The &lt;i&gt;Alu&lt;/i&gt; Yc1 subfamily: sorting the wheat from the chaff

Garber, Randall K.; Hedges, Dale J.; Herke, Scott W.; Hazard, Nicole; Batzer, Mark A.

doi:10.1159/000084986

Cited by 18 publications

(11 citation statements)

References 55 publications

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“…Whether this subfamily is identical by descent or state to its human counterpart is unclear, as AluYc1 differs from the canonical AluY sequence by a single G→A nucleotide substitution. Human AluYc1 insertions exhibit a relatively young (1 to 3 Myr) average age (Garber et al 2004). Our estimates of the chimpanzee AluYc1 family place it between 1.2 and 2.6 Myr old.…”

Section: Subfamily Compositionmentioning

confidence: 67%

Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages

Hedges

Callinan²,

Cordaux³

et al. 2004

Genome Res.

116

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Alu elements are primate-specific members of the SINE (short interspersed element) retroposon family, which comprise ∼10% of the human genome. Here we report the first chromosomal-level comparison examining the Alu retroposition dynamics following the divergence of humans and chimpanzees. We find a twofold increase in Alu insertions in humans in comparison to the common chimpanzee (Pan troglodytes). The genomic diversity (polymorphism for presence or absence of the Alu insertion) associated with these inserts indicates that, analogous to recent nucleotide diversity studies, the level of chimpanzee Alu diversity is ∼1.7 times higher than that of humans. Evolutionarily recent Alu subfamily structure differs markedly between the human and chimpanzee lineages, with the major human subfamilies remaining largely inactive in the chimpanzee lineage. We propose a population-based model to account for the observed fluctuation in Alu retroposition rates across primate taxa.[The sequence data from this study have been submitted to GenBank under accession nos. AY569161-AY569170.]Alu elements are primate-specific members of the SINE (short interspersed element) family of retroposons. They have enjoyed enormous success over the course of primate evolution and, by conservative estimates, comprise some 10% of the human genome (Schmid 1996;Lander et al. 2001). Largely as a result of the human genome project, a wealth of knowledge has been accumulated concerning the underlying biology, retroposition activity, and associated population genetics of Alu repeats (Schmid 1998;Batzer and Deininger 2002). The ubiquitous presence of Alu sequences within primate genomes has been the cumulative result of a "copy and paste" mechanism, in which an RNA polymerase III-generated transcript is reverse-transcribed and integrated into the genome (Burke et al. 1999). In addition to being wholly dependent upon host cellular processes for their transmission through the germline, Alu elements also lack the ability to generate the endonuclease and reverse transcriptase necessary for their own retroposition. Instead, they must appropriate the necessary enzymatic machinery from L1, a member of the LINE (long interspersed element) retroposon family (Jurka 1997;Kajikawa and Okada 2002). As a result of this obligatory relationship with their genomic host and other transposable elements, the Alu family has been characterized as a "parasite's parasite" (Schmid 2003). Despite the family's various designations as "junk," "parasites," and "selfish DNA," researchers have been reluctant to dismiss them as entirely self-serving genomic entities. A number of investigators have suggested a potential role for Alu elements within their host genomes, and recent implications of Alu element involvement in alternative splicing, segmental duplications, and DNA repair serve to further fuel these arguments (Morrish et al. 2002;Bailey et al. 2003;Lev-Maor et al. 2003;Salem et al. 2003a). Whether these observations constitute adaptations, exaptations (i.e., they have been comma...

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Section: Subfamily Compositionmentioning

confidence: 67%

Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages

Hedges

Callinan²,

Cordaux³

et al. 2004

Genome Res.

116

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“…Researchers familiar with Alu SINEs will be aware that distinct subfamilies of Alu exist in each primate lineage Hedges et al 2004;Otieno et al 2004;Garber et al 2005;Ray and Batzer 2005;Ray et al 2005b;Salem et al 2005b;Han et al 2007;Liu et al 2009;Locke et al 2011). Each of the methods described relies on sequence characteristics unique to particular subfamilies of elements.…”

Section: Extensions To Other Organismsmentioning

confidence: 99%

Reading TE leaves: New approaches to the identification of transposable element insertions

Ray¹,

Batzer²

2011

Genome Res.

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Transposable elements (TEs) are a tremendous source of genome instability and genetic variation. Of particular interest to investigators of human biology and human evolution are retrotransposon insertions that are recent and/or polymorphic in the human population. As a consequence, the ability to assay large numbers of polymorphic TEs in a given genome is valuable. Five recent manuscripts each propose methods to scan whole human genomes to identify, map, and, in some cases, genotype polymorphic retrotransposon insertions in multiple human genomes simultaneously. These technologies promise to revolutionize our ability to analyze human genomes for TE-based variation important to studies of human variability and human disease. Furthermore, the approaches hold promise for researchers interested in nonhuman genomic variability. Herein, we explore the methods reported in the manuscripts and discuss their applications to aspects of human biology and the biology of other organisms.

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“…The remaining 46 CHGS polymorphic elements were likely from the public human BAC sequences that may have not been used for the assembly of PHGS. To determine how many of the 800 polymorphic Alu elements had been previously identified and published, we compiled a database containing 1051 non-redundant polymorphic Alu insertions (http://falcon.roswellpark.org:9090; Wang et al, in press) from the over 1500 polymorphisms reported in the literature (Batzer et al, 1994Bennett et al, 2004;Callinan et al, 2003;Carroll et al, 2001;Carter et al, 2004;Garber et al, 2005;Mamedov et al, 2005;Otieno et al, 2004;Ray et al, 2005;Roy-Engel et al, 2001;Watkins et al, 2003;Xing et al, 2003). A comparison of the genomic locations of our 800 polymorphic Alu insertions with the list revealed that only 266 of the 800 Alu elements correspond with previously reported Alu repeats, suggesting that the remaining 534 insertions represent newly identified polymorphisms.…”

Section: Identification Of Alu Insertion Polymorphismsmentioning

confidence: 99%

“…The first study using such a strategy identified 106 polymorphic Alu insertions out of 475 Ya5 and Yb8 insertions (Carroll et al, 2001). Subsequently, this method has been extensively used to analyze almost all Y subfamilies including Ya (Otieno et al, 2004), Yb (Carter et al, 2004;Roy-Engel et al, 2001), Yc (Roy-Engel et al, 2001;Garber et al, 2005), Yd (Xing et al, 2003), Yg and Yi (Salem et al, 2003), Ye (Salem et al, 2005b) and multiple Y subfamily members on the X chromosome (Callinan et al, 2003). These studies are responsible for the identification of the majority of the known polymorphic Alu insertions.…”

Section: Introductionmentioning

confidence: 99%

Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms

Wang

Song

Gonder

et al. 2006

Gene

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Alu elements are the most active and predominant type of short interspersed elements (SINEs) in the human genome. Recently inserted polymorphic (for presence/absence) Alu elements contribute to genome diversity among different human populations, and they are useful genetic markers for population genetic studies. The objective of this study is to identify polymorphic Alu insertions through an in silico comparative genomics approach and to analyze their distribution pattern throughout the human genome. By computationally comparing the public and Celera sequence assemblies of the human genome, we identified a total of 800 polymorphic Alu elements. We used polymerase chain reaction-based assays to screen a randomly selected set of 16 of these 800 Alu insertion polymorphisms using a human diversity panel to demonstrate the efficiency of our approach. Based on sequence analysis of the 800 Alu polymorphisms, we report three new Alu subfamilies, Ya3, Ya4b, and Yb11, with Yb11 being the smallest known Alu subfamily. Analysis of retrotransposition activity revealed Yb11, Ya8, Ya5, Yb9, and Yb8 as the most active Alu subfamilies and the maintenance of a very low level of retrotransposition activity or recent gene conversion events involving S subfamilies. The 800 polymorphic Alu insertions are characterized by the presence of target site duplications (TSDs) and longer than average polyA-tail length. Their pre-integration sites largely follow an extended "NT-AARA" motif. Among chromosomes, the density of Alu insertion polymorphisms is positively correlated with the Alu-site availability and is inversely correlated with the densities of older Alu elements and genes.

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The <i>Alu</i> Yc1 subfamily: sorting the wheat from the chaff

Cited by 18 publications

References 55 publications

Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages

Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages

Reading TE leaves: New approaches to the identification of transposable element insertions

Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms

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