A new subfamily of recently retroposed human Alu repeats

Jurka, Jerzy

doi:10.1093/nar/21.9.2252

Cited by 57 publications

(57 citation statements)

References 13 publications

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“…According to Jurka and Milosavlievic (1991), AluY (Batzer et al 1996) was the youngest and it was divided further into AluYa5 (Batzer et al 1996), which was also known as PV (predicted variant) (Matera et al 1990) or HS (human specific) (Batzer et al 1990), and AluYb8 (Batzer et al 1996), which was previously known as Sb2 (Jurka 1993). In a recent study, Kapitonov and Jurka (1996) estimated the ages of Alu subfamilies.…”

Section: Discussionmentioning

confidence: 99%

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Characterization of Alu Repeats That Are Associated with Trinucleotide and Tetranucleotide Repeat Microsatellites

et al. 1997

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The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was characterized as a first step toward advancing our understanding of the evolution of microsatellite repeats. In addition, information regarding the association of specific classes of microsatellites with families of Alu elements was used to facilitate the development of genetic markers. Sequences containing Alu repeats were eliminated because unique primers could not be designed. Various classes of microsatellites are associated with different classes of Alu repeats. Very abundant and poly(A)-rich microsatellite classes (ATA, AATA) are frequently associated with an evolutionarily older subclass of Alu repeats, AluSx, whereas most of GATA and CA microsatellites are associated with a recent Alu subfamily, AluY. Our observations support all three possible mechanisms for the association of Alu repeats to microsatellites. Primers designed using a set of sequences from a particular microsatellite class showed higher homology with more sequences of that class than probes designed for other classes. We developed an efficient method of prescreening GGAA and ATA microsatellite clones for Alu repeats with probes designed in this study. We also showed that Alu probes labeled in a single reaction (multiplex labeling) could be used efficiently for prescreening of GGAA clones. Sequencing of these prescreened GGAA microsatellites revealed only 5% Alu repeats. Prescreening with primers designed for ATA microsatellite class resulted in the reduction of the loss of markers from ∼50% to 10%. The new Alu probes that were designed have also proved to be useful in Alu-Alu fingerprinting.

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Section: Discussionmentioning

confidence: 99%

“…Alu repeats can be classified into subfamilies based on DNA sequence divergence (Jurka and Smith 1988;Batzer et al 1990;Jurka and Milosavljevic 1991;Jurka 1993). Each subfamily was thought to arise from a distinct founder sequence.…”

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confidence: 99%

Characterization of Alu Repeats That Are Associated with Trinucleotide and Tetranucleotide Repeat Microsatellites

et al. 1997

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“…To gain additional insight into Alu subfamily propagation, we reconstructed the evolutionary history of the AluYb lineage, one of the largest and most active Alu lineages in the human genome (Jurka 1993;Carter et al 2004) that composes ∼40% of the human-specific Alu elements ). This lineage, originally termed Sb2, is characterized by a 7-nt duplication involving positions 246 through 252 of the AluY consensus sequence (Jurka 1993;Batzer et al 1996).…”

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confidence: 99%

“…This lineage, originally termed Sb2, is characterized by a 7-nt duplication involving positions 246 through 252 of the AluY consensus sequence (Jurka 1993;Batzer et al 1996). The AluYb lineage in the human genome is subdivided into three major subfamilies as follows: AluYb7, AluYb8, and AluYb9 (Batzer et al 1996;RoyEngel et al 2001;Jurka et al 2002;Carter et al 2004) based on diagnostic mutations following the standardized nomenclature for Alu repeats (Batzer et al 1996).…”

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confidence: 99%

Under the genomic radar: The Stealth model of Alu amplification

et al. 2005

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Alu elements are the most successful SINEs (Short INterspersed Elements) in primate genomes and have reached more than 1,000,000 copies in the human genome. The amplification of most Alu elements is thought to occur through a limited number of hyperactive "master" genes that produce a high number of copies during long evolutionary periods of time. However, the existence of long-lived, low-activity Alu lineages in the human genome suggests a more complex propagation mechanism. Using both computational and wet-bench approaches, we reconstructed the evolutionary history of the AluYb lineage, one of the most active Alu lineages in the human genome. We show that the major AluYb lineage expansion in humans is a species-specific event, as nonhuman primates possess only a handful of AluYb elements. However, the oldest existing AluYb element resided in an orthologous position in all hominoid primate genomes examined, demonstrating that the AluYb lineage originated 18-25 million years ago. Thus, the history of the AluYb lineage is characterized by ∼20 million years of retrotranspositional quiescence preceding a major expansion in the human genome within the past few million years. We suggest that the evolutionary success of the Alu family may be driven at least in part by "stealth-driver" elements that maintain low retrotranspositional activity over extended periods of time and occasionally produce short-lived hyperactive copies responsible for the formation and remarkable expansion of Alu elements within the genome.

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“…The amplification of Alu elements has been dominated by a small number of master genes as well as a few fortuitous source genes , resulting in the appearance of distinct subfamilies as defined by tightly linked diagnostic or subfamily-specific mutations (Slagel et al 1987;Britten et al 1988;Jurka and Smith 1988;Jurka and Milosavljevic 1991;Shen et al 1991). The youngest of these subfamilies, defined as Ya5/8 and Yb8 (Batzer et al 1996b), appeared around the time humans diverged from other primates; therefore, members of these subfamilies are largely restricted in their distribution to humans (Matera et al 1990a,b;Batzer et al 1990Batzer et al , 1995Batzer et al , 1996aJurka 1993). A number of polymorphic Alu insertions have been identified (Batzer et al , 1994(Batzer et al , 1996aBlonden et al 1994;Hammer 1994;Milewicz et al 1996) including some that are unique to single individuals (Wallace et al 1991;Vidaud et al 1993) or families (Muratani et al 1991).…”

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confidence: 99%

Alu fossil relics--distribution and insertion polymorphism.

Arcot¹,

Adamson²,

Lamerdin³

et al. 1996

Genome Res.

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Screening of a human genomic library with an oligonucleotide probe specific for one of the young subfamilies of Alu repeats I~YaS/8] resulted in the identification of several hundred positive clones. Thirty-three of these clones were analyzed in detail by DNA sequencing. Oligonucleotide primers complementary to the unique sequence regions flanking each Alu repeat were used in PCR-based assays to perform phylogenetic analyses, chromosomal localization, and insertion polymorphism analyses within different human population groups. All 33 Alu repeats were present only in humans and absent from orthologous positions in several nonhuman primate genomes. Seven Alu repeats were polymorphic for their presence/absence in three different human population groups, making them novel identical-by-descent markers for the analysis of human genetic diversity and evolution. Nucleotide sequence analysis of the polymorphic Alu repeats showed an extremely low nucleotide diversity compared with the subfamily consensus sequence with an average age of 1.63 million years old. The young Alu insertions do not appear to accumulate preferentially on any individual human chromosome.

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A new subfamily of recently retroposed human Alu repeats

Cited by 57 publications

References 13 publications

Characterization of Alu Repeats That Are Associated with Trinucleotide and Tetranucleotide Repeat Microsatellites

Characterization of Alu Repeats That Are Associated with Trinucleotide and Tetranucleotide Repeat Microsatellites

Under the genomic radar: The Stealth model of Alu amplification

Alu fossil relics--distribution and insertion polymorphism.

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