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Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli.

Kim SH, Spensley M, Choi SK, Calixto CP, Pendle AF, Koroleva O, Shaw PJ, Brown JW - Nucleic Acids Res. (2010)

Bottom Line: The nucleolar localization of a number of the snoRNAs and the localization to nuclear bodies of two putative scaRNAs was confirmed by in situ hybridization.The majority of the novel snoRNA genes were found in new gene clusters or as part of previously described clusters.These results expand the repertoire of Arabidopsis snoRNAs to 188 snoRNA genes with 294 gene variants.

View Article: PubMed Central - PubMed

Affiliation: Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK.

ABSTRACT
Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs) are non-coding RNAs whose main function in eukaryotes is to guide the modification of nucleotides in ribosomal and spliceosomal small nuclear RNAs, respectively. Full-length sequences of Arabidopsis snoRNAs and scaRNAs have been obtained from cDNA libraries of capped and uncapped small RNAs using RNA from isolated nucleoli from Arabidopsis cell cultures. We have identified 31 novel snoRNA genes (9 box C/D and 22 box H/ACA) and 15 new variants of previously described snoRNAs. Three related capped snoRNAs with a distinct gene organization and structure were identified as orthologues of animal U13snoRNAs. In addition, eight of the novel genes had no complementarity to rRNAs or snRNAs and are therefore putative orphan snoRNAs potentially reflecting wider functions for these RNAs. The nucleolar localization of a number of the snoRNAs and the localization to nuclear bodies of two putative scaRNAs was confirmed by in situ hybridization. The majority of the novel snoRNA genes were found in new gene clusters or as part of previously described clusters. These results expand the repertoire of Arabidopsis snoRNAs to 188 snoRNA genes with 294 gene variants.

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Sequence alignment of U13 snoRNAs. (A) The three plant U13 orthologues are aligned with human U13. Identical sequences are indicated by asterisks; for the three plant genes, sequence differences from snoR105 are highlighted white on black. Box C and D sequences are boxed; the two highly conserved regions in the plant genes are shaded grey; the two regions of complementarity to 18S rRNA in human U13 are boxed and labelled A and B [following human model: ref. (48)] and putative inverted repeats adjacent to boxes C and D are shown by arrows. (B) Putative base-pairing interactions between human U13snoRNA and Arabidopsis U13 (snoR146) with the 3′ regions of their cognate 18S rRNAs.
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Figure 3: Sequence alignment of U13 snoRNAs. (A) The three plant U13 orthologues are aligned with human U13. Identical sequences are indicated by asterisks; for the three plant genes, sequence differences from snoR105 are highlighted white on black. Box C and D sequences are boxed; the two highly conserved regions in the plant genes are shaded grey; the two regions of complementarity to 18S rRNA in human U13 are boxed and labelled A and B [following human model: ref. (48)] and putative inverted repeats adjacent to boxes C and D are shown by arrows. (B) Putative base-pairing interactions between human U13snoRNA and Arabidopsis U13 (snoR146) with the 3′ regions of their cognate 18S rRNAs.

Mentions: Of particular interest was the demonstration that three snoRNA species were highly abundant in the capped library. SnoR105, snoR108 and snoR146 are related monocistronic box C/D snoRNAs. SnoR105 and snoR108 were identified previously as partial sequences which contained recognized promoter elements of plant snRNA genes [an upstream sequence element (USE) at ∼−90 and a TATA-box at ∼30 bp upstream of the transcription start site—ref. (44)] in the upstream region of their genomic sequences (21). Here, we obtained full-length sequences of snoR105 and snoR108 as well as the related snoR146 (Figure 3). The genomic sequences upstream of all three genes have USE and TATA promoter elements in the RNA polymerase II configuration (44). The presence of snRNA promoter elements as well as their efficient isolation from the capped library strongly suggest that these snoRNAs are capped while the vast majority of Arabidopsis snoRNAs are processed from polycistronic snoRNA precursors and are uncapped. The three genes contain conserved C and D boxes except that the box C sequence is internal in the coding sequence lying ∼30 nt from the 5′ end (Figure 3). Like most box C/D snoRNAs, short inverted repeats are present directly up and downstream of the box C and D sequences, respectively, which may facilitate the formation of a K-turn in the C/D motif to which the core p15.5 kDa protein binds as the first stage in box C/D snoRNP assembly (47). Alignment of the three snoRNA sequences show two regions of high conservation: the first 24 nt which shows only a single nucleotide change and positions 83–96 (Figure 3A). The structural features of these snoRNAs were reminiscent of animal U8 and U13 snoRNAs which contain complementarity to rRNA sequences (48). Alignment with the human U13 sequence (49) clearly showed similarity in the two most highly conserved regions (above) (Figure 3A). The Arabidopsis sequences were complementary to the 3′-end of 18S rRNAs and formed similar putative base-pairing interactions (Figure 3B). A number of other plant orthologues of the U13 snoRNAs have been identified in EST libraries and all have complementarity to the 3′-end of 18S rRNA (results not shown).Figure 3.


Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli.

Kim SH, Spensley M, Choi SK, Calixto CP, Pendle AF, Koroleva O, Shaw PJ, Brown JW - Nucleic Acids Res. (2010)

Sequence alignment of U13 snoRNAs. (A) The three plant U13 orthologues are aligned with human U13. Identical sequences are indicated by asterisks; for the three plant genes, sequence differences from snoR105 are highlighted white on black. Box C and D sequences are boxed; the two highly conserved regions in the plant genes are shaded grey; the two regions of complementarity to 18S rRNA in human U13 are boxed and labelled A and B [following human model: ref. (48)] and putative inverted repeats adjacent to boxes C and D are shown by arrows. (B) Putative base-pairing interactions between human U13snoRNA and Arabidopsis U13 (snoR146) with the 3′ regions of their cognate 18S rRNAs.
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Related In: Results  -  Collection

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Figure 3: Sequence alignment of U13 snoRNAs. (A) The three plant U13 orthologues are aligned with human U13. Identical sequences are indicated by asterisks; for the three plant genes, sequence differences from snoR105 are highlighted white on black. Box C and D sequences are boxed; the two highly conserved regions in the plant genes are shaded grey; the two regions of complementarity to 18S rRNA in human U13 are boxed and labelled A and B [following human model: ref. (48)] and putative inverted repeats adjacent to boxes C and D are shown by arrows. (B) Putative base-pairing interactions between human U13snoRNA and Arabidopsis U13 (snoR146) with the 3′ regions of their cognate 18S rRNAs.
Mentions: Of particular interest was the demonstration that three snoRNA species were highly abundant in the capped library. SnoR105, snoR108 and snoR146 are related monocistronic box C/D snoRNAs. SnoR105 and snoR108 were identified previously as partial sequences which contained recognized promoter elements of plant snRNA genes [an upstream sequence element (USE) at ∼−90 and a TATA-box at ∼30 bp upstream of the transcription start site—ref. (44)] in the upstream region of their genomic sequences (21). Here, we obtained full-length sequences of snoR105 and snoR108 as well as the related snoR146 (Figure 3). The genomic sequences upstream of all three genes have USE and TATA promoter elements in the RNA polymerase II configuration (44). The presence of snRNA promoter elements as well as their efficient isolation from the capped library strongly suggest that these snoRNAs are capped while the vast majority of Arabidopsis snoRNAs are processed from polycistronic snoRNA precursors and are uncapped. The three genes contain conserved C and D boxes except that the box C sequence is internal in the coding sequence lying ∼30 nt from the 5′ end (Figure 3). Like most box C/D snoRNAs, short inverted repeats are present directly up and downstream of the box C and D sequences, respectively, which may facilitate the formation of a K-turn in the C/D motif to which the core p15.5 kDa protein binds as the first stage in box C/D snoRNP assembly (47). Alignment of the three snoRNA sequences show two regions of high conservation: the first 24 nt which shows only a single nucleotide change and positions 83–96 (Figure 3A). The structural features of these snoRNAs were reminiscent of animal U8 and U13 snoRNAs which contain complementarity to rRNA sequences (48). Alignment with the human U13 sequence (49) clearly showed similarity in the two most highly conserved regions (above) (Figure 3A). The Arabidopsis sequences were complementary to the 3′-end of 18S rRNAs and formed similar putative base-pairing interactions (Figure 3B). A number of other plant orthologues of the U13 snoRNAs have been identified in EST libraries and all have complementarity to the 3′-end of 18S rRNA (results not shown).Figure 3.

Bottom Line: The nucleolar localization of a number of the snoRNAs and the localization to nuclear bodies of two putative scaRNAs was confirmed by in situ hybridization.The majority of the novel snoRNA genes were found in new gene clusters or as part of previously described clusters.These results expand the repertoire of Arabidopsis snoRNAs to 188 snoRNA genes with 294 gene variants.

View Article: PubMed Central - PubMed

Affiliation: Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK.

ABSTRACT
Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs) are non-coding RNAs whose main function in eukaryotes is to guide the modification of nucleotides in ribosomal and spliceosomal small nuclear RNAs, respectively. Full-length sequences of Arabidopsis snoRNAs and scaRNAs have been obtained from cDNA libraries of capped and uncapped small RNAs using RNA from isolated nucleoli from Arabidopsis cell cultures. We have identified 31 novel snoRNA genes (9 box C/D and 22 box H/ACA) and 15 new variants of previously described snoRNAs. Three related capped snoRNAs with a distinct gene organization and structure were identified as orthologues of animal U13snoRNAs. In addition, eight of the novel genes had no complementarity to rRNAs or snRNAs and are therefore putative orphan snoRNAs potentially reflecting wider functions for these RNAs. The nucleolar localization of a number of the snoRNAs and the localization to nuclear bodies of two putative scaRNAs was confirmed by in situ hybridization. The majority of the novel snoRNA genes were found in new gene clusters or as part of previously described clusters. These results expand the repertoire of Arabidopsis snoRNAs to 188 snoRNA genes with 294 gene variants.

Show MeSH