title: A genomic-scale artificial microRNA library as a tool to investigate the functionally redundant gene space in Arabidopsis.
abstract: Traditional forward genetic screens are limited in the identification of homologous genes with overlapping functions. Here, we report the analyses and assembly of genome-wide protein family definitions that comprise the largest estimate for the potentially redundant gene space in Arabidopsis thaliana. On this basis, a computational design of genome-wide family-specific artificial microRNAs (amiRNAs) was performed using high-performance computing resources. The amiRNA designs are searchable online (http://phantomdb.ucsd.edu). A computationally derived library of 22,000 amiRNAs was synthesized in 10 sublibraries of 1505 to 4082 amiRNAs, each targeting defined functional protein classes. For example, 2964 amiRNAs target annotated DNA and RNA binding protein families and 1777 target transporter proteins, and another sublibrary targets proteins of unknown function. To evaluate the potential of an amiRNA-based screen, we tested 122 amiRNAs targeting transcription factor, protein kinase, and protein phosphatase families. Several amiRNA lines showed morphological phenotypes, either comparable to known phenotypes of single and double/triple mutants or caused by overexpression of microRNAs. Moreover, novel morphological and abscisic acid-insensitive seed germination mutants were identified for amiRNAs targeting zinc finger homeodomain transcription factors and mitogen-activated protein kinase kinase kinases, respectively. These resources provide an approach for genome-wide genetic screens of the functionally redundant gene space in Arabidopsis.
authors: Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, California 92093-0116.
authors: Felix
authors: F
authors: Hauser
authors: Wenxiao
authors: W
authors: Chen
authors: Ulrich
authors: U
authors: Deinlein
authors: Kenneth
authors: K
authors: Chang
authors: Stephan
authors: S
authors: Ossowski
authors: Joffrey
authors: J
authors: Fitz
authors: Gregory J
authors: GJ
authors: Hannon
authors: Julian I
authors: JI
authors: Schroeder
mesh_terms: D000040:Abscisic Acid / Q000494:pharmacology; D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D035264:Flowers / Q000187:drug effects / Q000254:growth & development; D017343:Genes, Plant / Q000235:genetics*; D005820:Genetic Testing; D015698:Genomic Library; D023281:Genomics / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D005810:Multigene Family; D009154:Mutation / Q000235:genetics; D010641:Phenotype; D018515:Plant Leaves / Q000187:drug effects / Q000254:growth & development; D020543:Proteome / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D035683:MicroRNAs; D020543:Proteome; D000040:Abscisic Acid
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