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doi:10.1534/genetics.107.071902
A more recent version of this article appeared on June 1, 2007.
REGULAR RESEARCH PAPERS |
The centromeric retrotransposons of rice are transcribed and differentially processed by RNAi
Pavel Neumann 1, Huihuang Yan 1 and Jiming Jiang 1*
1 University of Wisconsin-Madison
* To whom correspondence should be addressed. E-mail: jjiang1{at}facstaff.wisc.edu.
Submitted on February 9, 2007
Revised on March 7, 2007
Accepted on 12 March 2007
Retrotransposons consist of significant portions of many complex eukaryotic genomes and are often enriched in heterochromatin. The centromeric retrotransposon (CR) family in the grass species is colonized in the centromeres and highly conserved among species that have been diverged for more than 50 Myr. These unique characteristics have inspired scientists to speculate the roles of CR elements in organization and function of centromeric chromatin. Here we report that the CRR (CR of Rice) elements in rice are highly enriched in chromatin associated with H3K9me2, a hallmark for heterochromatin. CRR elements were transcribed in root, leaf and panicle tissues, suggesting a constitutive transcription of this retrotransposon family. However, the overall transcription level was low and the CRR transcripts appeared to be derived from relatively few loci. The majority of the CRR transcripts had chimerical structures and contained only partial CRR sequences. We detected small RNAs (smRNAs) cognate to nonautonomous CRR1 (noaCRR1) and CRR1, but not CRR2 elements. This result was also confirmed by in-silico analysis of rice smRNA sequences. These results suggest that different CRR subfamilies may play different roles in the RNAi-mediated pathway for formation and maintenance of centromeric heterochromatin.
Key Words: Centromeric retrotransposon, Heterochromatin, Small RNA, Transcription
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