Nov

13

Custom MicroRNA Microarray – a Tool for Plant Research

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coconut_chips_blog

Many recent studies report that miRNAs control the key components of signaling pathways and thereby regulate related development processes in plants.  LC Sciences offers several options for study of plant microRNA.  In addition to our standard microarrays designed for all plants in the miRBase 14.0 (1,117 unique miRs) and the Plant MicroRNA Database 1.0 (5,690 unique miRs), our custom microfluidic platform enables the synthesis of made to order custom plant microarrays.

Researchers at the Laboratory of Tropic Biological Resources, Hainan University, China utilized a custom plant microRNA microarray from LC Sciences to study cellular development in coconut, a key plantation crop in the tropical parts of the world1. The custom µparaflo® microfluidic chip contained 653 unique plant miRNAs of release version 10.1 (http://www.mirbase.org/), representing 877 miRNAs from 17 plant species. The 877 miRNAs comprised 154 from Arabidopsis thaliana, 115 from Oryza sativa, 187 from Physcomitrella patens, 100 from Populus trichocarpa, 43 from Zea mays and 278 from 12 other plant species.

Comparative analyses of the miRNA expression profiles between developmental stages of coconut endosperm showed that several miRNAs were differentially expressed in mature tissue. Differential expression was confirmed using real-time PCR. The contrasting expression patterns between the two developmental stages suggested that miRNAs play a role in tissue development and compound metabolism of coconut endosperm.

Li D, Zheng Y, Wan L, Zhu X, Wang Z. (2009) Differentially expressed microRNAs during solid endosperm development in coconut (Cocos nucifera L.). Scientia Horticulture 122(4), 666-69. [abstract]

Oct

8

Plant MicroRNA Database Arrays Now Available

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LC Sciences now has standard arrays available for all species listed in the newly created Plant MicroRNA Database (PMRD). 

The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated by the database organizers. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser.

In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, the possible target genes for each miRNA with a predicted interaction site are included in the database.  

In addition, miRNA expression profiles are provided in the PMRD, including some data generated with previous versions of  LC Sciences’ Plants microRNA Microarray.

The PMRD is freely available at http://bioinformatics.cau.edu.cn/PMRD.

  1. Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z.  (2009) PMRD: plant microRNA database.  Nucleic Acids Res  [Epub ahead of print]