Origin and evolution of LINE-1 derived “half-L1” retrotransposons (HAL1)

Bao, Weidong; Jurka, Jerzy

doi:10.1016/j.gene.2010.06.005

Cited by 19 publications

(16 citation statements)

References 42 publications

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“…Notably, the lack of a 3′ poly(A) tract on L1 “driver” plasmids did not lead to enhanced trans -complementation from a second “reporter” plasmid that resembles a Half-L1 (HAL1) retrotransposon (Figure S6A; pL1.3/ORF1 mneoI ) (Bao and Jurka, 2010; Jurka et al, 2005; Smit, 1999). Instead, the efficiency of L1.3 ORF1 mneoI trans -complementation generally correlated with the steady state level of ORF2p expressed from the respective “driver” plasmids (Figures S3C and S6B).…”

Section: Resultsmentioning

confidence: 99%

A 3′ Poly(A) Tract Is Required for LINE-1 Retrotransposition

et al. 2015

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Summary L1 retrotransposons express proteins (ORF1p and ORF2p) that preferentially mobilize their encoding RNA in cis, but they also can mobilize Alu RNA and, more rarely, cellular mRNAs in trans. Although these RNAs differ in sequence, each ends in a 3′ polyadenosine (poly(A)) tract. Here, we replace the L1 polyadenylation signal with sequences derived from a non-polyadenylated long noncoding RNA (MALAT1), which can form a stabilizing triple helix at the 3′ end of an RNA. L1/MALAT RNAs accumulate in cells, lack poly(A) tails, and are translated; however, they cannot retrotranspose in cis. Remarkably, the addition of a 16 or 40 base poly(A) tract downstream of the L1/MALAT triple helix restores retrotransposition in cis. The presence of a poly(A) tract also allows ORF2p to bind and mobilize RNAs in trans. Thus, a 3′ poly(A) tract is critical for the retrotransposition of sequences that comprise approximately one billion base pairs of human DNA.

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Section: Resultsmentioning

confidence: 99%

A 3′ Poly(A) Tract Is Required for LINE-1 Retrotransposition

et al. 2015

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“…This long lasting coding capability would seems unusual for a “non-autonomous” family ( CMe - 1A ) if no function is associated with the Fanzor1 protein. Analogous cases exist in the so-called HAL1 “non-autonomous” families derived from the L1 non-LTR retrotransposons, which encode the first open reading frame protein (ORF1p) only, instead of both ORF1p and ORF2p [35]. ORF1p is a “nucleic acid chaperone with RNA binding [36] and nucleic acid chaperone activity [37], but ORF2p codes for the major Tpase with its endonuclease (EN) and reverse transcriptase (RT) activity.…”

Section: Discussionmentioning

confidence: 99%

“…ORF1p is a “nucleic acid chaperone with RNA binding [36] and nucleic acid chaperone activity [37], but ORF2p codes for the major Tpase with its endonuclease (EN) and reverse transcriptase (RT) activity. In the guinea pig genome the coding capacity of the ORF1p in the HAL1 retrotransposons has been maintained for a relatively long time (approximately 29 to 44 Myr) [35], implying that both the cis -encoded ORF1p and trans-encoded ORF2p are required for transposition of HAL1 elements.…”

Section: Discussionmentioning

confidence: 99%

Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements

Bao

Jurka

2013

Mobile DNA

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BackgroundBacterial insertion sequences (IS) of IS200/IS605 and IS607 family often encode a transposase (TnpA) and a protein of unknown function, TnpB.ResultsHere we report two groups of TnpB-like proteins (Fanzor1 and Fanzor2) that are widespread in diverse eukaryotic transposable elements (TEs), and in large double-stranded DNA (dsDNA) viruses infecting eukaryotes. Fanzor and TnpB proteins share the same conserved amino acid motif in their C-terminal half regions: D-X(125, 275)-[TS]-[TS]-X-X-[C4 zinc finger]-X(5,50)-RD, but are highly variable in their N-terminal regions. Fanzor1 proteins are frequently captured by DNA transposons from different superfamilies including Helitron, Mariner, IS4-like, Sola and MuDr. In contrast, Fanzor2 proteins appear only in some IS607-type elements. We also analyze a new Helitron2 group from the Helitron superfamily, which contains elements with hairpin structures on both ends. Non-autonomous Helitron2 elements (CRe-1, 2, 3) in the genome of green alga Chlamydomonas reinhardtii are flanked by target site duplications (TSDs) of variable length (approximately 7 to 19 bp).ConclusionsThe phylogeny and distribution of the TnpB/Fanzor proteins indicate that they may be disseminated among eukaryotic species by viruses. We hypothesize that TnpB/Fanzor proteins may act as methyltransferases.

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“…Recombination between TE copies of the same family has been reported before [83-87], but the significance of this for TEs in general is rarely discussed. Our survey focused on variation in an approximately 1,600 bp sequence.…”

Section: Discussionmentioning

confidence: 99%

Evolution of a transposon in Daphnia hybrid genomes

et al. 2013

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BackgroundTransposable elements play a major role in genome evolution. Their capacity to move and/or multiply in the genome of their host may have profound impacts on phenotypes, and may have dramatic consequences on genome structure. Hybrid and polyploid clones have arisen multiple times in the Daphnia pulex complex and are thought to reproduce by obligate parthenogenesis. Our study examines the evolution of a DNA transposable element named Pokey in the D. pulex complex.ResultsPortions of Pokey elements inserted in the 28S rRNA genes from various Daphnia hybrids (diploids and polyploids) were sequenced and compared to sequences from a previous study to understand the evolutionary history of the elements. Pokey sequences show a complex phylogenetic pattern. We found evidence of recombination events in numerous Pokey alleles from diploid and polyploid hybrids and also from non-hybrid diploids. The recombination rate in Pokey elements is comparable to recombination rates previously estimated for 28S rRNA genes in the congener, Daphnia obtusa. Some recombinant Pokey alleles were encountered in Daphnia isolates from multiple locations and habitats.ConclusionsPhylogenetic and recombination analyses showed that recombination is a major force that shapes Pokey evolution. Based on Pokey phylogenies, reticulation has played and still plays an important role in shaping the diversity of the D. pulex complex. Horizontal transfer of Pokey seems to be rare and hybrids often possess Pokey elements derived from recombination among alleles encountered in the putative parental species. The insertion of Pokey in hotspots of recombination may have important impacts on the diversity and fitness of this transposable element.

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Origin and evolution of LINE-1 derived “half-L1” retrotransposons (HAL1)

Cited by 19 publications

References 42 publications

A 3′ Poly(A) Tract Is Required for LINE-1 Retrotransposition

A 3′ Poly(A) Tract Is Required for LINE-1 Retrotransposition

Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements

Evolution of a transposon in Daphnia hybrid genomes

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