Plant Hormones pp 121-132 | Cite as

Discovery of Plant MicroRNAs and Short-Interfering RNAs by Deep Parallel Sequencing

  • Padmanabhan Chellappan
  • Hailing Jin
Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 495)

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.

Key words

miRNA siRNA small RNA library construction, 454 SBS 
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Notes

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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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Padmanabhan Chellappan
    • 1
  • Hailing Jin
    • 1
  1. 1.Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome BiologyUniversity of California RiversideRiversideUSA

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