Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity

Carroll, Marion L.; Roy-Engel, Astrid M.; Nguyen, Son; Salem, Abdel Halim; Vogel, Erika; Vincent, Bethaney; Myers, Jeremy S.; Ahmad, Zahid; Nguyen, Linh P.; Sammarco, Mimi C.; Watkins, W. Scott; Henke, Jürgen; Makałowski, Wojciech; Jorde, Lynn B.; Deininger, Prescott L.; Batzer, Mark A.

doi:10.1006/jmbi.2001.4847

Cited by 152 publications

(157 citation statements)

References 43 publications

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“…Our results are the first direct demonstration that SINE copies engage in active sequence exchange during retrotransposition, leading to the rapid spread of the sequence tag to the SINE population, and generation of diversity. As mRNA transcripts are also templates of the same retrotransposition machinery during retropseudogene formation, it will be interesting to see if mRNA transcripts could also engage in similar recombination during reverse transcription 29 .…”

Section: Mismatchesmentioning

confidence: 99%

Recombinant SINEs are formed at high frequency during induced retrotransposition in vivo

et al. 2012

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non-long terminal repeat Retrotransposons are referred to as long interspersed nuclear elements (LInEs) and their non-autonomous partners are short interspersed nuclear elements (sInEs). It is believed that an active sInE copy, upon retrotransposition, generates near identical copies of itself, which subsequently accumulate mutations resulting in sequence polymorphism. Here we show that when a retrotransposition-competent cell line of the parasitic protist Entamoeba histolytica, transfected with a marked sInE copy, is induced to retrotranspose, > 20% of the newly retrotransposed copies are neither identical to the marked sInE nor to the mobilized resident sInEs. Rather they are recombinants of resident sInEs and the marked sInE. They are a consequence of retrotransposition and not DnA recombination, as they are absent in cells not expressing the retrotransposition functions. This high-frequency recombination provides a new explanation for the existence of mosaic sInEs, which may impact on genetic analysis of sInE lineages, and measurement of phylogenetic distances.

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Section: Mismatchesmentioning

confidence: 99%

Recombinant SINEs are formed at high frequency during induced retrotransposition in vivo

et al. 2012

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“…6). Data for up to six markers have been generated by Carroll et al [14] and Roy-Engel et al [7] for populations including African American, Greenland natives, Asian, European Caucasians, and Egyptians, and we have incorporated this information into the database (see view population data). As more data are collected, we can add these to the database.…”

Section: Menumentioning

confidence: 99%

“…Three possible genotypes can be generated; homozygosity for the presence form (þþ), homozygosity for the absence form (22), or heterozygosity (þ2) in which the amplicons of both sizes are visible on an agarose gel. Dimorphic (presence/absence) Alu elements have demonstrated usefulness as markers for paternity [8], forensics [9,10] including gender determination [11], population studies [7,[12][13][14], and notably as a useful teaching tool to study genetic variation [15,16].…”

mentioning

confidence: 99%

“…By analyzing eight presence/absence loci, a total of 6,561 genotypes are possible. We chose what are referred to as intermediate frequency (IF) Alu markers [7,14]; those markers in which both presence and absence forms are relatively common and therefore more informative.…”

mentioning

confidence: 99%

“…Additionally, students have the opportunity to compare each of eight loci for genetic distance between classes as well as among different ethnic groups. We have thus far incorporated the genetic profiles for up to six of these loci among different populations (ethnic groups) as determined by Carroll et al [14] and Roy-Engel et al [7], allowing students to contrast population variations for several loci providing more information than would be obtained for a single locus.…”

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confidence: 99%

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Web‐based analysis for student‐generated complex genetic profiles

Kass

LaRoe

2007

Biochem Molecular Bio Educ

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A simple, rapid method for generating complex genetic profiles using Alu-based markers was recently developed for students primarily at the undergraduate level to learn more about forensics and paternity analysis. On the basis of the Cold Spring Harbor Allele Server, which provides an excellent tool for analyzing a single Alu variant, we present a new web-based system for analyzing several genetic loci, including Hardy-Weinberg equilibrium, genetic drift, and Fst genetic-distance calculations, as well as analyzing eight loci profiles simultaneously for forensic purposes. By analyzing several loci, students can determine more precisely the relatedness of populations as well as develop a greater appreciation for the use of DNA markers in forensic analysis by concurrently assessing the frequencies of genotypes for eight genetic loci.

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Autosomal and X chromosome Alu insertions in Bolivian Aymaras and Quechuas: Two languages and one genetic pool

Gayà-Vidal

Dugoujon

Esteban

et al. 2009

American J Hum Biol

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Thirty-two polymorphic Alu insertions (18 autosomal and 14 from the X chromosome) were studied in 192 individuals from two Amerindian populations of the Bolivian Altiplano (Aymara and Quechua speakers: the two main Andean linguistic groups), to provide relevant information about their genetic relationships and demographic processes. The main objective was to determine from genetic data whether the expansion of the Quechua language into Bolivia could be associated with demographic (Inca migration of Quechua-speakers from Peru into Bolivia) or cultural (language imposition by the Inca Empire) processes. Allele frequencies were used to assess the genetic relationships between these two linguistic groups. Our results indicated that the two Bolivian samples showed a high genetic similarity for both sets of markers and were clearly differentiated from the two Peruvian Quechua samples available in the literature. Additionally, our data were compared with the available literature to determine the genetic and linguistic structure, and East-West differentiation in South America. The close genetic relationship between the two Bolivian samples and their differentiation from the Quechua-speakers from Peru suggests that the Quechua language expansion in Bolivia took place without any important demographic contribution. Moreover, no clear geographical or linguistic structure was found for the Alu variation among South Amerindians.

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Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity

Cited by 152 publications

References 43 publications

Recombinant SINEs are formed at high frequency during induced retrotransposition in vivo

Recombinant SINEs are formed at high frequency during induced retrotransposition in vivo

Web‐based analysis for student‐generated complex genetic profiles

Autosomal and X chromosome Alu insertions in Bolivian Aymaras and Quechuas: Two languages and one genetic pool

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