Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant

doi:10.1073/pnas.0808066105

Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant

*Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711;
^†BIO5 Institute and Department of Plant Sciences, University of Arizona, Tucson, AZ 85721; and
^‡Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007

Contributed by Vicki L. Chandler, August 15, 2008 (received for review June 28, 2008)

Abstract

Small RNAs from plants are known to be highly complex and abundant, with this complexity proportional to genome size. Most endogenous siRNAs in Arabidopsis are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. Recent work has demonstrated that the maize MEDIATOR OF PARAMUTATION1 (mop1) gene is a predicted ortholog of RDR2. The mop1 gene is required for establishment of paramutation and maintenance of transcriptional silencing of transposons and transgenes, suggesting the potential involvement of small RNAs. We analyzed small RNAs in wild-type maize and in the isogenic mop1-1 loss-of-function mutant by using Illumina's sequencing-by-synthesis (SBS) technology, which allowed us to characterize the complement of maize small RNAs to considerable depth. Similar to rdr2 in Arabidopsis, in mop1-1, the 24-nucleotide (nt) endogenous heterochromatic short-interfering siRNAs were dramatically reduced, resulting in an enrichment of miRNAs and transacting siRNAs. In contrast to the Arabidopsis rdr2 mutant, the mop1-1 plants retained a highly abundant heterochromatic ≈22-nt class of small RNAs, suggesting a second mechanism for heterochromatic siRNA production. The enrichment of miRNAs and loss of 24-nt heterochromatic siRNAs in mop1-1 should be advantageous for miRNA discovery as the maize genome becomes more fully sequenced.

Footnotes

^§To whom correspondence may be addressed. E-mail: chandler{at}ag.arizona.edu or meyers{at}dbi.udel.edu
Author contributions: L.S. and V.L.C. designed research; K.N., C.L., M.A.-V., P.J.G., and B.C.M. performed research; M.A., D.-H.J., and Y.Y. contributed new reagents/analytic tools; R.S., M.P., and E.D.P. analyzed data; and K.N., C.L., P.J.G., V.L.C., and B.C.M. wrote the paper.
The authors declare no conflict of interest.
Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo [accession nos. GSE12173 (series identifier), GPL7071 (platform identifier), and GSM306487 and GSM306488 (sample identifiers)]. The raw and normalized SBS data are also available at http://mpss.udel.edu/maize; this web site allows users to query data based on physical location, gene identifiers, or by sequence.
This article contains supporting information online at www.pnas.org/cgi/content/full/0808066105/DCSupplemental.