Target site analysis of RTE1_LA and its AfroSINE partner in the elephant genome

Gilbert, Clément; Pace, John K.; Waters, Paul D.

doi:10.1016/j.gene.2008.08.013

Cited by 8 publications

(6 citation statements)

References 53 publications

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“…Animal SINEs, which share a specific nucleotide sequence of the 3′-terminal region with animal RTE-clade LINEs, were two types: one that ends in (CAA)n and has A as the first nucleotide of its TSD, and the other that ends in T-rich repeats and has T as the first nucleotide of its TSD. Interestingly, these two types of SINEs coexist in the elephant genome ( table 2 and supplementary table S3 , Supplementary Material online; Gilbert et al. 2008 ; Bao et al.…”

Section: Resultsmentioning

confidence: 99%

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Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons

Nishiyama

Ohshima

2018

Genome Biology and Evolution

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In multicellular organisms, such as vertebrates and flowering plants, horizontal transfer (HT) of genetic information is thought to be a rare event. However, recent findings unveiled unexpectedly frequent HT of RTE-clade LINEs. To elucidate the molecular footprints of the genomic integration machinery of RTE-related retroposons, the sequence patterns surrounding the insertion sites of plant Au-like SINE families were analyzed in the genomes of a wide variety of flowering plants. A novel and remarkable finding regarding target site duplications (TSDs) for SINEs was they start with thymine approximately one helical pitch (ten nucleotides) downstream of a thymine stretch. This TSD pattern was found in RTE-clade LINEs, which share the 3′-end sequence of these SINEs, in the genome of leguminous plants. These results demonstrably show that Au-like SINEs were mobilized by the enzymatic machinery of RTE-clade LINEs. Further, we discovered the same TSD pattern in animal SINEs from lizard and mammals, in which the RTE-clade LINEs sharing the 3′-end sequence with these animal SINEs showed a distinct TSD pattern. Moreover, a significant correlation was observed between the first nucleotide of TSDs and microsatellite-like sequences found at the 3′-ends of SINEs and LINEs. We propose that RTE-encoded protein could preferentially bind to a DNA region that contains a thymine stretch to cleave a phosphodiester bond downstream of the stretch. Further, determination of cleavage sites and/or efficiency of primer sites for reverse transcription may depend on microsatellite-like repeats in the RNA template. Such a unique mechanism may have enabled retroposons to successfully expand in frontier genomes after HT.

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Section: Resultsmentioning

confidence: 99%

“…2008 ). Because AfroSINEs and known elephant RTE-clade LINE are not terminated by the same tandem repeat motifs, Gilbert et al. (2008) proposed that these differences reflect constraints imposed by base pairing interactions between the mRNA 3′ terminal tandem repeats and the target DNA at the initiation of TPRT.…”

Section: Introductionmentioning

confidence: 99%

Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons

Nishiyama

Ohshima

2018

Genome Biology and Evolution

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“…But most of them are based on the sequence alignment, statistical approaches or utilisation of the functional properties proprietary to specific elements (Geurts et al, 2006; Gilbert et al, 2008). …”

Section: Related Workmentioning

confidence: 99%

Breaking the computational barrier: a divide-conquer and aggregate based approach for Alu insertion site characterisation

Zhang

Wang

Deininger

et al. 2009

IJCBDD

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Insertion site characterisation of Alu elements is an important problem in primate-specific bioinformatics research. Key characteristics of this challenging problem include: • Data are not in the pre-defined feature vectors for predictive model construction. • Without any prior knowledge, can we discover the general patterns that could exist and also make biological insights? • How to obtain the compact yet discriminative patterns given a search space of 4200? This paper provides an integrated algorithmic framework for fulfilling the above mining tasks. Compared to the benchmark biological study, our results provide a further refined analysis of the patterns involved in Alu insertion. In particular, we acquire a 200nt predictive profile around the primary insertion site which not only contains the widely accepted consensus, but also suggests a longer pattern (T)7AA[G|A]AATAA. This pattern provides more insight into the favourable sequence variations allowed for preferred binding and cleavage by the L1 ORF2 endonuclease. The proposed method is general enough that can be also applied to other sequence detection problems, such as microRNA target prediction.

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“…Most other TE types (SINEs, LTRs, LINEs (L1 and L2), and DNA transposons) in mammoth DNA were on par with or in fewer numbers than in other mammalian genomes. Significantly, RTE elements are absent in armadillo [13], cetartiodactyls, primates, carnivores and rodents [28] but are found in ruminants and at least two afrotherian clades, tenrec and the modern elephant [29] (Figure 1). This distribution of RTEs lends support to the idea that each repeat is a unique genomic invasion by a lineage of LINEs with an unprecedented ability to spread via horizontal transfer [28, 30, 31].…”

Section: Te Content and Genome Dynamics In Mammothmentioning

confidence: 99%

“…Indeed, the power of next-generation sequencing for understanding the evolutionary patterns of repetitive sequences and their impact on genome evolution has recently been shown in work in the pea ( Pisum sativa ) genome [28] and in the soybean genome [29]. The use of 454 sequencing technology seems particularly well suited to genome-wide TE analysis.…”

Section: Subgenomic Targeting Using Next-generation Sequencing Technomentioning

confidence: 99%

Reading between the LINEs to see into the past

2009

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Transposable elements are an important source of genome diversity and have crucial role in genome evolution.. A recent study by Zhao et al. describes novel patterns of transposable element (TE) diversification in the genome of the extinct mammoth, Mammuthus primigenius. Analysis of Mammuthus has provided a unique genome landscape, a pivotal species for understanding TEs and genome evolution, and hints at the diversity we verge on discovering by expanding our taxonomic sampling among genomes. Strategies based on the work. might also revolutionize investigations of the interface between TE dynamics and genome diversity. Discovering TEs in the mammoth genomeTransposable elements (TEs, Box 1) have had substantial impacts on eukaryotic genomes throughout life's history, being responsible either directly or indirectly for much of the genomic diversity we see today. Not surprisingly, studies of TE impacts on human and non-human primate genomes are numerous and well developed. We know for example how the movement of TEs has impacted human diseases [1], genome size [2][3][4][5][6][7][8], and the transcriptome [9][10][11]. But how well does our little corner of the genomic world reflect TE diversity and impact in a more general sense? The broader mammalian perspective is only now being investigated, and although we are starting to answer this question (see Ref [12] for an example), many gaps in our knowledge remain. Recently, Zhao et al.[13] applied next-generation sequencing (454) to address the question in a unique way -by investigating TE amplification dynamics in the woolly mammoth (Mammuthus primigenius), a species that has been extinct for ~10 000 years. Using the massive data available from the mammoth genome project, they determined likely TE content using an iterative process to identify relatives of known TE families. It was immediately clear that the sheer volume of TEs within the mammoth genome sets it apart from other mammals. The uniqueness of the mammoth genome can been seen in several TE-related areas, including genomic expansion, TE diversity, and a likely case of horizontal transfer of a Class I TE. Such observations hint at tremendous potential for finding a vast array of TE associated diversity in mammals as their genomes are explored. Zhao et al. [1] also demonstrate the impressive potential of next-generation sequencing with regard to subgenomic analysis. The increased throughput provided by platforms such as the 454, Illumina, and SOLiD systems has

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Target site analysis of RTE1_LA and its AfroSINE partner in the elephant genome

Cited by 8 publications

References 53 publications

Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons

Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons

Breaking the computational barrier: a divide-conquer and aggregate based approach for Alu insertion site characterisation

Reading between the LINEs to see into the past

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