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Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency.

Deschamps-Francoeur G, Garneau D, Dupuis-Sandoval F, Roy A, Frappier M, Catala M, Couture S, Barbe-Marcoux M, Abou-Elela S, Scott MS - Nucleic Acids Res. (2014)

Bottom Line: The results indicate that C/D snoRNAs are expressed as two distinct forms differing in their ends with respect to boxes C and D and in their terminal stem length.Analysis of the potential secondary structure of both forms indicates that the k-turn motif required for binding of NOP58 is less stable in short forms which are thus less likely to mature into a canonical snoRNP.Taken together the data suggest that C/D snoRNAs are divided into at least two groups with distinct maturation and functional preferences.

View Article: PubMed Central - PubMed

Affiliation: Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.

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Intronic snoRNA processing model. (A) Intronic snoRNAs displaying canonical features including a strong k-turn and/or proximity to the downstream exon are more likely to follow the canonical processing pathway including dependency on core box C/D snoRNP proteins such as NOP58. (B) In contrast, snoRNAs displaying non-canonical features are more likely to depend on non-canonical snoRNA binding proteins such as RBFOX2.
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Figure 6: Intronic snoRNA processing model. (A) Intronic snoRNAs displaying canonical features including a strong k-turn and/or proximity to the downstream exon are more likely to follow the canonical processing pathway including dependency on core box C/D snoRNP proteins such as NOP58. (B) In contrast, snoRNAs displaying non-canonical features are more likely to depend on non-canonical snoRNA binding proteins such as RBFOX2.

Mentions: The data obtained in this study suggest a snoRNA processing model (Figure 6) where snoRNAs forming a k-turn motif stabilized by a long terminal stem, and typically located close to a 3′ splice site, are likely to bind to the NOP58 complex leading to the formation of canonical snoRNPs that mostly target rRNA for modification. In cases where the k-turn is unstable (e.g. snoRNASH) and the snoRNA is positioned further upstream from the 3′ splice site, binding of the NOP58 complex becomes less efficient, making the snoRNA available for association with other protein factors like RBFOX2. According to this model, non-canonical snoRNAs that do not have conventional targets or activity are more likely to be generated by an alternative processing mechanism independent of the snoRNP core proteins that obligatorily associate with NOP58. This group of non-canonical snoRNAs may include those serving as precursors for miRNAs or involved in rRNA independent functions such as splicing regulation and chromatin modulation (30,32,35–37,74–76). Many of these snoRNAs are not affected by either NOP58 or RBFOX2 depletions, suggesting that other protein factors might be involved in forming specific subclasses of snoRNAs. Detailed analysis of the effects of different RNA binding proteins on snoRNA may shed light on the breadth and depth of the snoRNA super family. Meanwhile, the data presented here provide a clear example of snoRNA subclasses and challenges the notion that all box C/D snoRNAs are obligatorily dependent on core snoRNA binding proteins.


Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency.

Deschamps-Francoeur G, Garneau D, Dupuis-Sandoval F, Roy A, Frappier M, Catala M, Couture S, Barbe-Marcoux M, Abou-Elela S, Scott MS - Nucleic Acids Res. (2014)

Intronic snoRNA processing model. (A) Intronic snoRNAs displaying canonical features including a strong k-turn and/or proximity to the downstream exon are more likely to follow the canonical processing pathway including dependency on core box C/D snoRNP proteins such as NOP58. (B) In contrast, snoRNAs displaying non-canonical features are more likely to depend on non-canonical snoRNA binding proteins such as RBFOX2.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150776&req=5

Figure 6: Intronic snoRNA processing model. (A) Intronic snoRNAs displaying canonical features including a strong k-turn and/or proximity to the downstream exon are more likely to follow the canonical processing pathway including dependency on core box C/D snoRNP proteins such as NOP58. (B) In contrast, snoRNAs displaying non-canonical features are more likely to depend on non-canonical snoRNA binding proteins such as RBFOX2.
Mentions: The data obtained in this study suggest a snoRNA processing model (Figure 6) where snoRNAs forming a k-turn motif stabilized by a long terminal stem, and typically located close to a 3′ splice site, are likely to bind to the NOP58 complex leading to the formation of canonical snoRNPs that mostly target rRNA for modification. In cases where the k-turn is unstable (e.g. snoRNASH) and the snoRNA is positioned further upstream from the 3′ splice site, binding of the NOP58 complex becomes less efficient, making the snoRNA available for association with other protein factors like RBFOX2. According to this model, non-canonical snoRNAs that do not have conventional targets or activity are more likely to be generated by an alternative processing mechanism independent of the snoRNP core proteins that obligatorily associate with NOP58. This group of non-canonical snoRNAs may include those serving as precursors for miRNAs or involved in rRNA independent functions such as splicing regulation and chromatin modulation (30,32,35–37,74–76). Many of these snoRNAs are not affected by either NOP58 or RBFOX2 depletions, suggesting that other protein factors might be involved in forming specific subclasses of snoRNAs. Detailed analysis of the effects of different RNA binding proteins on snoRNA may shed light on the breadth and depth of the snoRNA super family. Meanwhile, the data presented here provide a clear example of snoRNA subclasses and challenges the notion that all box C/D snoRNAs are obligatorily dependent on core snoRNA binding proteins.

Bottom Line: The results indicate that C/D snoRNAs are expressed as two distinct forms differing in their ends with respect to boxes C and D and in their terminal stem length.Analysis of the potential secondary structure of both forms indicates that the k-turn motif required for binding of NOP58 is less stable in short forms which are thus less likely to mature into a canonical snoRNP.Taken together the data suggest that C/D snoRNAs are divided into at least two groups with distinct maturation and functional preferences.

View Article: PubMed Central - PubMed

Affiliation: Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.

Show MeSH
Related in: MedlinePlus