RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats.
In plants, heterochromatin is maintained by a small RNA-based gene silencing mechanism known as RNA-directed DNA methylation (RdDM). RdDM requires the non-redundant functions of two plant-specific DNA-dependent RNA polymerases (RNAP), RNAP IV and RNAP V. RNAP IV plays a major role in siRNA biogenesis, while RNAP V may recruit DNA methylation machinery to target endogenous loci for silencing. Although small RNA-generating regions that are dependent on both RNAP IV and RNAP V have been identified previously, the genomic loci targeted by RNAP V for siRNA accumulation and silencing have not been described extensively. To characterize the RNAP V-dependent, heterochromatic siRNA-generating regions in the Arabidopsis genome, we deeply sequenced the small RNA populations of wild-type and RNAP V null mutant (nrpe1) plants. Our results showed that RNAP V-dependent siRNA-generating loci are associated predominately with short repetitive sequences in intergenic regions. Suppression of small RNA production from short repetitive sequences was also prominent in RdDM mutants including dms4, drd1, dms3 and rdm1, reflecting the known association of these RdDM effectors with RNAP V. The genomic regions targeted by RNAP V were small, with an estimated average length of 238 bp. Our results suggest that RNAP V affects siRNA production from genomic loci with features dissimilar to known RNAP IV-dependent loci. RNAP V, along with RNAP IV and DRM1/2, may target and silence a set of small, intergenic transposable elements located in dispersed genomic regions for silencing. Silencing at these loci may be actively reinforced by RdDM.
Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
Tzuu-fen
TF
Lee
Sai Guna Ranjan
SG
Gurazada
Jixian
J
Zhai
Shengben
S
Li
Stacey A
SA
Simon
Marjori A
MA
Matzke
Xuemei
X
Chen
Blake C
BC
Meyers
D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000378:metabolism*; D019175:DNA Methylation; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D020868:Gene Silencing; D017343:Genes, Plant; D056426:Genetic Loci; D059014:High-Throughput Nucleotide Sequencing; D034741:RNA, Small Interfering / Q000096:biosynthesis* / Q000235:genetics; D017422:Sequence Analysis, DNA; D020086:Short Interspersed Nucleotide Elements
D029681:Arabidopsis Proteins; D034741:RNA, Small Interfering; C499181:RNA polymerase IV, Arabidopsis; C538841:RNA polymerase V, Arabidopsis; D012321:DNA-Directed RNA Polymerases