scholarly journals Non-long terminal repeat (non-LTR) retrotransposons: mechanisms, recent developments, and unanswered questions

Mobile DNA ◽  
2010 ◽  
Vol 1 (1) ◽  
pp. 15 ◽  
Author(s):  
Jeffrey S Han
Keyword(s):  
Long Terminal Repeat ◽  
Terminal Repeat ◽  
Ltr Retrotransposons ◽  
Recent Developments

scholarly journals Role of RNA Polymerase III Transcription Factors in the Selection of Integration Sites by the Dictyostelium Non-Long Terminal Repeat Retrotransposon TRE5-A

2006 ◽  
Vol 26 (22) ◽  
pp. 8242-8251 ◽  
Author(s):  
Oliver Siol ◽  
Moustapha Boutliliss ◽  
Thanh Chung ◽  
Gernot Glöckner ◽  
Theodor Dingermann ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase ◽  
Long Terminal Repeat ◽  
Integration Site ◽  
Rna Polymerase Iii ◽  
Terminal Repeat ◽  
Trna Genes ◽  
Ltr Retrotransposons ◽  
Polymerase Iii

ABSTRACT In the compact Dictyostelium discoideum genome, non-long terminal repeat (non-LTR) retrotransposons known as TREs avoid accidental integration-mediated gene disruption by targeting the vicinity of tRNA genes. In this study we provide the first evidence that proteins of a non-LTR retrotransposon interact with a target-specific transcription factor to direct its integration. We applied an in vivo selection system that allows for the isolation of natural TRE5-A integrations into a known genomic location upstream of tRNA genes. TRE5-A frequently modified the integration site in a way characteristic of other non-LTR retrotransposons by adding nontemplated extra nucleotides and generating small and extended target site deletions. Mutations within the B-box promoter of the targeted tRNA genes interfered with both the in vitro binding of RNA polymerase III transcription factor TFIIIC and the ability of TRE5-A to target these genes. An isolated B box was sufficient to enhance TRE5-A integration in the absence of a surrounding tRNA gene. The RNA polymerase III-transcribed ribosomal 5S gene recruits TFIIIC in a B-box-independent manner, yet it was readily targeted by TRE5-A in our assay. These results suggest a direct role of an RNA polymerase III transcription factor in the targeting process.

scholarly journals LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Shujun Ou ◽  
Ning Jiang
Keyword(s):  
Triticum Aestivum ◽  
Long Terminal Repeat ◽  
Bread Wheat ◽  
Repetitive Sequences ◽  
Long Terminal Repeat Retrotransposons ◽  
Rapid Identification ◽  
Terminal Repeat ◽  
Parallel Operation ◽  
Ltr Retrotransposons ◽  
Plant Genomes

AbstractAnnotation of plant genomes is still a challenging task due to the abundance of repetitive sequences, especially long terminal repeat (LTR) retrotransposons. LTR_FINDER is a widely used program for the identification of LTR retrotransposons but its application on large genomes is hindered by its single-threaded processes. Here we report an accessory program that allows parallel operation of LTR_FINDER, resulting in up to 8500X faster identification of LTR elements. It takes only 72 min to process the 14.5 Gb bread wheat (Triticum aestivum) genome in comparison to 1.16 years required by the original sequential version. LTR_FINDER_parallel is freely available at https://github.com/oushujun/LTR_FINDER_parallel.

scholarly journals Targeted Nuclear Import of Open Reading Frame 1 Protein Is Required for In Vivo Retrotransposition of a Telomere-Specific Non-Long Terminal Repeat Retrotransposon, SART1

2004 ◽  
Vol 24 (1) ◽  
pp. 105-122 ◽  
Author(s):  
Takumi Matsumoto ◽  
Hidekazu Takahashi ◽  
Haruhiko Fujiwara
Keyword(s):  
Long Terminal Repeat ◽  
Nuclear Import ◽  
Fluorescent Protein ◽  
Open Reading Frames ◽  
Terminal Repeat ◽  
Ltr Retrotransposons ◽  
Reading Frame ◽  
Localization Pattern ◽  
Nuclear Localization Signals

ABSTRACT Non-long terminal repeat (non-LTR) retrotransposons, most of which carry two open reading frames (ORFs), are abundant mobile elements that are distributed widely among eukaryotes. ORF2 encodes enzymatic domains, such as reverse transcriptase, that are conserved in all retroelements, but the functional roles of ORF1 in vivo are little understood. We show with green fluorescent protein-ORF1 fusion proteins that the ORF1 proteins of SART1, a telomeric repeat-specific non-LTR retrotransposon in Bombyx mori, are transported into the nucleus to produce a dotted localization pattern. Nuclear localization signals N1 (RRKR) and N2 (PSKRGRG) at the N terminus and a highly basic region in the center of SART1 ORF1 are involved in nuclear import and the dotted localization pattern in the nucleus, respectively. An in vivo retrotransposition assay clarified that at least three ORF1 domains, N1/N2, the central basic domain, and CCHC zinc fingers are required for SART1 retrotransposition. The nuclear import activity of SART1 ORF1 makes it clear that the ORF1 proteins of non-LTR retrotransposons work mainly in the nucleus, in contrast to the cytoplasmic action of Gag proteins of LTR elements. The functional domains found here in SART1 ORF1 will be useful for developing a more efficient and target-specific LINE-based gene delivery vector.

scholarly journals Eukaryotic Translational Coupling in UAAUG Stop-Start Codons for the Bicistronic RNA Translation of the Non-Long Terminal Repeat Retrotransposon SART1

2005 ◽  
Vol 25 (17) ◽  
pp. 7675-7686 ◽  
Author(s):  
Kenji K. Kojima ◽  
Takumi Matsumoto ◽  
Haruhiko Fujiwara
Keyword(s):  
Long Terminal Repeat ◽  
Stop Codon ◽  
Expression System ◽  
Terminal Repeat ◽  
Start Codon ◽  
General Mechanism ◽  
Translation Efficiency ◽  
Ltr Retrotransposons ◽  
Translational Coupling ◽  
Rna Translation

ABSTRACT Most eukaryotic cellular mRNAs are monocistronic; however, many retroviruses and long terminal repeat (LTR) retrotransposons encode multiple proteins on a single RNA transcript using ribosomal frameshifting. Non-long terminal repeat (non-LTR) retrotransposons are considered the ancestor of LTR retrotransposons and retroviruses, but their translational mechanism of bicistronic RNA remains unknown. We used a baculovirus expression system to produce a large amount of the bicistronic RNA of SART1, a non-LTR retrotransposon of the silkworm, and were able to detect the second open reading frame protein (ORF2) by Western blotting. The ORF2 protein was translated as an independent protein, not as an ORF1-ORF2 fusion protein. We revealed by mutagenesis that the UAAUG overlapping stop-start codon and the downstream RNA secondary structure are necessary for efficient ORF2 translation. Increasing the distance between the ORF1 stop codon and the ORF2 start codon decreased translation efficiency. These results are different from the eukaryotic translation reinitiation mechanism represented by the yeast GCN4 gene, in which the probability of reinitiation increases as the distance between the two ORFs increases. The translational mechanism of SART1 ORF2 is analogous to translational coupling observed in prokaryotes and viruses. Our results indicate that translational coupling is a general mechanism for bicistronic RNA translation.

scholarly journals Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon

2021 ◽  
Author(s):  
Nusrat Sultana ◽  
Gerhard Menzel ◽  
Kathrin M. Seibt ◽  
Sonia Garcia ◽  
Beatrice Weber ◽  
...  
Keyword(s):  
Long Terminal Repeat ◽  
Genome Assembly ◽  
In Silico ◽  
Transcriptional Activity ◽  
Long Terminal Repeat Retrotransposons ◽  
Genomic Variation ◽  
Terminal Repeat ◽  
Vaccinium Macrocarpon ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons

BACKGROUND: Long terminal repeat (LTR) retrotransposons are widespread in plant genomes and play a large role in the generation of genomic variation. Despite this, their identification and characterization remains challenging, especially for non-model genomes. Hence, LTR retrotransposons remain undercharacterized in Vaccinium genomes, although they may be beneficial for current berry breeding efforts. OBJECTIVE: Exemplarily focusing on the genome of American cranberry (Vaccinium macrocarpon Aiton), we aim to generate an overview of the LTR retrotransposon landscape, highlighting the abundance, transcriptional activity, sequence, and structure of the major retrotransposon lineages. METHODS: Graph-based clustering of whole genome shotgun Illumina reads was performed to identify the most abundant LTR retrotransposons and to reconstruct representative in silico full-length elements. To generate insights into the LTR retrotransposon diversity in V. macrocarpon, we also queried the genome assembly for presence of reverse transcriptases (RTs), the key domain of LTR retrotransposons. Using transcriptomic data, transcriptional activity of retrotransposons corresponding to the consensuses was analyzed. RESULTS: We provide an in-depth characterization of the LTR retrotransposon landscape in the V. macrocarpon genome. Based on 475 RTs harvested from the genome assembly, we detect a high retrotransposon variety, with all major lineages present. To better understand their structural hallmarks, we reconstructed 26 Ty1-copia and 28 Ty3-gypsyin silico consensuses that capture the detected diversity. Accordingly, we frequently identify association with tandemly repeated motifs, extra open reading frames, and specialized, lineage-typical domains. Based on the overall high genomic abundance and transcriptional activity, we suggest that retrotransposons of the Ale and Athila lineages are most promising to monitor retrotransposon-derived polymorphisms across accessions. CONCLUSIONS: We conclude that LTR retrotransposons are major components of the V. macrocarpon genome. The representative consensuses provide an entry point for further Vaccinium genome analyses and may be applied to derive molecular markers for enhancing cranberry selection and breeding.

scholarly journals Essential Domains for Ribonucleoprotein Complex Formation Required for Retrotransposition of Telomere-Specific Non-Long Terminal Repeat Retrotransposon SART1

2006 ◽  
Vol 26 (13) ◽  
pp. 5168-5179 ◽  
Author(s):  
Takumi Matsumoto ◽  
Mitsuhiro Hamada ◽  
Mizuko Osanai ◽  
Haruhiko Fujiwara
Keyword(s):  
Long Terminal Repeat ◽  
Expression System ◽  
Baculovirus Expression System ◽  
Open Reading Frames ◽  
Terminal Repeat ◽  
Ltr Retrotransposons ◽  
C Terminus ◽  
Functional Features

ABSTRACT Non-long terminal repeat (LTR) retrotransposons are major components of the higher eukaryotic genome. Most of them have two open reading frames (ORFs): ORF2 encodes mainly the endonuclease and reverse transcriptase domains, but the functional features of ORF1 remain largely unknown. We used telomere-specific non-LTR retrotransposon SART1 in Bombyx mori and clarified essential roles of the ORF1 protein (ORF1p) in ribonucleoprotein (RNP) formation by novel approaches: in vitro reconstitution and in vivo/in vitro retrotransposition assays using the baculovirus expression system. Detailed mutation analyses showed that each of the three CCHC motifs at the ORF1 C terminus are essential for SART1 retrotransposition and are involved in packaging the SART1 mRNA specifically into RNP. We also demonstrated that amino acid residues 555 to 567 and 285 to 567 in the SART1 ORF1p are crucial for the ORF1p-ORF1p and ORF1p-ORF2p interactions, respectively. The loss of these domains abolishes protein-protein interaction, leading to SART1 retrotransposition deficiency. These data suggest that systematic formation of RNP composed of ORF1p, ORF2p, and mRNA is mainly mediated by ORF1p domains and is a common, essential step for many non-LTR retrotransposons encoding the two ORFs.

scholarly journals New Insights into Long Terminal Repeat Retrotransposons in Mulberry Species

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 285 ◽  
Author(s):  
Bi Ma ◽  
Lulu Kuang ◽  
Youchao Xin ◽  
Ningjia He
Keyword(s):  
Long Terminal Repeat ◽  
Life Histories ◽  
Evolutionary Dynamics ◽  
Long Terminal Repeat Retrotransposons ◽  
Terminal Repeat ◽  
Ltr Retrotransposons ◽  
Positive Selection Pressure ◽  
Insertion And Deletion ◽  
Mulberry Tree ◽  
Dominant Influence

The evolutionary dynamics of long terminal repeat (LTR) retrotransposons in tree genomes has remained largely unknown. The availability of the complete genome sequences of the mulberry tree (Morus notabilis) has offered an unprecedented opportunity for us to characterize these retrotransposon elements. We investigated 202 and 114 families of Copia and Gypsy superfamilies, respectively, comprising 2916 intact elements in the mulberry genome. The tRNAMet was the most frequently used type of tRNA in both superfamilies. Phylogenetic analysis suggested that Copia and Gypsy from mulberry can be grouped into eight and six lineages, respectively. All previously characterized families of such elements could also be found in the mulberry genome. About 95% of the identified Copia and Gypsy full elements were estimated to have been inserted into the mulberry genome within the past 2–3 million years. Meanwhile, the estimated insertion times of members of the three most abundant families of the Copia superfamily (908 members from the three most abundant families) and Gypsy superfamily (783 members from the three most abundant families) revealed divergent life histories. Compared with the situation in Gypsy elements, three families of Copia elements are under positive selection pressure, which suggested that Copia elements may have a dominant influence in the evolution of mulberry genes. Analysis of insertion and deletion dynamics suggested that Copia and Gypsy elements exhibited a very long half-life in the mulberry genome. The present work provides new insights into the insertion and deletion dynamics of LTR retrotransposons, and it will greatly improve our understanding of the important roles transposable elements play in the architecture of the mulberry genome.

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