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Originally published as Genetics Published Articles Ahead of Print on April 3, 2007.

Genetics, Vol. 176, 749-761, June 2007, Copyright © 2007
doi:10.1534/genetics.107.071902

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The Centromeric Retrotransposons of Rice Are Transcribed and Differentially Processed by RNA Interference

Pavel Neumann, Huihuang Yan and Jiming Jiang1

Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706

1 Corresponding author: Department of Horticulture, University of Wisconsin, 1575 Linden Dr., Madison, WI 53706.
E-mail: jjiang1{at}wisc.edu

Retrotransposons consist of significant portions of many complex eukaryotic genomes and are often enriched in heterochromatin. The centromeric retrotransposon (CR) family in grass species is colonized in the centromeres and highly conserved among species that have been diverged for >50 MY. These unique characteristics have inspired scientists to speculate about 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.




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X. Li, X. Wang, K. He, Y. Ma, N. Su, H. He, V. Stolc, W. Tongprasit, W. Jin, J. Jiang, et al.
High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression
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[Abstract] [Full Text] [PDF]


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Copyright © 2007 by the Genetics Society of America.