Working with Natural Antisense Transcripts

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Published on: September 27, 2012

In January of this year Nucleic Acids Research published a paper describing a database of plant natural antisense transcripts (NATs), PlantNATsDB (Chen, Yuan et al., 2012). It contains around 2 million NATs from 69 plant species, and has a simple viewer showing the two loci involved in each NAT, any overlap, the NAT type, and an option for more detail. It is also possible for search for NATs for specific loci. It is important to note however that the database was last updated a year ago, in September 2011.

This month’s Plant Methods also features a NATs tool, a protocol for NAT identification in plant tissue (Collani and Baraccia, 2012).  It is a simple PCR based method, and relies on prior knowledge of the existence of a NAT, as specific primers are needed. Used in association with PlantNATsDB, this is a useful technique. A researcher who wants to investigate NAT-mediated gene regulation in their favourite molecular process can search PlantNATsDB for the loci that encode relevant proteins or transcription factors, and if they are found, use Collani and Baraccia’s method to find tissue localisation.

A third NATs method was published in May in Plant Molecular Biology (Lembke, Nichiyama Jr, et al., 2012). This time, the researchers used a custom oligonucleotide array to identify groups of antisense transcripts in sugar cane which were affected by drought treatment. They found a set of 22 genes with sense and antisense transcripts that behave the same as each other in normal and drought conditions, and used qPCR to validate the results.

The Lembeke, Nichiyama et al. (2012) approach appears to be the most revealing and in depth way of exploring sense and antisense transcripts, and is able to find novel NATs. However making a custom array is time and energy intensive, so PlantNATsDB is a highly useful resource for researchers investigating natural antisense transcripts.

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