Identification of a novel helitron transposon in the genome of Antarctic fish

Cocca, Ennio; Iorio, S. De; Capriglione, Teresa

doi:10.1016/j.ympev.2010.12.020

Cited by 20 publications

(15 citation statements)

References 44 publications

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“…Helentrons also carry other highly conserved genes, suggesting that the encoded proteins probably function in the life cycle of these elements (11,56). Some Helentron encoded Rep/ Helicase/Endonuclease proteins have an additional two domains that share strong sequence identity with the Ovarian Tumor protein of Drososphila (OTU) (11,54,56,62). The OTU proteins are a family of cysteine proteases (54,63,64).…”

Section: Structure and Coding Capacitymentioning

confidence: 99%

Helitrons , the Eukaryotic Rolling-circle Transposable Elements

Thomas

Pritham

2015

Microbiol Spectr

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Helitrons, the eukaryotic rolling-circle transposable elements, are widespread but most prevalent among plant and animal genomes. Recent studies have identified three additional coding and structural variants of Helitrons called Helentrons, Proto-Helentron, and Helitron2. Helitrons and Helentrons make up a substantial fraction of many genomes where nonautonomous elements frequently outnumber the putative autonomous partner. This includes the previously ambiguously classified DINE-1-like repeats, which are highly abundant in Drosophila and many other animal genomes. The purpose of this review is to summarize what we have learned about Helitrons in the decade since their discovery. First, we describe the history of autonomous Helitrons, and their variants. Second, we explain the common coding features and difference in structure of canonical Helitrons versus the endonuclease-encoding Helentrons. Third, we review how Helitrons and Helentrons are classified and discuss why the system used for other transposable element families is not applicable. We also touch upon how genome-wide identification of candidate Helitrons is carried out and how to validate candidate Helitrons. We then shift our focus to a model of transposition and the report of an excision event. We discuss the different proposed models for the mechanism of gene capture. Finally, we will talk about where Helitrons are found, including discussions of vertical versus horizontal transfer, the propensity of Helitrons and Helentrons to capture and shuffle genes and how they impact the genome. We will end the review with a summary of open questions concerning the biology of this intriguing group of transposable elements.

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Section: Structure and Coding Capacitymentioning

confidence: 99%

Helitrons , the Eukaryotic Rolling-circle Transposable Elements

Thomas

Pritham

2015

Microbiol Spectr

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“…Helentrons are so called because of the presence of an apurinic/apyrimidinic (AP) endonuclease domain fused to the C-terminus of the Rep/Helicase protein [38]. Helentrons encode additional ORFs with homology to OTU cysteine proteases [40,41] and RPA proteins [2]. The structural features of Helentrons are not known despite reports describing the coding capacity [38,40,41].…”

Section: Introductionmentioning

confidence: 99%

“…Helentrons encode additional ORFs with homology to OTU cysteine proteases [40,41] and RPA proteins [2]. The structural features of Helentrons are not known despite reports describing the coding capacity [38,40,41]. The Helitron2 elements have asymmetrical terminal inverted repeats and palindromic sequences on both ends.…”

Section: Introductionmentioning

confidence: 99%

DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons)

2014

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BackgroundThe Drosophila INterspersed Elements-1 (DINE-1/INE1) transposable elements (TEs) are the most abundant component of the Drosophila melanogaster genome and have been associated with functional gene duplications. DINE-1 TEs do not encode any proteins (non-autonomous) thus are moved by autonomous partners. The identity of the autonomous partners has been a mystery. They have been allied to Helitrons (rolling-circle transposons), MITEs (DNA transposons), and non-LTR retrotransposons by different authors.ResultsWe report multiple lines of bioinformatic evidence that illustrate the relationship of DINE-1 like TEs to endonuclease-encoding rolling-circle TEs (Helentrons). The structural features of Helentrons are described, which resemble the organization of the non-autonomous partners, but differ significantly from canonical Helitrons. In addition to the presence of an endonuclease domain fused to the Rep/Helicase protein, Helentrons have distinct structural features. Evidence is presented that illustrates that Helentrons are widely distributed in invertebrate, fish, and fungal genomes. We describe an intermediate family from the Phytophthora infestans genome that phylogenetically groups with Helentrons but that displays Helitron structure. In addition, evidence is presented that Helentrons can capture gene fragments in a pattern reminiscent of canonical Helitrons.ConclusionsWe illustrate the relationship of DINE-1 and related TE families to autonomous partners, the Helentrons. These findings will allow their proper classification and enable a more accurate understanding of the contribution of rolling-circle transposition to the birth of new genes, gene networks, and genome composition.

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“…This technique offers the possibility to encode DNA into several signals according to a well-defined order. Three levels of the representation are taken into account: FCGS 2 , FCGS 4 and FCGS 6 .…”

Section: Discussionmentioning

confidence: 99%

“…For this, chromosomes sequences from the NCBI data base for the C.elegans model (http://www.ncbi.nlm.nih.gov/Genbank) are extracted. Then, 1-D signals are generated by applying the Frequency Chaos Game Signal of order i: FCGS i, (i=2, 4,6) for the whole chromosomes. This coding technique is based on the apparition"s probability of N successive nucleotides groups in an entry DNA sequence [29]- [31].…”

Section: Methodology Of Helitron"s Identificationmentioning

confidence: 99%

Helitron’s Periodicities Identification in C.Elegans based on the Smoothed Spectral Analysis and the Frequency Chaos Game Signal Coding

Touati¹,

Messaoudi²,

Ouesleti³

et al. 2018

ijacsa

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Abstract-Helitrons are typical rolling circle transposons which make up the bulk of eukaryotic genomes. Unlike of other DNA transposons, these transposable elements (TEs), don't create target site duplications or end in inverted repeats, which make them particular challenge to identify and more difficult to annotate. To date, these elements are not well studied; they only attracted the interest of researchers in biology. The focus of this paper is oriented towards identifying the helitrons in C.elegans genome in the perspective of signal processing. Aiming at the helitron's identification, a novel methodology including two steps is proposed: the coding and the spectral analysis. The first step consists in converting DNA into a 1-D signal based on the statistical features of the sequence (FCGS coding). As for the second step, it aims to identify the global periodicities in helitrons using the Smoothed Fourier Transform. The resulting spectrum and spectrogram are shown to present a specific signature of each helitron's type.

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Identification of a novel helitron transposon in the genome of Antarctic fish

Cited by 20 publications

References 44 publications

Helitrons , the Eukaryotic Rolling-circle Transposable Elements

Helitrons , the Eukaryotic Rolling-circle Transposable Elements

DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons)

Helitron’s Periodicities Identification in C.Elegans based on the Smoothed Spectral Analysis and the Frequency Chaos Game Signal Coding

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