Isolation and characterization of retrotransposition-competent LINEs from zebrafish

Sugano, Tomohiro; Kajikawa, Masaki; Okada, Norihiro

doi:10.1016/j.gene.2005.09.037

Cited by 45 publications

(89 citation statements)

References 32 publications

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“…20 Other transposable elements have also had their composition evidenced in fish species other than those participating in chromosome mapping studies. This is the case of the elements of the families HE1 and HER1 in elasmobranchs, 54 CORE-SINE isolated elements in salmonids, 55 Mermaid, 56 Zfl2-1 and Zfl2-2 isolated in zebrafish, 57 and tdr1 isolated in Danio rerio, 58 among others. It is considered that the marking of these elements and their respective mapping in the genome of the species could substantially increase knowledge of the structure and function of these genomic components in fish, and consequently in vertebrates.…”

Section: ©2 0 1 1 L a N D E S B I O S C I E N C E D O N O T D I S Tmentioning

confidence: 98%

Transposable elements as a potential source for understanding the fish genome

Ferreira

Porto‐Foresti

Oliveira

et al. 2011

Mobile Genetic Elements

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Section: ©2 0 1 1 L a N D E S B I O S C I E N C E D O N O T D I S Tmentioning

confidence: 98%

Transposable elements as a potential source for understanding the fish genome

Ferreira

Porto‐Foresti

Oliveira

et al. 2011

Mobile Genetic Elements

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“…Type III ORF1p is found in the heterogeneous CR1 clade, which also harbors ORF1p proteins of type IV. These contain a functional esterase domain that enhances retrotransposition (40,41). Finally, there are numerous NLR ORF1p proteins (type V) that cannot be classified so far (Fig.…”

Section: Orf1pmentioning

confidence: 99%

Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame

Khazina

Weichenrieder

2009

Proc. Natl. Acad. Sci. U.S.A.

137

200

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Non-LTR retrotransposons (NLRs) are a unique class of mobile genetic elements that have significant impact on the evolution of eukaryotic genomes. However, the molecular details and functions of their encoded proteins, in particular of the accessory ORF1p proteins, are poorly understood. Here, we identify noncanonical RNA-recognitionmotifs (RRMs) in several phylogenetically unrelated NLR ORF1p proteins. This provides an explanation for their RNA-binding properties and clearly shows that they are not related to the retroviral nucleocapsid protein Gag, despite the frequent presence of CCHC zinc knuckles. In particular, we characterize the ORF1p protein of the human long interspersed nuclear element 1 (LINE-1 or L1). We show that L1ORF1p is a multidomain protein, consisting of a coiled coil (cc), RRM, and C-terminal domain (CTD). Most importantly, we solved the crystal structure of the RRM domain, which is characterized by extended loops stabilized by unique salt bridges. Furthermore, we demonstrate that L1ORF1p trimerizes via its N-terminal cc domain, and we suggest that this property is functionally important for all homologues. The formation of distinct complexes with singlestranded nucleic acids requires the presence of the RRM and CTD domains on the same polypeptide chain as well as their close cooperation. Finally, the phylogenetic analysis of mammalian L1ORF1p shows an ancient origin of the RRM domain and supports a modular evolution of NLRs.genome evolution ͉ LINE-1 ͉ nucleic acid chaperone ͉ RNP ͉ crystal structure

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“…The zebrafish genome harbors at least three active NLRs of the L2 clade: CR1-1_DR, CR1-2_DR, and CR1-3_DR, which are also called ZfL2-1, ZfL2-2, and ZfL2-3, respectively (Kapitonov and Jurka 2003;Sugano et al 2006). CR1-1_DR and CR1-3_DR carry two ORFs.…”

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confidence: 99%

Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts

Ichiyanagi¹,

Nakajima²,

Kajikawa³

et al. 2006

Genome Res.

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Autonomous non-long-terminal-repeat retrotransposons (NLRs) proliferate by retrotransposition via coordinated reactions of target DNA cleavage and reverse transcription by a mechanism called target-primed reverse transcription (TPRT). Whereas this mechanism guarantees the covalent attachment of the NLR and its target site at the 3Ј junction, mechanisms for the joining at the 5Ј junction have been conjectural. To better understand the retrotransposition pathways, we analyzed target-NLR junctions of zebrafish NLRs with a new method of identifying genomic copies that reside within other transposons, termed "target analysis of nested transposons" (TANT). Application of the TANT method revealed various features of the zebrafish NLR integrants; for example, half of the integrants carry extra nucleotides at the 5Ј junction, which is in stark contrast to the major human NLR, LINE-1. Interestingly, in a cell culture assay, retrotransposition of the zebrafish NLR in heterologous human cells did not bear extra 5Ј nucleotides, indicating that the choice of the 5Ј joining pathway is affected by the host. Our results suggest that several pathways exist for NLR retrotransposition and argue in favor of host protein involvement. With genomic sequence information accumulating exponentially, our data demonstrate the general applicability of the TANT method for the analysis of a wide variety of retrotransposons.

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Isolation and characterization of retrotransposition-competent LINEs from zebrafish

Cited by 45 publications

References 32 publications

Transposable elements as a potential source for understanding the fish genome

Transposable elements as a potential source for understanding the fish genome

Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame

Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts

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