Small RNAs have a demonstrated and important role in plant development, stress responses, and epigenetic regulation primarily through their role in transcriptional and post-transcriptional silencing of specific target genes and other loci. While most studies have been limited to Arabidopsis, the little that is known about small RNA diversity and evolution suggests that miRNAs are a well-conserved gene regulatory system dating back to lower plants and green algae. This project will develop a sequence dataset of plant small RNAs based on the hypothesis that most if not all plants utilize important small RNA signaling networks. Different plant families are likely to have both common and lineage-specific miRNAs or other small RNAs with important biological roles. Comparative genomics approaches can be applied to distinguish potential miRNAs from siRNAs and to match the miRNAs to the target sequences. This project will develop an unparalleled resource of millions of plant small RNAs for comparative analyses. The project includes sequencing of small RNAs from a diverse and agronomically-relevant set of plant species, focused analyses of important members of the Solanaceae and Poaceae, and development of a small RNA database and web interface for public access and analysis of data. These data will allow the experimental characterization of the majority of biologically important small RNAs for a range of plant species, and will be tremendously useful to a broad set of plant biologists interested in development, stress responses, epigenetics, evolution, RNA biology and other traits impacted by small RNAs.
Publications from the project:
Nobuta et al. (2008) Proc Natl Acad Sci U S A. 105:14958-63. Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant.
Wei et al. (2009) PLoS Genet. 5:e1000728. Detailed analysis of a contiguous 22-Mb region of the maize genome.
De Paoli et al. (2009) RNA. 15:1965-70. Distinct extremely abundant siRNAs associated with cosuppression in petunia.
Swaminathan et al. (2010) Genome Biol. 11:R12. Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses.
Protocols:
Accerbi et al. (2010) Methods Mol Biol. 592:31-50. Methods for isolation of total RNA to recover miRNAs and other small RNAs from diverse species.
Mahalingam et al. (2010) Methods Mol Biol. 592:163-81. Computational methods for comparative analysis of plant small RNAs.
Nobuta et al. (2010) Methods Mol Biol. 592:89-106. Bioinformatics analysis of small RNAs in plants using next generation sequencing technologies.
While this publication was not supported by the NSF award for this project, the libraries were predominantly constructed using this method: Lu et al. (2007) Methods. 43:110-7. Construction of small RNA cDNA libraries for deep sequencing.
While this publication was not supported by the NSF award for this project, the libraries were predominantly constructed using this method: Lu et al. (2007) Methods. 43:110-7. Construction of small RNA cDNA libraries for deep sequencing.
Project Participants
- PI: Blake C. Meyers
- Co-PI: Pamela J. Green
- Post-Doc: Emanuele DePaoli, Kan Nobuta
- Research Scientist: Monica Accerbi
- Web-Masters: Mayumi Nakano, Gayathri Mahalingam, Feray Demirci
- Informatics Students: Prakash Janardhanan, Giriprasad Sridhara, Xia Cheng, Varun Notibula