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Originally published as Genetics Published Articles Ahead of Print on October 1, 2008.
Genetics, Vol. 180, 1927-1944, December 2008, Copyright © 2008
doi:10.1534/genetics.108.092395
Unstable RNAi Effects Through Epigenetic Silencing of an Inverted Repeat Transgene in Chlamydomonas reinhardtii
Tomohito Yamasaki*,
Hitoshi Miyasaka
and
Takeshi Ohama*,1
* Department of Environmental Systems Engineering, Kochi University of Technology, Tosayamada, Kochi 782-8502, Japan and Environmental Research Center, Kansai Electric Power Co., 1-7 Seika-cho, Souraku-gun, Kyoto 619-0237, Japan
1 Corresponding author: Department of Environmental Systems Engineering, Kochi University of Technology (KUT), Tosayamada, Kochi 782-8502, Japan.
E-mail: ohama.takeshi{at}kochi-tech.ac.jp
RNA interferences in the unicellular green alga, Chlamydomonas reinhardtii, can be silenced. We have used the silencing of a transgene (aadA) that confers resistance to spectinomycin to investigate the mechanisms responsible for silencing by an artificial inverted repeat (IR) of the aadA gene. The IR construct provided strong silencing, but the RNAi efficiency varied among subclones of a single RNAi-transformed strain with successive cell divisions. Northern blot analyses revealed an inverse correlation between the copy number of the hairpin RNA and the spectinomycin resistance of the subclones. There is an inverse correlation between the efficiency of RNAi and the frequency of methylated CpG (*CpG) in the silenced region. No significant methylated cytosine was observed in the target aadA gene, which suggests the absence of RNA-directed DNA methylation in trans. Several experiments suggest the existence of an intrinsic IR sequence-dependent but a transcription-independent DNA methylation system in C. reinhardtii. The correlation between the *CpG levels and the IR transcript implies the existence of IR DNA-dependent DNA methylation. Treatment of RNAi-induced cells with a histone deacetylase inhibitor, Trichostatin A, rapidly increased the amount of the hairpin RNA and suggests that transcription of the silencer construct was repressed by *CpG-related silencing mechanisms.