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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 KD of the RBFOX2 splicing factor preferentially downregulates the expression of short snoRNA forms. (A) KD of RBFOX2 inhibits the expression of select box C/D and H/ACA snoRNAs. RBFOX2 was knocked down in SKOV3ip1 using two independent siRNAs and the impact on the abundance of RNA shorter than 200 nt (snoRNA, miRNA, snRNA, YRNA and tRNA) was calculated relative to the level in mock-transfected cells (LF). The log2 fold change in RNA abundance is shown in the form of scatter plots. The different small RNA members are indicated by blue dots, while the box C/D (left panel) and H/ACA snoRNA (right panel) are highlighted in red. The dashed lines represent a decrease of 2-fold in the RBFOX2 depletion. (B) Effect of the RBFOX2 KD on the different forms of box C/D snoRNA. The number of long (snoRNAL), short (snoRNASH) and other (that differ from the snoRNAL and snoRNASH) forms of box C/D snoRNAs was determined and plotted relative to binned values of the log2 fold change in expression after the RBFOX2 KD. The enrichment in snoRNASH downregulated by the KD is shown at bottom.
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Figure 4: The KD of the RBFOX2 splicing factor preferentially downregulates the expression of short snoRNA forms. (A) KD of RBFOX2 inhibits the expression of select box C/D and H/ACA snoRNAs. RBFOX2 was knocked down in SKOV3ip1 using two independent siRNAs and the impact on the abundance of RNA shorter than 200 nt (snoRNA, miRNA, snRNA, YRNA and tRNA) was calculated relative to the level in mock-transfected cells (LF). The log2 fold change in RNA abundance is shown in the form of scatter plots. The different small RNA members are indicated by blue dots, while the box C/D (left panel) and H/ACA snoRNA (right panel) are highlighted in red. The dashed lines represent a decrease of 2-fold in the RBFOX2 depletion. (B) Effect of the RBFOX2 KD on the different forms of box C/D snoRNA. The number of long (snoRNAL), short (snoRNASH) and other (that differ from the snoRNAL and snoRNASH) forms of box C/D snoRNAs was determined and plotted relative to binned values of the log2 fold change in expression after the RBFOX2 KD. The enrichment in snoRNASH downregulated by the KD is shown at bottom.

Mentions: To be considered in these analyses, snoRNAs had to be represented by at least 10 reads covering at least 77% of the full-length snoRNA as defined in snoRNAbase (28). For analyses considering all reads mapping to full-length snoRNAs regardless of forms (Figures 3A and 4A), the normalized abundance value per snoRNA (one value per snoRNA) as well as per miRNA, per tRNA, per rRNA, per YRNA and per snRNA was calculated using DESeq (55). The fold change following the depletions (Figures 3A and 4A) was calculated as the average normalized abundance value in the two depletion samples divided by the average normalized abundance in the three mock-treated (Lipofectamine) samples.


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 KD of the RBFOX2 splicing factor preferentially downregulates the expression of short snoRNA forms. (A) KD of RBFOX2 inhibits the expression of select box C/D and H/ACA snoRNAs. RBFOX2 was knocked down in SKOV3ip1 using two independent siRNAs and the impact on the abundance of RNA shorter than 200 nt (snoRNA, miRNA, snRNA, YRNA and tRNA) was calculated relative to the level in mock-transfected cells (LF). The log2 fold change in RNA abundance is shown in the form of scatter plots. The different small RNA members are indicated by blue dots, while the box C/D (left panel) and H/ACA snoRNA (right panel) are highlighted in red. The dashed lines represent a decrease of 2-fold in the RBFOX2 depletion. (B) Effect of the RBFOX2 KD on the different forms of box C/D snoRNA. The number of long (snoRNAL), short (snoRNASH) and other (that differ from the snoRNAL and snoRNASH) forms of box C/D snoRNAs was determined and plotted relative to binned values of the log2 fold change in expression after the RBFOX2 KD. The enrichment in snoRNASH downregulated by the KD is shown at bottom.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
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Figure 4: The KD of the RBFOX2 splicing factor preferentially downregulates the expression of short snoRNA forms. (A) KD of RBFOX2 inhibits the expression of select box C/D and H/ACA snoRNAs. RBFOX2 was knocked down in SKOV3ip1 using two independent siRNAs and the impact on the abundance of RNA shorter than 200 nt (snoRNA, miRNA, snRNA, YRNA and tRNA) was calculated relative to the level in mock-transfected cells (LF). The log2 fold change in RNA abundance is shown in the form of scatter plots. The different small RNA members are indicated by blue dots, while the box C/D (left panel) and H/ACA snoRNA (right panel) are highlighted in red. The dashed lines represent a decrease of 2-fold in the RBFOX2 depletion. (B) Effect of the RBFOX2 KD on the different forms of box C/D snoRNA. The number of long (snoRNAL), short (snoRNASH) and other (that differ from the snoRNAL and snoRNASH) forms of box C/D snoRNAs was determined and plotted relative to binned values of the log2 fold change in expression after the RBFOX2 KD. The enrichment in snoRNASH downregulated by the KD is shown at bottom.
Mentions: To be considered in these analyses, snoRNAs had to be represented by at least 10 reads covering at least 77% of the full-length snoRNA as defined in snoRNAbase (28). For analyses considering all reads mapping to full-length snoRNAs regardless of forms (Figures 3A and 4A), the normalized abundance value per snoRNA (one value per snoRNA) as well as per miRNA, per tRNA, per rRNA, per YRNA and per snRNA was calculated using DESeq (55). The fold change following the depletions (Figures 3A and 4A) was calculated as the average normalized abundance value in the two depletion samples divided by the average normalized abundance in the three mock-treated (Lipofectamine) samples.

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