Abstract
Endogenous small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), play important regulatory roles in development, hormone signaling, stress responses, and genome stability. These small RNAs induce transcriptional or posttranscriptional gene silencing by guiding heterochromatin formation, mRNA degradation, or translational inhibition. In this chapter, we describe the methods for small RNA discovery in plants by small RNA cloning and deep parallel sequencing. We compare two methods of small RNA library construction: the 5’ phosphate (P)-independent and 5’ phosphate (P)-dependent methods. Deep parallel sequencing of small RNA libraries is discussed by comparing among 454, SBS, and SOLiD technologies.
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Acknowledgments
Research in Jin Laboratory is supported by NSF Career Award MCB-0642843 and a University of California Discovery Grant Bio06-10566 and AES-CE Research Allocation Award PPA-7517H.
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Chellappan, P., Jin, H. (2009). Discovery of Plant MicroRNAs and Short-Interfering RNAs by Deep Parallel Sequencing. In: Cutler, S., Bonetta, D. (eds) Plant Hormones. Methods in Molecular Biology, vol 495. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59745-477-3_11
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DOI: https://doi.org/10.1007/978-1-59745-477-3_11
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