Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007 Mar 13;104(11):4536-41.
doi: 10.1073/pnas.0611456104. Epub 2007 Mar 5.

Role of RNA polymerase IV in plant small RNA metabolism

Xiaoyu Zhang  1 , Ian R Henderson, Cheng Lu, Pamela J Green, Steven E Jacobsen
Affiliations

Role of RNA polymerase IV in plant small RNA metabolism

Xiaoyu Zhang et al. Proc Natl Acad Sci U S A. .

Abstract

In addition to the three RNA polymerases (RNAP I-III) shared by all eukaryotic organisms, plant genomes encode a fourth RNAP (RNAP IV) that appears to be specialized in the production of siRNAs. Available data support a model in which dsRNAs are generated by RNAP IV and RNA-dependent RNAP 2 (RDR2) and processed by DICER (DCL) enzymes into 21- to 24-nt siRNAs, which are associated with different ARGONAUTE (AGO) proteins for transcriptional or posttranscriptional gene silencing. However, it is not yet clear what fraction of genomic siRNA production is RNAP IV-dependent, and to what extent these siRNAs are preferentially processed by certain DCL(s) or associated with specific AGOs for distinct downstream functions. To address these questions on a genome-wide scale, we sequenced approximately 335,000 siRNAs from wild-type and RNAP IV mutant Arabidopsis plants by using 454 technology. The results show that RNAP IV is required for the production of >90% of all siRNAs, which are faithfully produced from a discrete set of genomic loci. Comparisons of these siRNAs with those accumulated in rdr2 and dcl2 dcl3 dcl4 and those associated with AGO1 and AGO4 provide important information regarding the processing, channeling, and functions of plant siRNAs. We also describe a class of RNAP IV-independent siRNAs produced from endogenous single-stranded hairpin RNA precursors.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
The lengths of sRNAs that perfectly matched the Arabidopsis genomic sequence in wild-type, nrpd1a/1b, nrpd2a/2b, and the F1 progenies from a cross between nrpd1a/1b and nrpd2a/2b. (a) All sRNAs. (b) siRNAs (miRNAs and tasiRNAs were excluded). y axis, the number of individual sRNA sequences of a certain size.
Fig. 2.
Fig. 2.
The locus IR71 as an example of siRNAs produced from single-stranded hairpin RNA precursors. (a) All individual siRNAs at IR71 that matched a unique position in the genome isolated from wild type (454 or MPSS), nrpd1a/1b (454), and rdr2 (MPSS). Vertical color bars, individual siRNAs; pink horizontal bars, the two arms of the inverted repeat. siRNAs shown above the inverted repeats matched the Watson strand, and those below matched the Crick strand of the genome. (b) Examples of siRNAs produced from the imperfectly matched regions (red dots) of the predicted single-stranded hairpin of IR71. Horizontal bars, siRNAs that match the left (above the alignment) or right arm (below the alignment).
Fig. 3.
Fig. 3.
Immediate restoration of siRNA production and RNA-directed DNA methylation. (a) Northern blot analysis of siRNAs derived from the FWA and siRNA02 loci (16, 19, 38). miRNA 159 is shown as control. (b) Bisulfite sequencing analysis of DNA methylation at MEA-ISR.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Wassenegger M. Cell. 2005;122:13–16. - PubMed
    1. Jones-Rhoades MW, Bartel DP, Bartel B. Annu Rev Plant Biol. 2006;57:19–53. - PubMed
    1. Zhang B, Pan X, Cobb GP, Anderson TA. Dev Biol. 2006;289:3–16. - PubMed
    1. Meins F, Jr, Si-Ammour A, Blevins T. Annu Rev Cell Dev Biol. 2005;21:297–318. - PubMed
    1. Vaucheret H. Genes Dev. 2006;20:759–771. - PubMed

Publication types