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Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap structures in Caenorhabditis elegans.

Jia D, Cai L, He H, Skogerbø G, Li T, Aftab MN, Chen R - BMC Mol. Biol. (2007)

Bottom Line: All snRNAs known to have a TMG cap structure were found in the precipitate, indicating that our identification system was efficient.Further analysis showed that the SL RNAs and the Sm Y RNAs shared a very similar Sm binding site element (AAU4-5GGA), which sequence composition differed somewhat from those of other U snRNAs.Our results showed that most ncRNAs predicted to be transcribed by RNA polymerase II had a TMG cap, while those predicted to be transcribed by RNA plymerase III or located in introns did not have a TMG cap structure.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. donging@gmail.com

ABSTRACT

Background: The 2,2,7-trimethylguanosine (TMG) cap structure is an important functional characteristic of ncRNAs with critical cellular roles, such as some snRNAs. Here we used immunoprecipitation with both K121 and R1131 anti-TMG antibodies to systematically identify the TMG cap structures for all presently characterized ncRNAs in C. elegans.

Results: The two anti-TMG antibodies precipitated a similar group of the C. elegans ncRNAs. All snRNAs known to have a TMG cap structure were found in the precipitate, indicating that our identification system was efficient. Other ncRNA families related to splicing, such as SL RNAs and Sm Y RNAs, were also found in the precipitate, as were 7 C/D box snoRNAs. Further analysis showed that the SL RNAs and the Sm Y RNAs shared a very similar Sm binding site element (AAU4-5GGA), which sequence composition differed somewhat from those of other U snRNAs. There were also 16 ncRNAs without an Sm binding site element in the precipitate, suggesting that for these ncRNAs, TMG formation may occur independently of Sm proteins.

Conclusion: Our results showed that most ncRNAs predicted to be transcribed by RNA polymerase II had a TMG cap, while those predicted to be transcribed by RNA plymerase III or located in introns did not have a TMG cap structure. Compared to ncRNAs without a TMG cap, TMG-capped ncRNAs tended to have higher expression levels. Five functionally non-annotated ncRNAs also have a TMG cap structure, which might be helpful for identifying the cellular roles of these ncRNAs.

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Cap structure and predicted mode of biogenesis. The ncRNAs were divided into four groups: those predicted to be transcribed by RNA polymerase II (Pol II) or III (Pol III), those located in introns with no evident upstream motifs (Intronic), and those with intergenic loci with no distinct upstream motifs (Other). The numbers of TMG-capped and non-TMG-capped ncRNAs were shown for each group.
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Figure 3: Cap structure and predicted mode of biogenesis. The ncRNAs were divided into four groups: those predicted to be transcribed by RNA polymerase II (Pol II) or III (Pol III), those located in introns with no evident upstream motifs (Intronic), and those with intergenic loci with no distinct upstream motifs (Other). The numbers of TMG-capped and non-TMG-capped ncRNAs were shown for each group.

Mentions: Primary transcripts synthesized by RNA polymerase II are modified by addition of a 7-methylguanosine residue to their triphosphate 5'-end shortly after emergence from the polymerase. The 7-methylguanosine "caps" of small nuclear and small nucleolar RNAs are subsequently hypermethylated to a 2,2,7-trimethylguanosine cap. We therefore analyzed the relationship between TMG cap structure and the predicted mode of biogenesis for ncRNAs in C. elegans. Based on upstream motifs and other characteristics, ncRNAs in C. elegans have been divided into four groups [19], of which the first two were assumed to be transcribed by RNA polymerase II or III, respectively. The third group comprised ncRNAs processed from spliced introns with no evident upstream motif, and the fourth group was composed of other ncRNAs for which no predictions could be made. Twenty-eight of the 32 ncRNAs predicted to be transcribed by polymerase II [19], have a TMG-cap structure, the exceptions being four C/D box snoRNAs (CeN117, CeN121, CeN28 and CeN33), two of which were precipitated by K121 antibody. On the other hand, only one of 52 ncRNAs predicted to be transcribed by RNA polymerase III were assigned to the TMG-capped group. All the 34 intronic snoRNA without upstream motifs were also in the non-TMG-capped group. Eight of 9 intergenic ncRNA loci with no distinct upstream motif were in TMG-capped group, whereas one (CeN113) had intensity ratios (precipitation/supernatant) around 1.0 and the last one was assigned to the non-TMG group (Figure 3).


Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap structures in Caenorhabditis elegans.

Jia D, Cai L, He H, Skogerbø G, Li T, Aftab MN, Chen R - BMC Mol. Biol. (2007)

Cap structure and predicted mode of biogenesis. The ncRNAs were divided into four groups: those predicted to be transcribed by RNA polymerase II (Pol II) or III (Pol III), those located in introns with no evident upstream motifs (Intronic), and those with intergenic loci with no distinct upstream motifs (Other). The numbers of TMG-capped and non-TMG-capped ncRNAs were shown for each group.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2200864&req=5

Figure 3: Cap structure and predicted mode of biogenesis. The ncRNAs were divided into four groups: those predicted to be transcribed by RNA polymerase II (Pol II) or III (Pol III), those located in introns with no evident upstream motifs (Intronic), and those with intergenic loci with no distinct upstream motifs (Other). The numbers of TMG-capped and non-TMG-capped ncRNAs were shown for each group.
Mentions: Primary transcripts synthesized by RNA polymerase II are modified by addition of a 7-methylguanosine residue to their triphosphate 5'-end shortly after emergence from the polymerase. The 7-methylguanosine "caps" of small nuclear and small nucleolar RNAs are subsequently hypermethylated to a 2,2,7-trimethylguanosine cap. We therefore analyzed the relationship between TMG cap structure and the predicted mode of biogenesis for ncRNAs in C. elegans. Based on upstream motifs and other characteristics, ncRNAs in C. elegans have been divided into four groups [19], of which the first two were assumed to be transcribed by RNA polymerase II or III, respectively. The third group comprised ncRNAs processed from spliced introns with no evident upstream motif, and the fourth group was composed of other ncRNAs for which no predictions could be made. Twenty-eight of the 32 ncRNAs predicted to be transcribed by polymerase II [19], have a TMG-cap structure, the exceptions being four C/D box snoRNAs (CeN117, CeN121, CeN28 and CeN33), two of which were precipitated by K121 antibody. On the other hand, only one of 52 ncRNAs predicted to be transcribed by RNA polymerase III were assigned to the TMG-capped group. All the 34 intronic snoRNA without upstream motifs were also in the non-TMG-capped group. Eight of 9 intergenic ncRNA loci with no distinct upstream motif were in TMG-capped group, whereas one (CeN113) had intensity ratios (precipitation/supernatant) around 1.0 and the last one was assigned to the non-TMG group (Figure 3).

Bottom Line: All snRNAs known to have a TMG cap structure were found in the precipitate, indicating that our identification system was efficient.Further analysis showed that the SL RNAs and the Sm Y RNAs shared a very similar Sm binding site element (AAU4-5GGA), which sequence composition differed somewhat from those of other U snRNAs.Our results showed that most ncRNAs predicted to be transcribed by RNA polymerase II had a TMG cap, while those predicted to be transcribed by RNA plymerase III or located in introns did not have a TMG cap structure.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. donging@gmail.com

ABSTRACT

Background: The 2,2,7-trimethylguanosine (TMG) cap structure is an important functional characteristic of ncRNAs with critical cellular roles, such as some snRNAs. Here we used immunoprecipitation with both K121 and R1131 anti-TMG antibodies to systematically identify the TMG cap structures for all presently characterized ncRNAs in C. elegans.

Results: The two anti-TMG antibodies precipitated a similar group of the C. elegans ncRNAs. All snRNAs known to have a TMG cap structure were found in the precipitate, indicating that our identification system was efficient. Other ncRNA families related to splicing, such as SL RNAs and Sm Y RNAs, were also found in the precipitate, as were 7 C/D box snoRNAs. Further analysis showed that the SL RNAs and the Sm Y RNAs shared a very similar Sm binding site element (AAU4-5GGA), which sequence composition differed somewhat from those of other U snRNAs. There were also 16 ncRNAs without an Sm binding site element in the precipitate, suggesting that for these ncRNAs, TMG formation may occur independently of Sm proteins.

Conclusion: Our results showed that most ncRNAs predicted to be transcribed by RNA polymerase II had a TMG cap, while those predicted to be transcribed by RNA plymerase III or located in introns did not have a TMG cap structure. Compared to ncRNAs without a TMG cap, TMG-capped ncRNAs tended to have higher expression levels. Five functionally non-annotated ncRNAs also have a TMG cap structure, which might be helpful for identifying the cellular roles of these ncRNAs.

Show MeSH
Related in: MedlinePlus