SINEs and LINEs share common 3′ sequences: a review

Okada, Norihiro; Hamada, Mitsuhiro; Ogiwara, Ikuo; Ohshima, Kousei

doi:10.1016/s0378-1119(97)00409-5

Cited by 244 publications

(176 citation statements)

References 58 publications

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“…We observed that all other SINE families also possess primary sequence homologies in their 39 ends with at least one LINE consensus sequence from the RandI family (see supplemental Figure 11B). This suggests that most SINE/ LINE partnerships in C. reinhardtii are based on primary sequence homologies and are not of the ''relaxed'' type (Okada et al 1997).…”

Section: Resultsmentioning

confidence: 99%

On the Evolution and Expression of Chlamydomonas reinhardtii Nucleus-Encoded Transfer RNA Genes

et al. 2008

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In Chlamydomonas reinhardtii, 259 tRNA genes were identified and classified into 49 tRNA isoaccepting families. By constructing phylogenetic trees, we determined the evolutionary history for each tRNA gene family. The majority of the tRNA sequences are more closely related to their plant counterparts than to animals ones. Northern experiments also permitted us to show that at least one member of each tRNA isoacceptor family is transcribed and correctly processed in vivo. A short stretch of T residues known to be a signal for termination of polymerase III transcription was found downstream of most tRNA genes. It allowed us to propose that the vast majority of the tRNA genes are expressed and to confirm that numerous tRNA genes separated by short spacers are indeed cotranscribed. Interestingly, in silico analyses and hybridization experiments show that the cellular tRNA abundance is correlated with the number of tRNA genes and is adjusted to the codon usage to optimize translation efficiency. Finally, we studied the origin of SINEs, short interspersed elements related to tRNAs, whose presence in Chlamydomonas is exceptional. Phylogenetic analysis strongly suggests that tRNA Asp -related SINEs originate from a prokaryotic-type tRNA either horizontally transferred from a bacterium or originally present in mitochondria or chloroplasts.

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Section: Resultsmentioning

confidence: 99%

On the Evolution and Expression of Chlamydomonas reinhardtii Nucleus-Encoded Transfer RNA Genes

et al. 2008

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“…The amplification of a LINE occurs when its primary transcript is reverse transcribed, copied, and then integrated into another area of the genome. SINEs operate essentially the same way but rely on LINEs, at least in part, for their own retroposition, amplification, and genomic integration (34)(35)(36).…”

Section: Discussionmentioning

confidence: 99%

Evolution of a large ribosomal RNA multigene family in filamentous fungi: Birth and death of a concerted evolution paradigm

Rooney

Ward

2005

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

163

151

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In eukaryotes, the primary components of the ribosome are encoded by multicopy nuclear ribosomal RNA (rRNA) genes: 28͞26S, 18S, 5.8S, and 5S. Copies of these genes are typically localized within tandem arrays and homogenized within a genome. As a result, nuclear rRNA gene families have become a paradigm of concerted evolution. In filamentous fungi of the subphylum Pezizomycotina, 5S rRNA genes exist as a large and dispersed multigene family, with between 50 and 100 copies per genome. To determine whether these genes defy the concerted evolution paradigm, we examined the patterns of evolution of these genes by using sequences from the complete genomes of four species. Analyses of these sequences revealed (i) multiple 5S gene types within a genome, (ii) interspecies clustering of gene types, (iii) multiple identical gene types shared among species, (iv) multiple pseudogenes within a genome, and (v) presence͞absence variation of individual 5S copies in comparisons of closely related species. These results demonstrate that the 5S family in these species is characterized by birth-and-death evolution under strong purifying selection. Furthermore, our results suggest that birth-and-death evolution occurs at different rates in the genera examined, and that the multiplication and movement of 5S genes across the genome are highly dynamic. As such, we hypothesize that a mechanism resembling retroposition controls 5S rRNA gene amplification, dispersal, and integration in the genomes of filamentous fungi.5S rRNA ͉ retroposition

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“…Non-LTR LINE-1-like elements are widely distributed in eucaryotes and comprise approximately 30% of the human genome; a recent study has shown that the X chromosome is rich in non-LTR retrotransposon Alu repetitive sequences relative to the Y chromosome and autosomes (Jurka et al, 2004). Bm1 elements are a family of short (130-470 bp) tRNA/U1RNA-derived retroposons or SINEs containing variable 3 0 poly (A) tracts, which comprise an estimated 5% of the silkworm genome (Okada et al, 1997). The silkworm Z chromosome has double the repetitive elements of autosomes, a trend which is similar to the X chromosomes in mammals and D. melanogaster.…”

Section: Sequencing and Characterizing Of Z-linked Markersmentioning

confidence: 99%

Genetic mapping of Z chromosome and identification of W chromosome-specific markers in the silkworm, Bombyx mori

Nagaraja

Mahesh

et al. 2005

Heredity

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In the silkworm, Bombyx mori, the female is the heterogametic (ZW) sex and the male is homogametic (ZZ). The female heterogamety is a typical situation in the insect order Lepidoptera. Although the W chromosome in silkworm is strongly female determining, no W-linked gene for a morphological character has been found on it. The Z chromosome carries important traits of economic value as well as genes for various phenotypic traits, but only 2% of molecular information based on its relative size is known. Studies conducted so far indicate that the Z-linked genes are not dosage compensated. In the present study, we constructed a genetic map of randomly amplified polymorphic DNA fragments (RAPD), simple sequence repeats (SSR), and fluorescent intersimple sequence repeat PCR (FISSR) markers for the Z chromosome using a backcross mapping population. A total of 16 Zlinked markers were identified, characterized, and mapped using od, a recessive trait for translucent skin as an anchor marker yielding a total recombination map of 334.5 cM. The linkage distances obtained suggested that the markers were distributed throughout the Z chromosome. Four RAPD and four SSR markers that were linked to W chromosome were also identified. The proposed mapping approach should be useful to identify and map sex-linked traits in the silkworm. The economic and evolutionary significance of Z-and W-linked genes in silkworm, in particular, and lepidopterans, in general, is discussed. Heredity (2005) 95, 148-157.

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SINEs and LINEs share common 3′ sequences: a review

Cited by 244 publications

References 58 publications

On the Evolution and Expression of Chlamydomonas reinhardtii Nucleus-Encoded Transfer RNA Genes

On the Evolution and Expression of Chlamydomonas reinhardtii Nucleus-Encoded Transfer RNA Genes

Evolution of a large ribosomal RNA multigene family in filamentous fungi: Birth and death of a concerted evolution paradigm

Genetic mapping of Z chromosome and identification of W chromosome-specific markers in the silkworm, Bombyx mori

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