TY - JOUR
T1 - siRNAs from miRNA sites mediate DNA methylation of target genes
AU - Chellappan, Padmanabhan
AU - Xia, Jing
AU - Zhou, Xuefeng
AU - Gao, Shang
AU - Zhang, Xiaoming
AU - Coutino, Gabriela
AU - Vazquez, Franck
AU - Zhang, Weixiong
AU - Jin, Hailing
N1 - Funding Information:
NSF Career Award MCB-0642843; National Institute of Health R01GM093008-01; University of California Discovery (grant Bio06-10566); AES-CE Research Allocation Award PPA-7517H (to H.J.); NSF (grant DBI-0743797); National Institute of Health (grants RC1AR05868101 and U54AI05716006S1); Monsanto Company (to W.Z.); Swiss National Science Foundation Ambizione (grant PZ00P3_126329/1 to F.V.). Funding for open access charge: NSF Career Award (MCB-0642843).
PY - 2010/11
Y1 - 2010/11
N2 - Arabidopsis microRNA (miRNA) genes (MIR) give rise to 20- to 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicerlike 1 (DCL1) but do not require any RNA-dependent RNA Polymerases (RDRs) or RNA Polymerase IV (Pol IV). Here, we identify a novel class of non-conserved MIR genes that give rise to two small RNA species, a 20- to 22-nt species and a 23- to 27-nt species, at the same site. Genetic analysis using small RNA pathway mutants reveals that the 20- to 22-nt small RNAs are typical miRNAs generated by DCL1 and are associated with Argonaute 1 (AGO1). In contrast, the accumulation of the 23- to 27-nt small RNAs from the miRNA-generating sites is dependent on DCL3, RDR2 and Pol IV, components of the typical heterochromatic small interfering RNA (hc-siRNA) pathway. We further demonstrate that these MIR-derived siRNAs associate with AGO4 and direct DNA methylation at some of their target loci in trans. In addition, we find that at the miRNA-generating sites, some conserved canonical MIR genes also produce siRNAs, which also induce DNA methylation at some of their target sites. Our systematic examination of published small RNA deep sequencing datasets of rice and moss suggests that this type of dual functional MIRs exist broadly in plants.
AB - Arabidopsis microRNA (miRNA) genes (MIR) give rise to 20- to 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicerlike 1 (DCL1) but do not require any RNA-dependent RNA Polymerases (RDRs) or RNA Polymerase IV (Pol IV). Here, we identify a novel class of non-conserved MIR genes that give rise to two small RNA species, a 20- to 22-nt species and a 23- to 27-nt species, at the same site. Genetic analysis using small RNA pathway mutants reveals that the 20- to 22-nt small RNAs are typical miRNAs generated by DCL1 and are associated with Argonaute 1 (AGO1). In contrast, the accumulation of the 23- to 27-nt small RNAs from the miRNA-generating sites is dependent on DCL3, RDR2 and Pol IV, components of the typical heterochromatic small interfering RNA (hc-siRNA) pathway. We further demonstrate that these MIR-derived siRNAs associate with AGO4 and direct DNA methylation at some of their target loci in trans. In addition, we find that at the miRNA-generating sites, some conserved canonical MIR genes also produce siRNAs, which also induce DNA methylation at some of their target sites. Our systematic examination of published small RNA deep sequencing datasets of rice and moss suggests that this type of dual functional MIRs exist broadly in plants.
UR - https://www.scopus.com/pages/publications/78650514497
U2 - 10.1093/nar/gkq590
DO - 10.1093/nar/gkq590
M3 - Article
C2 - 20621980
AN - SCOPUS:78650514497
SN - 0305-1048
VL - 38
SP - 6883
EP - 6894
JO - Nucleic acids research
JF - Nucleic acids research
IS - 20
ER -