The pericentromeric heterochromatin of the grass Zingeria biebersteiniana (2n = 4) is composed of Zbcen1-type tandem repeats that are intermingled with accumulated dispersedly organized sequences.

DNA reassociation and hydroxyapatite chromatography were used to isolate high-copy DNA of the grass Zingeria biebersteiniana (2n = 4). In situ hybridization demonstrated that the DNA isolated was enriched for pericentromere-specific repetitive sequences. One abundant pericentromere-specific component is the differentially methylated tandem-repeat family Zbcen1. Other sequences isolated, Zb46 and Zb47A, are dispersed and display similarity to parts of the gypsy- and copia-like retrotransposable elements of other grasses. In situ hybridization with the copia-like sequence Zb47A resulted in dispersed labelling along the chromosome arms, with a significant signal accumulation in the pericentromeric region of all chromosomes. It is concluded that the pericentromeric heterochromatin of Z. biebersteiniana is composed of members of the Zbcen1 tandem repeat family and that these tandem arrays are intermingled with accumulated putative copia-like retrotransposon sequences. An observed Rab1 interphase orientation suggests that the length of the chromosomes rather than the genome size is the determining factor of the Rab1 phenomenon.     

绿豆Ty1／Copia类反转录转座子逆转录酶序列的克隆和分析

利用Ty1/copia类反转录转座子的保守位点设计简并引物,从绿豆(Vignaradiata(L.)Wilczek)基因组中扩增得到了反转录转座子的逆转录酶序列。对扩增得到的约270bp的片段进行分离和克隆,并随机挑选了40个克隆进行测序,结果得到了36个单独的核酸序列,其中18个含有移码突变或终止子。根据序列比对,这些克隆可分为9组以及单个的9种。这40个克隆中,核酸序列相似性从8%到100%,显示出其核酸序列的高度异质性。将这些克隆的核酸序列与来自其他种植物的相应序列进行谱系分析,发现有些克隆与来自其他种植物的相应序列的亲缘关系比这些克隆之间更为接近。斑点杂交显示Ty1/copia反转录转座子约占绿豆基因组的9.3%。     

Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon

Sequence similarities exist between terminal inverted repeats (TIRs) of some miniature inverted-repeat transposable element (MITE) families isolated from a wide range of organisms, including plants, insects, and humans, and TIRs of DNA transposons from the pogo family. We present here evidence that one of these MITE families, previously described for Arabidopsis thaliana, is derived from a larger element encoding a putative transposase. We have named this novel class II transposon Lemi1. We show that its putative product is related to transposases of the Tc1/mariner superfamily, being closer to the pogo family. A similar truncated element was found in a tomato DNA sequence, indicating an ancient origin and/or horizontal transfer for this family of elements. These results are reminiscent of those recently reported for the human genome, where other members of the pogo family, named Tiggers, are believed to be responsible for the generation of abundant MITE-like elements in an early primate ancestor. These results further suggest that some MITE families, which are highly reiterated in plant, insect, and human genomes, could have arisen from a similar mechanism, implicating pogo-like elements.     

Isolation and Characterization of Ty1/copia-like Reverse Transcriptase Sequences from Mung Bean (Vigna radiata)

Ty1/copia-like sequences were amplified from mung bean (Vigna radiata (L.) Wilczek) genomic DNA, by PCR with degenerate oligonucleotide primers corresponding to highly conserved domains in the Ty1/copia-like retrotransposons. PCR fragments of roughly 270 bp were isolated and cloned, and forty clones were sequenced. Thirty-six of the forty clones had unique nucleotide sequences, and eighteen clones had a frameshift, a stop codon, or both. Alignment of the nucleotide sequences indicated that these clones, denoted Tvr, fell into nine subgroups and nine ungrouped sequences. The nucleotide sequence similarity between these elements ranged from 8% to 100%, which indicates high level of sequence heterogeneity among these clones. A phylogenetic analysis comparing these clones with corresponding sequences from other plant species showed that some of the Tvr clones are more closely related to Ty1/copia-like retrotransposons from other species than to other Tvr clones. Dot blot analysis revealed that Ty1/copia-like retrotransposons comprise about 9.3% of the mung bean genome.     

Nucleotide sequence of the intracisternal A-particle genome inserted 5'' to the interleukin-3 gene of the leukemia cell line WEHI-3B.

The nucleotide sequence of the intracisternal A-particle genome IAP-IL3 is presented. This IAP element was found to have inserted upstream of the promoter of the interleukin-3 gene of the leukemia cell line WEHI-3B. IAP-IL3 is 5095 bp in length, with identical long terminal repeats (LTRs) of 337 bp. The LTRs show many of the conserved sequence elements identified in other retroviruses. Comparison with other available sequences of IAP genomes indicates that IAP-IL3 is a deleted type I element. It carries a deletion covering the 3' end of the putative IAP gag gene and extending into the 5' end of the putative IAP pol gene. IAP-IL3 has extensive sequence homology with an IgE-binding factor cDNA and evidence is presented indicating that it was derived from a member of the mouse IAP sequence family. Comparison between the pol region of IAP-IL3 and other retroviruses suggests that IAP-IL3 is most closely related to type B and type D retroviruses.     

Functional and Structural Divergence of an Unusual LTR Retrotransposon Family in Plants

Retrotransposons with long terminal repeats (LTRs) more than 3 kb are not frequent in most eukaryotic genomes. Rice LTR retrotransposon, Retrosat2, has LTRs greater than 3.2 kb and two open reading frames (ORF): ORF1 encodes enzymes for retrotransposition whereas no function can be assigned to ORF0 as it is not found in any other organism. A variety of experimental and in silico approaches were used to determine the origin of Retrosat2 and putative function of ORF0. Our data show that not only is Retrosat2 highly abundant in the Oryza genus, it may yet be active in rice. Homologs of Retrosat2 were identified in maize, sorghum, Arabidopsis and other plant genomes suggesting that the Retrosat2 family is of ancient origin. Several putatively cis-acting elements, some multicopy, that regulate retrotransposon replication or responsiveness to environmental factors were found in the LTRs of Retrosat2. Unlike the ORF1, the ORF0 sequences from Retrosat2 and homologs are divergent at the sequence level, 3D-structures and predicted biological functions. In contrast to other retrotransposon families, Retrosat2 and its homologs are dispersed throughout genomes and not concentrated in the specific chromosomal regions, such as centromeres. The genomic distribution of Retrosat2 homologs varies across species which likely reflects the differing evolutionary trajectories of this retrotransposon family across diverse species.