Academic journal article Genetics

Large-Scale Survey of Cytosine Methylation of Retrotransposons and the Impact of Readout Transcription from Long Terminal Repeats on Expression of Adjacent Rice Genes

Academic journal article Genetics

Large-Scale Survey of Cytosine Methylation of Retrotransposons and the Impact of Readout Transcription from Long Terminal Repeats on Expression of Adjacent Rice Genes

Article excerpt

ABSTRACT

Transposable elements (TEs) represent ~45% of the human genome and 50-90% of some grass genomes. While most elements contain inactivating mutations, others are reversibly inactivated (silenced) by epigenetic mechanisms, including cytosine methylation. Previous studies have shown that retrotransposons can influence the expression of adjacent host genes. In this study, the methylation patterns of TEs and their flanking sequences in different tissues were undertaken using a novel technique called transposon methylation display (TMD). TMD was successfully applied on a highly copied (~1000 copies), newly amplified LTR retrotransposon family in rice called Dasheng. We determined that the methylation status of a subset of LTRs varies in leaves vs. roots. In addition, we determined that tissue-specific LTR methylation correlated with tissue-specific expression of the flanking rice gene. Genes showing tissue-specific expression were in opposite orientation relative to the LTR. Antisense transcripts were detected in the tissue where the sense transcripts from that gene were not detected. Comparative analysis of Dasheng LTR methylation in the two subspecies, japonica vs. indica revealed LTR-mediated differences in subspecies gene expression. Subspecies-specific expression was due either to polymorphic Dasheng insertion sites between the two subspecies or to subspecies-specific methylation of LTRs at the same locus accounted for observed differences in the expression of adjacent genes.

TRANSPOSABLE elements (TEs) are mobile DNA sequences that have the ability to "jump" to new locations in the genome. They are divided into two classes. Class I retrotransposons, or retroelements, move to a new genomic location via an RNA intermediate that is reverse-transcribed into an extrachromosomal cDNA that then integrates into a new location (FINNEGAN 1989). There are two types of retrotransposons: LTR retrotransposons, flanked by long terminal repeats (LTRs) that include the promoter and terminator regions and non-LTR elements (such as long interspersed nuclear elements, (LINEs) and short interspersed nuclear elements, (SINEs) that use an internal promoter or are transcribed from a flanking gene's promoter. Transcription of LTR retrotransposons initiates from a promoter in the 59 LTR and terminates in the 39 LTR. However, because the 59 and 39 LTRs are identical upon insertion, transcripts can initiate from the promoter in the 39 LTR and read out into flanking host sequences. In addition, transcripts can read out from solo LTRs, which are produced by homologous recombination between LTRs. The replicative mode of transposition of retroelements allows them to reach a high copy number (up to 1 million copies). In some plants they represent up to 80% of the genome (BENNETZEN and KELLOGG 1997; FESCHOTTE et al. 2002). On the other hand, class II elements, also called DNA elements or transposons, move directly by a cut and paste mechanism (FINNEGAN 1989).

Plants protect their genes by targeting TEs for methylation (KUMAR and BENNETZEN 1999; ZILBERMAN and HENIKOFF 2004). As such, TEs in plant genomes are hypermethylated in comparison with host genes and are said to be epigenetically silenced (BENNETZEN et al. 1994; FLAVELL 1994; MARTIENSSEN 1998; RABINOWICZ et al. 2003; KHODOSEVICH et al. 2004; OKAHARA et al. 2004; LAVIE et al. 2005). Inactive TEs in plants are often heavily methylated (BENNETZEN et al. 1994; FLAVELL 1994; MARTIENSSEN 1998) and can be reactivated in genetic backgrounds containing methylation-defective mutants or during tissue culture (MIURA et al. 2001; SINGER et al. 2001). For example, in Arabidopsis thaliana, a higher frequency of mutation in genetic backgrounds containing methylation-defectivemutations, such as ddm1, has been associated with the transcriptional activation of endogenous TEs and the subsequent insertion of a member of at least one TE family into Arabidopsis genes (MIURA et al. 2001; SINGER et al. …

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