Apr

14

High-Throughput Approaches for miRNA Expression Analysis

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Book Series Methods in Molecular Biology
ISSN 1064-3745 (Print) 1940-6029 (Online)
Volume Volume 592
Book Plant MicroRNAs
Publisher Humana Press
DOI 10.1007/978-1-60327-005-2
Copyright 2010
ISBN 978-1-60327-004-5 (Print) 978-1-60327-005-2 (Online)
DOI 10.1007/978-1-60327-005-2_8
Pages 107-125
Subject Collection Biomedical and Life Sciences
SpringerLink Date Saturday, October 03, 2009

By: Cheng Lu1, Frédéric Souret2

miRNAs have emerged as key regulators of gene expression in both plants and animals. These small (generally 21–22 nt) RNA molecules, originated from primary “hairpin” transcripts, can induce translational suppression or direct mRNA cleavage. Similar to regular mRNAs, the expression of miRNAs is highly regulated. Their expression pattern could provide critical clues to understanding miRNA functions. However, many previously identified miRNA families have multiple paralogous loci. Within each family, different members are often closely related and sometimes give rise to identical miRNAs. This poses critical challenges in the analysis of individual miRNA genes. This chapter describes several methods that are commonly used for miRNA expression analysis, including high-throughput sequencing, microarrays, and briefly discusses qRT-PCR, northern blotting, and other approaches used for data validation.

Oct

26

Tools And Information for Plant Scientists Studying microRNA

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Web Links

PMRD:  plant miRNA Database
http://bioinformatics.cau.edu.cn/PMRD/

This site offers a complete list of all publicly known plant miRNA sequences.  The database is composed of a total of 8,433 sequences including all known sequences in the miRBase database.

PlantGDB
http://www.plantgdb.org/

This website is dedicated entirely to plant miRNA and provides many useful tools such as sequence browser & assemblies, genome browser, and other tools and datasets.

miRU: Plant miRNA Potential Target Finder
http://bioinfo3.noble.org/miRNA/miRU.htm

This website allows users to predict plant miRNA target genes.  By entering a small RNA sequence (19-28nt) the program will report all potential complimentary sequences.

UPC: A Resource for Predicting and Comparing Plant microRNAs
http://www3a.biotec.or.th/micropc/index.html

Here users can predict and compare plant miRNA sequences.  This site includes 128 miRNA families, 125 plant species, and 2,995 protein targets.

The UEA plant sRNA toolkit
http://srna-tools.cmp.uea.ac.uk/targets/

Users can input sequences up to 50 nucleotides in length in FASTA format to run target predictions for their sequence dataset.

  Read more

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]