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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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The long form of box C/D snoRNA (snoRNAL) features extended base pairing downstream of the k-turn structural motif. (A) The long and short snoRNA forms share the basic structural features of box C/D snoRNA. The characteristic box C, box D and k-turn were identified and their level of sequence conservation in each class of snoRNA was determined using the sequence obtained from the SKOV3ip1 cell line. The number and percent of snoRNAs displaying each feature are shown. Only predominant snoRNA forms expressed above 1 CPM in both replicates were counted. (B) The snoRNAL form features more stable k-turn structure. The length of the external stem was measured using SKOV3ip1 RNA for snoRNAs only expressed as short or only expressed as long forms. The proportion of snoRNAs from these two groups is expressed as a function of the number of paired nucleotides in their external stem. (C) Schematic representation of the external stem observed in snoRNAs only expressed as long or short snoRNA forms. The percentage of snoRNAs containing the different number of base pairs downstream of box D is shown on the right of each form. The orange and blue boxes indicate the position of the C and D motifs, respectively.
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Figure 2: The long form of box C/D snoRNA (snoRNAL) features extended base pairing downstream of the k-turn structural motif. (A) The long and short snoRNA forms share the basic structural features of box C/D snoRNA. The characteristic box C, box D and k-turn were identified and their level of sequence conservation in each class of snoRNA was determined using the sequence obtained from the SKOV3ip1 cell line. The number and percent of snoRNAs displaying each feature are shown. Only predominant snoRNA forms expressed above 1 CPM in both replicates were counted. (B) The snoRNAL form features more stable k-turn structure. The length of the external stem was measured using SKOV3ip1 RNA for snoRNAs only expressed as short or only expressed as long forms. The proportion of snoRNAs from these two groups is expressed as a function of the number of paired nucleotides in their external stem. (C) Schematic representation of the external stem observed in snoRNAs only expressed as long or short snoRNA forms. The percentage of snoRNAs containing the different number of base pairs downstream of box D is shown on the right of each form. The orange and blue boxes indicate the position of the C and D motifs, respectively.

Mentions: To understand the relevance of the different snoRNA forms, we investigated their structural and functional differences and their impact if any on the basic features of box C/D snoRNA. As summarized in Figure 2A, no significant differences between the long and short forms were found in the consensus sequences of boxes C and D, or in their k-turn characteristics as defined in Figure 1A. However, the external stem, which is expected to increase the stability of the k-turn motif and believed to be important for canonical snoRNP assembly (17,61,62), is significantly shorter in snoRNASH (P-value < 10−4 by Kolmogorov–Smirnov goodness-of-fit test). As shown in Figure 2B and C, while 30% of snoRNAs produced only as short forms have no external stem (i.e. 0 or 1 consecutive paired residues in this region), over 75% of snoRNAs produced only as long forms have a stem of over five base pairs and many extend well passed the end of the actual mature snoRNA (but are present in the genomic DNA and could be present as long stems before the snoRNA is excised and processed from the intron). Thermodynamic analyses using mfold (63) on a small number of snoRNAs produced as both long and short forms indicate that the longer forms have an average 4 kcal/mol lower free energy than the shorter forms, when folding to form k-turns (e.g. compare Supplementary File1, Figure S7A and B, D and E as well as G and H). The short forms are often more likely to fold in a way that maximizes canonical base pairing, but makes k-turn formation unlikely (e.g. Supplementary File 1, Figure S7C, F and I). Therefore, the long snoRNA forms are more likely to preserve the structure of the k-turn motif needed for the assembly of core snoRNA proteins, such as NOP58, than the short form.


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)

The long form of box C/D snoRNA (snoRNAL) features extended base pairing downstream of the k-turn structural motif. (A) The long and short snoRNA forms share the basic structural features of box C/D snoRNA. The characteristic box C, box D and k-turn were identified and their level of sequence conservation in each class of snoRNA was determined using the sequence obtained from the SKOV3ip1 cell line. The number and percent of snoRNAs displaying each feature are shown. Only predominant snoRNA forms expressed above 1 CPM in both replicates were counted. (B) The snoRNAL form features more stable k-turn structure. The length of the external stem was measured using SKOV3ip1 RNA for snoRNAs only expressed as short or only expressed as long forms. The proportion of snoRNAs from these two groups is expressed as a function of the number of paired nucleotides in their external stem. (C) Schematic representation of the external stem observed in snoRNAs only expressed as long or short snoRNA forms. The percentage of snoRNAs containing the different number of base pairs downstream of box D is shown on the right of each form. The orange and blue boxes indicate the position of the C and D motifs, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: The long form of box C/D snoRNA (snoRNAL) features extended base pairing downstream of the k-turn structural motif. (A) The long and short snoRNA forms share the basic structural features of box C/D snoRNA. The characteristic box C, box D and k-turn were identified and their level of sequence conservation in each class of snoRNA was determined using the sequence obtained from the SKOV3ip1 cell line. The number and percent of snoRNAs displaying each feature are shown. Only predominant snoRNA forms expressed above 1 CPM in both replicates were counted. (B) The snoRNAL form features more stable k-turn structure. The length of the external stem was measured using SKOV3ip1 RNA for snoRNAs only expressed as short or only expressed as long forms. The proportion of snoRNAs from these two groups is expressed as a function of the number of paired nucleotides in their external stem. (C) Schematic representation of the external stem observed in snoRNAs only expressed as long or short snoRNA forms. The percentage of snoRNAs containing the different number of base pairs downstream of box D is shown on the right of each form. The orange and blue boxes indicate the position of the C and D motifs, respectively.
Mentions: To understand the relevance of the different snoRNA forms, we investigated their structural and functional differences and their impact if any on the basic features of box C/D snoRNA. As summarized in Figure 2A, no significant differences between the long and short forms were found in the consensus sequences of boxes C and D, or in their k-turn characteristics as defined in Figure 1A. However, the external stem, which is expected to increase the stability of the k-turn motif and believed to be important for canonical snoRNP assembly (17,61,62), is significantly shorter in snoRNASH (P-value < 10−4 by Kolmogorov–Smirnov goodness-of-fit test). As shown in Figure 2B and C, while 30% of snoRNAs produced only as short forms have no external stem (i.e. 0 or 1 consecutive paired residues in this region), over 75% of snoRNAs produced only as long forms have a stem of over five base pairs and many extend well passed the end of the actual mature snoRNA (but are present in the genomic DNA and could be present as long stems before the snoRNA is excised and processed from the intron). Thermodynamic analyses using mfold (63) on a small number of snoRNAs produced as both long and short forms indicate that the longer forms have an average 4 kcal/mol lower free energy than the shorter forms, when folding to form k-turns (e.g. compare Supplementary File1, Figure S7A and B, D and E as well as G and H). The short forms are often more likely to fold in a way that maximizes canonical base pairing, but makes k-turn formation unlikely (e.g. Supplementary File 1, Figure S7C, F and I). Therefore, the long snoRNA forms are more likely to preserve the structure of the k-turn motif needed for the assembly of core snoRNA proteins, such as NOP58, than the short form.

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