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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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NOP58 and RBFOX2 snoRNA targets are form-dependent. The abundance of the different forms generated from each snoRNA was determined before and after the KD of either NOP58 or RBFOX2 and plotted relative to the number of nucleotides upstream of box C and downstream of box D. Shown are three examples representing snoRNAs producing only long (A), only short (B) or both long and short (C) forms. The snoRNA names are shown on top, while the enrichment of the short and long forms are illustrated at bottom. CPM and LF respectively indicate counts per million reads mapped and mock transfection (Lipofectamine). The data obtained after the transfection of two independent siRNAs targeting either NOP58 (blue bars) or RBFOX2 (red bars) and three mock transfections (black bars) are shown.
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Figure 5: NOP58 and RBFOX2 snoRNA targets are form-dependent. The abundance of the different forms generated from each snoRNA was determined before and after the KD of either NOP58 or RBFOX2 and plotted relative to the number of nucleotides upstream of box C and downstream of box D. Shown are three examples representing snoRNAs producing only long (A), only short (B) or both long and short (C) forms. The snoRNA names are shown on top, while the enrichment of the short and long forms are illustrated at bottom. CPM and LF respectively indicate counts per million reads mapped and mock transfection (Lipofectamine). The data obtained after the transfection of two independent siRNAs targeting either NOP58 (blue bars) or RBFOX2 (red bars) and three mock transfections (black bars) are shown.

Mentions: For form-specific analyses (Figures 1, 2, 3B, 4B, 5 and Supplementary File 1, Figures S3–S9), for any given snoRNA, all sequences differing by as little as 1 nt but present with a count of at least 10 reads were considered as different forms of the same snoRNA. Predominant forms were defined as forms representing at least 20% of the total number of reads mapping to the full-length snoRNAs as defined above (i.e. these reads must cover at least 77% of the full-length snoRNA). The different snoRNA forms were compared to the positions of the boxes C and D as defined in snoRNAbase (28) and sno/scaRNAbase (56). Most box C/D snoRNA sequences start 4–6 nt before the box C and end 2–5 nt after the box D. Short snoRNA forms were defined as sequences starting 4 or 5 nt before the box C and ending 2 to 3 nt after the box D, while long snoRNA forms were defined as sequences starting 5 or 6 nt before the box C and ending 4 or 5 nt after the box D. The abundance of each different snoRNA form was calculated by normalizing the read count corresponding to the form by the total number of reads mapped to the genome for the given sample and multiplying by 1 000 000, obtaining abundance values in count per million (CPM). For all figures analyzing short and long snoRNA forms separately, only predominant forms with a minimum abundance of 1 CPM were considered. The fold change following the NOP58 depletion was calculated as the average normalized abundance for the NOP58 depletions divided by the average normalized abundance in the mock-treated samples. The fold change following the RBFOX2 depletion was calculated using the same procedure. The U3 family members were not considered in the analysis as their length exceeds the size cutoff of 200 nt used to isolate the RNA.


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)

NOP58 and RBFOX2 snoRNA targets are form-dependent. The abundance of the different forms generated from each snoRNA was determined before and after the KD of either NOP58 or RBFOX2 and plotted relative to the number of nucleotides upstream of box C and downstream of box D. Shown are three examples representing snoRNAs producing only long (A), only short (B) or both long and short (C) forms. The snoRNA names are shown on top, while the enrichment of the short and long forms are illustrated at bottom. CPM and LF respectively indicate counts per million reads mapped and mock transfection (Lipofectamine). The data obtained after the transfection of two independent siRNAs targeting either NOP58 (blue bars) or RBFOX2 (red bars) and three mock transfections (black bars) are shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4150776&req=5

Figure 5: NOP58 and RBFOX2 snoRNA targets are form-dependent. The abundance of the different forms generated from each snoRNA was determined before and after the KD of either NOP58 or RBFOX2 and plotted relative to the number of nucleotides upstream of box C and downstream of box D. Shown are three examples representing snoRNAs producing only long (A), only short (B) or both long and short (C) forms. The snoRNA names are shown on top, while the enrichment of the short and long forms are illustrated at bottom. CPM and LF respectively indicate counts per million reads mapped and mock transfection (Lipofectamine). The data obtained after the transfection of two independent siRNAs targeting either NOP58 (blue bars) or RBFOX2 (red bars) and three mock transfections (black bars) are shown.
Mentions: For form-specific analyses (Figures 1, 2, 3B, 4B, 5 and Supplementary File 1, Figures S3–S9), for any given snoRNA, all sequences differing by as little as 1 nt but present with a count of at least 10 reads were considered as different forms of the same snoRNA. Predominant forms were defined as forms representing at least 20% of the total number of reads mapping to the full-length snoRNAs as defined above (i.e. these reads must cover at least 77% of the full-length snoRNA). The different snoRNA forms were compared to the positions of the boxes C and D as defined in snoRNAbase (28) and sno/scaRNAbase (56). Most box C/D snoRNA sequences start 4–6 nt before the box C and end 2–5 nt after the box D. Short snoRNA forms were defined as sequences starting 4 or 5 nt before the box C and ending 2 to 3 nt after the box D, while long snoRNA forms were defined as sequences starting 5 or 6 nt before the box C and ending 4 or 5 nt after the box D. The abundance of each different snoRNA form was calculated by normalizing the read count corresponding to the form by the total number of reads mapped to the genome for the given sample and multiplying by 1 000 000, obtaining abundance values in count per million (CPM). For all figures analyzing short and long snoRNA forms separately, only predominant forms with a minimum abundance of 1 CPM were considered. The fold change following the NOP58 depletion was calculated as the average normalized abundance for the NOP58 depletions divided by the average normalized abundance in the mock-treated samples. The fold change following the RBFOX2 depletion was calculated using the same procedure. The U3 family members were not considered in the analysis as their length exceeds the size cutoff of 200 nt used to isolate the RNA.

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