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Open Access Correspondence

SNOntology: Myriads of novel snornas or just a mirage?

Julia A Makarova and Dmitri A Kramerov*

Author Affiliations

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia

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BMC Genomics 2011, 12:543  doi:10.1186/1471-2164-12-543

Published: 3 November 2011

Additional files

Additional file 1:

NcRNAs whose expression has not been detected by Zhang et al. [18]by Nothern hybridization in chicken, mouse, and human but was detected previously by other authors as well as by Zhang et al.[19]. The order of RNAs is as in Table one from Zhang et al. [18].

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Additional file 2:

Controversial results of ncRNA detections in chicken and rhesus monkey (14 extra examples). Hybridization of RNA isolated from different tissues of rhesus monkey, chicken, human, and mouse with rhesus snoRNA probes (left panel; from [18]) and with chicken snoRNA probes (right panel; from [19]). The same RNAs are shown side-by-side. Chicken ncRNAs were cloned by Zhang et al. but not identified as homologs of human snoRNAs [19] (shown on the right). The same RNAs are presented in Table 2.

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Additional file 3:

The majority of chicken ncRNAs cloned and presented as novel RNAs by Zhang at al. [19] are homologs of ncRNAs described previously. Alignments of chicken ncRNAs with the homologs in human or sometimes other vertebrates are shown. GGN sequences are from Zhang et al. [19]. Vault RNA sequence corresponds to the GenBank AF045143 sequence. Other sequences are from snoRNABase [3] and Additional file 4 in this paper. C, D/D', H, ACA, and CAB boxes are underlined; antisense elements are boxed; sequence numbering corresponds to human rRNAs in snoRNABase. In C/D snoRNAs, the nucleotide complementary to the modification site is indicated by the red arrowhead. For the vault RNAs, the secondary structures predicted by mfold [42,43] are shown. The order of ncRNAs is as in Table 2. The SNORD102B transcript has a longer antisense element, and thus can guide the modification of the rRNA nucleotide adjacent to that modified by SNORD102A (marked with black and red arrowheads, respectively) [16].

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Additional file 4:

Nucleotide sequences of C/D box snoRNA genes in different vertebrate species. Boxes C, D, and D' are shown in gray, and sequences of the antisense elements are highlighted in yellow. The G-T complementarity in the antisense elements or terminal stems is indicated in olive. The 5' and 3' terminal complementary regions forming the stem in snoRNAs are shown in blue. Species-specific complementary substitutions in the antisense elements are marked in pink. Pseudogenes are indicated by Ψ. SNORD115 gene clusters are not listed. They have been found only in eutherian mammals and are available in snoRNABase [3] and UCSC Genome Browser. The following genome assemblies were used: human, March 2006, NCBI Build 36.1; mouse, July 2007, NCBI Build 37; rat, November 2004, version 3.4; dog, May 2005, whole genome shotgun assembly v2.0, cow, October 2007, Baylor release Btau_4.0; horse, January 2007, UCSC version equCab1; opossum, January 2006, monDom4; platypus, March 2007, the v5.0.1 draft assembly; chicken, May 2006, galGal3 version 2.1 draft assembly; lizard, February 2007, Broad Institute AnoCar 1.0; frog, August 2005, whole genome shotgun assembly version 4.1; zebrafish, July 2007, Zv7 assembly; fugu, October 2004, v4.0 whole genome shotgun assembly; tetraodon, February 2004, V7 assembly; stickleback, February 2006, v 1.0 draft assembly; medaka, October 2005, v 1.0 draft assembly.

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Additional file 5:

SnoRNA genes not found in the genomes of studied species by Zhang et al. [18] but found in the same species by other researchers. Gene names are listed in the same order as in Figure three in [18].

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Additional file 6:

Nearly all examples of independent transcription of snoRNA genes in Li et al. [20] are erroneous. Screenshots of UCSC Genome Browser (March 2006, NCBI Build 36.1) and nucleotide sequence alignments of snoRNA genes and pseudogenes are shown. The antisense elements are boxed; H, ACA, C, and D/D' sequences are underlined. The nucleotides whose modification is guided by snoRNA are indicated in some cases. SnoRNA genes and pseudogenes (designated as pseudo or Ψ) are listed in the same order as in Tables three, four, and five of Li et al. [20]. The secondary structures were predicted by mfold [42,43].

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