires a number of RNA helicases that drive molecular rearrangements at various points of the assembly pathway. While many ribosome synthesis factors are conserved among all eukaryotes, certain features of ribosome maturation, such as U8 snoRNA-assisted processing of the 5.8S and 28S rRNA precursors, are observed only in metazoan cells. Here, we identify the mammalian DEAD box helicase family member Ddx51 as a novel ribosome synthesis factor and an interacting partner of the nucleolar GTP-binding protein Nog1. Unlike any previously studied yeast helicases, Ddx51 is required for the formation of the 3 end of 28S rRNA. Ddx51 binds to pre-60S subunit complexes and promotes displacement of U8 snoRNA from pre-rRNA, which is necessary for the removal of the 3 external transcribed spacer from 28S rRNA and productive downstream processing. These data demonstrate the emergence of a novel factor that facilitates a pre-rRNA processing event specific for higher eukaryotes.Synthesis of ribosomes is a highly complicated process that consumes a large amount of cellular resources and requires a large array of auxiliary factors. rRNAs, the main structural component of the ribosome, are transcribed as precursors (pre-rRNAs) that are processed to mature forms through cleavages, exonucleolytic trimming, and nucleotide modifications (34). Studies in the yeast Saccharomyces cerevisiae have led to the identification of more than 150 proteins acting in pre-rRNA processing and ribosome assembly (reviewed in references 14, 22, and 33). A variety of putative helicases, GTPases, and ATPases identified among ribosome synthesis factors are believed to facilitate extensive rearrangements in RNA and RNA-protein complexes occurring in the course of ribosome maturation (52). Functions of the majority of ribosome synthesis factors are still not completely understood. Based on sequence similarity, many yeast ribosome assembly factors have putative orthologs in higher eukaryotic species including humans (23). The overall pathway for ribosome maturation has also been conserved in eukaryotic evolution, but there are differences between organisms in the organization of the nucleolus (55) and pre-rRNA processing steps (12), pointing to the underlying mechanistic variations in this process.In addition to protein factors, several dozen to hundreds of small nucleolar RNAs (snoRNAs) participate in eukaryotic ribosome maturation (reviewed in references 3, 16, and 31).The majority of snoRNAs act as guides for posttranscriptional nucleotide modifications in rRNA (2Ј-O-ribose methylation or pseudouridylation) that fine-tune ribosome performance (13, 30, 39). However, several snoRNAs, including U3, U14, and U17/snR30, are required for cleavages within pre-rRNA and therefore are essential for ribosome production and cell viability (2,24,28,37,42). Two additional snoRNAs, U8 and U22, participate in rRNA cleavages in vertebrates (44, 59), underscoring variability in the pre-rRNA processing machinery between different eukaryotes...

show abstract

Functional importance of individual rRNA 2′-O-ribose methylations revealed by high-resolution phenotyping

Cited by 60 publications

References 36 publications

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

Novel small Cajal-body-specific RNAs identified in Drosophila: probing guide RNA function

Mammalian DEAD Box Protein Ddx51 Acts in 3′ End Maturation of 28S rRNA by Promoting the Release of U8 snoRNA

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