Site specific cytosine methylation in rice nonautonomous transposable element nDart

Transposition behavior of nonautonomous a hAT superfamily transposon nDart in rice (Oryza sativa L.)

Transposable elements (TEs) have a significant impact on the evolution of gene function and genome structures. An endogenous nonautonomous transposable element nDart was discovered in an albino mutant that had an insertion in the Mg-protoporphyrin IX methyltransferase gene in rice. In this study, we elucidated the transposition behavior of nDart, the frequency of nDart transposition and characterized the footprint of nDart. Novel independent nDart insertions in backcrossed progenies were detected by DNA blotting analysis. In addition, germinal excision of nDart occurred at very low frequency compared with that of somatic excision, 0-13.3%, in the nDart1-4(3-2) and nDart1-A loci by a locus-specific PCR strategy. A total of 253 clones from somatic excision at five nDart loci in 10 varieties were determined. nDart rarely caused deletions beyond target site duplication (TSD). The footprint of nDart contained few transversions of nucleotides flanking to both sides of the TSD. The predominant footprint of nDart was an 8-bp addition. Precise excision of nDart was detected at a rate of only 2.2%, which occurred at two loci among the five loci examined. Furthermore, the results in this study revealed that a highly conserved mechanism of transposition is involved between maize Ac/Ds and rice Dart/nDart, which are two-component transposon systems of the hAT superfamily transposons in plant species.

Analysis of SCAR marker nucleotide sequences in maize (Zea mays L.) somaclones

SCAR (sequence characterized amplified region) markers allow the reliable identification of unique somaclonal variations. Six SCAR markers were developed previously and were thought to be exclusively characteristic of eight maize somaclones. However, we detected two of these markers in maize lines and a cultivar unrelated to the progenitor line of the somaclones. Therefore, we sequenced these markers and performed bioinformatic searches to understand the molecular events that may underlie the variability observed in the somaclones. All changes were found in noncoding sequences and were induced by different molecular events, such as the insertion of long terminal repeat (LTR) transposon(s), precise miniature inverted repeat transposable element (MITE) excision, microdeletion, recombination, and a change in the pool of mitochondrial DNA. For example, the SCAR marker QR is represented by the two variants QR-A and QR-2. The sequences of the two variants were similar, except for a 457-bp fragment found only in QR-A; this region was denoted as Q. Region Q was flanked by the direct 3-bp repeat 5'-TAA-3' (target site duplication; TSD) and the inverted 14-bp repeat 5'-GGGCCTGTTTGGAA-3' (terminal inverted repeats; TIRs). These features confer the Q region with similarity to the nonautonomic Tourist-like MITE. In two groups of independently produced somaclones, the same features (morphological, molecular) were variable, which confirms the theory of 'hot spots' occurring in the genome. The distribution of one of the SCAR markers was confirmed using Southern blot hybridization. The presence of the same molecular markers in the somaclones and in different non-somaclonal maize variants suggests that in some cases, the same mechanisms determine both in vitro and in vivo variability and that cell culture enhances the rate of heritable genomic changes that naturally occur in living organisms.

Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia

BACKGROUND

It is widely recognized that interspecific hybridization may induce "genome shock", and lead to genetic and epigenetic instabilities in the resultant hybrids and/or backcrossed introgressants. A prominent component involved in the genome shock is reactivation of cryptic transposable elements (TEs) in the hybrid genome, which is often associated with alteration in the elements' epigenetic modifications like cytosine DNA methylation. We have previously reported that introgressants derived from hybridization between Oryza sativa (rice) and Zizania latifolia manifested substantial methylation re-patterning and rampant mobilization of two TEs, a copia retrotransposon Tos17 and a MITE mPing. It was not known however whether other types of TEs had also been transpositionally reactivated in these introgressants, their relevance to alteration in cytosine methylation, and their impact on expression of adjacent cellular genes.

RESULTS

We document in this study that the Dart TE family was transpositionally reactivated followed by stabilization in all three studied introgressants (RZ1, RZ2 and RZ35) derived from introgressive hybridization between rice (cv. Matsumae) and Z. latifolia, while the TEs remained quiescent in the recipient rice genome. Transposon-display (TD) and sequencing verified the element's mobility and mapped the excisions and re-insertions to the rice chromosomes. Methylation-sensitive Southern blotting showed that the Dart TEs were heavily methylated along their entire length, and moderate alteration in cytosine methylation patterns occurred in the introgressants relative to their rice parental line. Real-time qRT-PCR quantification on the relative transcript abundance of six single-copy genes flanking the newly excised or inserted Dart-related TE copies indicated that whereas marked difference in the expression of all four genes in both tissues (leaf and root) were detected between the introgressants and their rice parental line under both normal and various stress conditions, the difference showed little association with the presence or absence of the newly mobilized Dart-related TEs.

CONCLUSION

Introgressive hybridization has induced transpositional reactivation of the otherwise immobile Dart-related TEs in the parental rice line (cv. Matsumae), which was accompanied with a moderate alteration in the element's cytosine methylation. Significant difference in expression of the Dart-adjacent genes occurred between the introgressants and their rice parental line under both normal and various abiotic stress conditions, but the alteration in gene expression was not coupled with the TEs.

Transcriptional activity of rice autonomous transposable element Dart

The rice Dart/nDart transposon system belongs to the hAT superfamily of class II transposons. The nonautonomous element nDart is active in intact rice plants. The autonomous element Dart was identified based on sequence similarity to nDart. Because the rice genome sequence of Nipponbare contains at least 51 Dart elements, it is not clear whether Dart elements are expressed or whether they are transposable. This study characterized for the expression of the predicted ORF of Dart. RNA blotting analysis revealed three transcripts of different lengths. Only the longest transcript (2.5kb) corresponding to the predicted ORF of the Dart element produced a functional TPase. The other transcripts had a frame-shift generating a premature stop codon through alternative splicing. These transcripts were expressed from either of two potentially autonomous Dart elements, Dart01/28 and Dart02. The frequency of alternative splicing differed between the transcripts of the derivative elements. More than 90% of the transcripts from Dart02 were alternatively spliced, compared with only 3% from Dart01/28. The element-specific expression and alternative splicing may control the transposition of nDart.