Antisense transcription is a widespread and pervasive phenomenon affecting about 25% of eukaryotic genes, but its origins and functions are unknown. Small RNAs such as microRNAs (miRNAs) and trans- acting small-interfering RNAs (ta-siRNAs) are also pervasive in metazoans and plants and play important roles in gene regulation, development, and disease, but to date the predictive power of computational methods for plant and animal small RNA discovery is limited. Based on computational analysis of four independent Arabidopsis transcriptome databases, it is hypothesized that miRNAs and ta-siRNAs are triggers for antisense transcription in Arabidopsis. This hypothesis will be rigorously tested using computational and statistical methods on the entire Arabidopsis and rice genomes. Using known and hypothesized miRNA and ta-siRNA target gene antisense transcription as a learning set, a new algorithm will be developed based on antisense transcription combined with established miRNA prediction methods to discover new candidate miRNAs, ta-siRNAs and their hypothetical target genes. The identified putative small RNA target genes would be inherently """"""""interesting"""""""" as potential key regulators of growth and development. The predicted novel small RNAs and their targets will be experimentally validated with a facile transient assay system, RNA blots and rapid amplification of cDNA ends (RACE) to prove novel small RNA- directed cleavage of targets. Transcriptome profiling on whole genome tiling arrays of known mutants that affect small RNAs and antisense transcription will determine the extent of causality of antisense and small RNAs. A novel algorithm for small RNA prediction based on a phenomenon shared between plants and animals may have general utility for small RNA discovery in any organism for which deep genomic resources exist, for genome annotation, and for better understanding of human disease etiologies. Such a predictive tool would also have utility in the fields of functional genomics and evolutionary biology. A better understanding of small RNAs and their roles in gene regulation may shed light on """"""""the RNA World"""""""" and the origins of life.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Exploratory/Developmental Grants (R21)
Project #
3R21GM077245-02S1
Application #
7906357
Study Section
Special Emphasis Panel (ZRG1-GGG-J (10))
Program Officer
Hagan, Ann A
Project Start
2007-09-28
Project End
2010-08-31
Budget Start
2009-09-01
Budget End
2010-08-31
Support Year
2
Fiscal Year
2009
Total Cost
$48,286
Indirect Cost
Name
Texas Tech University
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
041367053
City
Lubbock
State
TX
Country
United States
Zip Code
79409
Rock, Christopher D (2013) Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development? Trends Plant Sci 18:601-10
Ou-Yang, Fangqian; Luo, Qing-Jun; Zhang, Yue et al. (2013) Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice. Funct Integr Genomics 13:207-16
Jia, Fan; Rock, Christopher D (2013) Jacalin lectin At5g28520 is regulated by ABA and miR846. Plant Signal Behav 8:e24563
Jia, Fan; Rock, Christopher D (2013) MIR846 and MIR842 comprise a cistronic MIRNA pair that is regulated by abscisic acid by alternative splicing in roots of Arabidopsis. Plant Mol Biol 81:447-60
Luo, Qing-Jun; Mittal, Amandeep; Jia, Fan et al. (2012) An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis. Plant Mol Biol 80:117-29
Richardson, Casey R; Luo, Qing-Jun; Gontcharova, Viktoria et al. (2010) Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes. PLoS One 5:e10710
Luo, Qing-Jun; Samanta, Manoj P; Köksal, Fatih et al. (2009) Evidence for antisense transcription associated with microRNA target mRNAs in Arabidopsis. PLoS Genet 5:e1000457
Jia, Fan; Gampala, Srinivas S L; Mittal, Amandeep et al. (2009) Cre-lox univector acceptor vectors for functional screening in protoplasts: analysis of Arabidopsis donor cDNAs encoding ABSCISIC ACID INSENSITIVE1-like protein phosphatases. Plant Mol Biol 70:693-708