SnOPY: A small nucleolar RNA orthological gene database

被引：73

作者：

Yoshihama M. ^{[1
]}

Nakao A. ^{[1
,2
]}

Kenmochi N. ^{[1
]}

机构：

[1] Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake

[2] Hymena and Co., Minato, Tokyo 108-0075, 1-21-3 Ebisu, Shibuya

来源：

BMC Research Notes | / 6卷 / 1期

基金：

日本学术振兴会;

关键词：

Intron; RNA modification; snoRNA;

D O I：

10.1186/1756-0500-6-426

中图分类号：

学科分类号：

摘要：

Background: Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs that guide the modification of specific nucleotides in ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). Although most non-coding RNAs undergo post-transcriptional modifications prior to maturation, the functional significance of these modifications remains unknown. Here, we introduce the snoRNA orthological gene database (snOPY) as a tool for studying RNA modifications. Findings. snOPY provides comprehensive information about snoRNAs, snoRNA gene loci, and target RNAs. It also contains data for orthologues from various species, which enables users to analyze the evolution of snoRNA genes. In total, 13,770 snoRNA genes, 10,345 snoRNA gene loci, and 133 target RNAs have been registered. Users can search and access the data efficiently using a simple web interface with a series of internal links. snOPY is freely available on the web at. Conclusions: snOPY is the database that provides information about the small nucleolar RNAs and their orthologues. It will help users to study RNA modifications and snoRNA gene evolution. © 2013 Yoshihama et al.; licensee BioMed Central Ltd.

引用

共 20 条

[1]

An integrated encyclopedia of DNA elements in the human genome, Nature, 489, pp. 57-74, (2012)

[2]

Amaral P.P., Dinger M.E., Mercer T.R., Mattick J.S., The eukaryotic genome as an RNA machine, Science, 319, 5871, pp. 1787-1789, (2008)

[3]

Decatur W.A., Fournier M.J., RRNA modifications and ribosome function, Trends in Biochemical Sciences, 27, 7, pp. 344-351, (2002)

[4]

Darzacq X., Jady B.E., Verheggen C., Kiss A.M., Bertrand E., Kiss T., Cajal body-specific small nuclear RNAs: A novel class of 2′-O-methylation and pseudouridylation guide RNAs, EMBO Journal, 21, 11, pp. 2746-2756, (2002)

[5]

Johansson M., Bystrom A., Transfer RNA modifications and modifying enzymes in Saccharomyces cerevisiae, Fine-Tuning of RNA Functions by Modification and Editing, Topics in Current Genetics. Volume 12, pp. 87-120, (2005)

[6]

Newton K., Petfalski E., Tollervey D., Caceres J.F., Fibrillarin Is Essential for Early Development and Required for Accumulation of an Intron-Encoded Small Nucleolar RNA in the Mouse, Molecular and Cellular Biology, 23, 23, pp. 8519-8527, (2003)

[7]

Higa-Nakamine S., Suzuki T., Uechi T., Chakraborty A., Nakajima Y., Nakamura M., Hirano N., Suzuki T., Kenmochi N., Loss of ribosomal RNA modification causes developmental defects in zebrafish, Nucleic Acids Res, 40, pp. 391-398, (2012)

[8]

Machnicka M.A., Milanowska K., Osman Oglou O., Purta E., Kurkowska M., Olchowik A., Januszewski W., Kalinowski S., Dunin-Horkawicz S., Rother K.M., Helm M., Bujnicki J.M., Grosjean H., MODOMICS: A database of RNA modification pathways - 2013 update, Nucleic Acids Res, 41, DATABASE ISSUE 262, (2013)

[9]

Matera A.G., Terns R.M., Terns M.P., Non-coding RNAs: Lessons from the small nuclear and small nucleolar RNAs, Nat Rev Mol Cell Biol, 8, pp. 209-220, (2007)

[10]

Castle J.C., Armour C.D., Lower M., Haynor D., Biery M., Bouzek H., Chen R., Jackson S., Johnson J.M., Rohl C.A., Raymond C.K., Digital genome-wide ncRNA expression, including snoRNAs, across 11 human tissues using polyA-neutral amplification, PLoS One, 5, (2010)

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