The Cornucopia of Small RNAs in Plant Genomes

Stacey A Simon,Jia Zeng,Blake C Meyers,Jixian Zhai

doi:10.1007/s12284-008-9008-5

Stacey A Simon, Jia Zeng + Show 2 more

Open Access

https://doi.org/10.1007/s12284-008-9008-5

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Journal: Rice	Publication Date: Aug 15, 2008
Citations: 77	License type: CC BY 2.0

Affiliation: University of Delaware, Biotechnology Institute

Abstract

AbstractRegulatory small RNAs (approximately 20 to 24 nt in length) are produced through pathways that involve several key evolutionarily conserved protein families; the variants of these proteins found in plants are encoded by multigene families and are known as Dicer-like, Argonaute, and RNA-dependent RNA polymerase proteins. Small RNAs include the well-known classes of microRNAs (miRNAs, ~21 nt) and the small-interfering RNAs (siRNAs, ~24 nt). Both of these types of molecules are found across a broad set of eukaryotic species, although the siRNAs are a much larger and more diverse class in plants due to the abundance of heterochromatic siRNAs. Well-studied species such asArabidopsishave provided a foundation for understanding in rice and other species how small RNAs function as key regulators of gene expression. In this paper, we review the current understanding of plant small RNA pathways, including the biogenesis and function of miRNAs, siRNAs, trans-acting siRNAs, and heterochromatic siRNAs. We also examine the evolutionary relationship among plant species of both their miRNAs and the key enzymatic components of the small RNA pathways. Many of the most recent advances in describing small RNAs have resulted from advances in sequencing technologies used for identifying and measuring small RNAs, and these technologies are discussed. Combined with the plethora of genetic tools available to researchers, we expect that the continued elucidation of the identity and functions of plant small RNAs will be both exciting and rewarding.

Highlights

Introduction to small RNAs in plantsSmall RNAs are short (20 to 30 nt), non-coding RNAs that play important roles in both transcriptional and post-transcriptional gene silencing
In a study performed by Nagasaki et al [14], the rice genes known as SHOOTLESS2 (SHL2), SHL4/SHOOT ORGANIZATION2 (SHO2), and SHO1, encoding orthologs of the small RNA-associated Arabidopsis proteins RNAdependent RNA polymerase 6 (RDR6), AGO7, and DCL4, respectively, were shown to play a role in leaf development through the ta-short-interfering RNAs (siRNAs) pathway
Many of the major players in small RNA biogenesis have been identified from intensive work in Arabidopsis

Summary

Introduction

Introduction to small RNAs in plantsSmall RNAs (sRNAs) are short (20 to 30 nt), non-coding RNAs that play important roles in both transcriptional and post-transcriptional gene silencing. This suggests that each plant lineage, including rice, may evolve a unique set of miRNAs. Direct cloning, traditional sequencing, and deep sequencing approaches have discovered many non-conserved miRNAs in rice, and their predicted target genes encode a broad range of proteins, including some transcription factors (Supplementary Table 1).

Results

Conclusion