Discovery of plant microRNAs and short-interfering RNAs by deep parallel sequencing.
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.
Chellappan
Padmanabhan
P
Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California Riverside, CA, USA.
Jin
Hailing
H
D001483:Base Sequence; D003001:Cloning, Molecular / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D035683:MicroRNAs / Q000235:genetics*; D010944:Plants / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods*
D035683:MicroRNAs; D018749:RNA, Plant; D034741:RNA, Small Interfering