Resources for Small Regulatory RNAs
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- Abstract
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- Literature Cited
Abstract
In the past fifteen years, new classes of regulatory RNAs have been discovered, previously hidden in the transcriptome mostly due to their small size. These small regulatory RNAs include small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi?interacting RNAs (piRNAs). Numerous databases have been developed to store information about these small regulatory RNAs, and many tools have been developed to work with the data. This overview introduces the reader to the many resources available for working with small regulatory RNAs. Curr. Protoc. Mol. Biol. 87:19.8.1?19.8.13. © 2009 by John Wiley & Sons, Inc.
Keywords: miRNA; piRNA; siRNA; regulatory RNAs
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PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Exogenous Small RNAs: siRNAs and shRNAs
- MicroRNA Genes
- Piwi‐Interacting RNAs
- General Resources that Include Small Regulatory RNAs
- Concluding Remarks
- Acknowledgments
- Literature Cited
- Figures
- Tables
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Figure 19.8.1 Partial results page from searching the NCBI Probe Database. To get to this screen, enter the terms egr1 human siRNA into the Entrez Probe Database search box. This will result in a list of probes containing these search terms. Click on the first entry (Pr000209.1) and information about that probe is displayed. This figure shows the details of an entry and includes information including the Sequence, Experimental Results, References, Submission Details, and other information about the probe. View Image -
Figure 19.8.2 Output of Experimental Results from searching the Probe Database. This figure shows the details of the experimental results for Probe 000209.1. Click on the link below the publication information in the Results section to view the page in this figure. View Image -
Figure 19.8.3 A screen shot from the UCSC Genome Browser (human hg18 assembly) showing some representative small regulatory RNA features in the region chr15:60,330,001‐60,930,000. The “piRNA clusters” track was generated by clicking on “add custom tracks” and using data from Aravin et al. () after converting genome coordinates from the hg17 assembly. See the accompanying text for details of BED browser files and genome coordinate conversion. Several gene sets (RefSeq and Ensembl) of primarily protein‐coding genes are shown. Note that the miRNA miR‐90 appears in the Ensembl track, as well as the RNA Genes and snoRNABase/miRBase tracks. The EvoFold track indicates predicted functional RNA structures, and the TargetScan track (displayed in dense format) shows predicted miRNA regulatory target sites (in the TLN2 3′ UTR). The highly configurable Conservation track shows the range of conservation across this genome region. Note that miR‐190 and exons of the protein‐coding gene TLN2 are conserved to zebrafish, whereas many other regions tend to be conserved in placental mammals (including armadillo) but not in other vertebrates. View Image
Videos
Literature Cited
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