Sequence diversity and chromosomal distribution of “young” Alu repeats

Arcot, Santosh S.; Shaikh, Tamim H.; Kim, Joomyeong; Bennett, Lesley; Alegria-Hartman, Michelle; Nelson, David; Deininger, Prescott L.; Batzer, Mark A.

doi:10.1016/0378-1119(95)00317-y

Cited by 42 publications

(28 citation statements)

References 21 publications

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“…Amplification and mobilization is limited to the young Alu subfamily sequences (i.e., Alu-Y, AluYa1, Alu-Yb8, Alu-Ya5, and Alu-Ya8) that have been inserted in the last 1.5 million years (Arcot et al 1995). We therefore analyzed the distribution of Alu pairs in order to explore the relationship between age, orientation, and distance between aligned sequences.…”

Section: Age Of Alus In Pairs Differs With Distancementioning

confidence: 99%

“…Among the reasons are that some regions diverge less readily than others, the full-length Alus have long polyA tails that would contribute to overall sequence identity, and possibly there are greater opportunities for homologous interactions. Also, long Alus tend to be younger and less diverged (Arcot et al 1995;Batzer et al 1996).…”

Section: Direct Alu Repeats and Preferencesmentioning

confidence: 99%

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Biased Distribution of Inverted and Direct Alus in the Human Genome: Implications for Insertion, Exclusion, and Genome Stability

Stenger

Lobachev²,

Gordenin³

et al. 2001

Genome Res.

117

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Alu sequences, the most abundant class of large dispersed DNA repeats in human chromosomes, contribute to human genome dynamics. Recently we reported that long inverted repeats, including human Alus, can be strong initiators of genetic change in yeast. We proposed that the potential for interactions between adjacent, closely related Alus would influence their stability and this would be reflected in their distribution. We have undertaken an extensive computational analysis of all Alus (the database is at http://dir.niehs.nih.gov/ALU) to better understand their distribution and circumstances under which Alu sequences might affect genome stability. Alus separated by <650 bp were categorized according to orientation, length of regions sharing high sequence identity, distance between highly identical regions, and extent of sequence identity. Nearly 50% of all Alu pairs have long alignable regions (>275 bp), corresponding to nearly full-length Alus, regardless of orientation. There are dramatic differences in the distributions and character of Alu pairs with closely spaced, nearly identical regions. For Alu pairs that are directly repetitive, ∼30% have highly identical regions separated by <20 bp, but only when the alignments correspond to near full-size or half-size Alus. The opposite is found for the distribution of inverted repeats: Alu pairs with aligned regions separated by <20 bp are rare. Furthermore, closely spaced direct and inverted Alus differ in their truncation patterns, suggesting differences in the mechanisms of insertion. At larger distances, the direct and inverted Alu pairs have similar distributions. We propose that sequence identity, orientation, and distance are important factors determining insertion of adjacent Alus, the frequency and spectrum of Alu-associated changes in the genome, and the contribution of Alu pairs to genome instability. Based on results in model systems and the present analysis, closely spaced inverted Alu pairs with long regions of alignment are likely at-risk motifs (ARMs) for genome instability.

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Section: Age Of Alus In Pairs Differs With Distancementioning

confidence: 99%

Section: Direct Alu Repeats and Preferencesmentioning

confidence: 99%

Biased Distribution of Inverted and Direct Alus in the Human Genome: Implications for Insertion, Exclusion, and Genome Stability

Stenger

Lobachev²,

Gordenin³

et al. 2001

Genome Res.

117

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“…The clones that did not sequence well probably contained random mutations in the regions where the subfamily-specific sequencing primers anneal. The flanking se-ALU FOSSIL RELICS quences were verified by comparing the sequences of the direct repeats of each Alu element, because the majority of young Alu elements are flanked by perfect direct repeats as compared with older Alu elements in which the flanking direct repeats have been subjected to random mutations after the genomic integration of these elements (Batzer et al 1990;Matera et al 1990a;Arcot et al 1995b).…”

Section: Dna Sequence Analysismentioning

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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“…To extract DNA we used the Chelex ® solution protocol as described by Walsh et al (1991). Each DNA sample was amplified by polymerase chain reaction (PCR) using locus-specific primers as described in Arcot et al (1995). PCR reactions were carried out in a total volume of 25 μl, with a final concentration of 1× Reaction Buffer, 2.5 mM MgCl 2 , 5% DMSO, 0.25 mM dNTPs and 50 pmol of each primer, according to the conditions reported in literature (Arcot et al, 1995).…”

Section: Laboratory Analysesmentioning

confidence: 99%

“…Each DNA sample was amplified by polymerase chain reaction (PCR) using locus-specific primers as described in Arcot et al (1995). PCR reactions were carried out in a total volume of 25 μl, with a final concentration of 1× Reaction Buffer, 2.5 mM MgCl 2 , 5% DMSO, 0.25 mM dNTPs and 50 pmol of each primer, according to the conditions reported in literature (Arcot et al, 1995). Amplified PCR products were run on 2.5% agarose gel, stained with ethidium bromide, and visualized under UV light.…”

Section: Laboratory Analysesmentioning

confidence: 99%

<i>Alu</i> insertion polymorphisms in four ethnic groups from northern Ivory Coast

Santovito

Cervella

Delpero

2014

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Patterns of genetic variation among geographically and ethnically diverse African populations have been under-represented in human genetics studies despite their importance for describing the evolutionary history of modern human populations. We conducted a study on 133 individuals, belonging to four northern Ivorian ethnic groups, based on the allele distribution of 11 Alu insertion loci, and compared the results with other African populations. All loci proved to be polymorphic in all ethnic groups, with the exception of HS2.43 and HS3.23, which were fixed for the absence and for the presence, respectively, of the Alu element. No significant departure from Hardy-Weinberg equilibrium was found among polymorphic loci, except for TPA25 loci in the Baoulé and Bété groups. Average heterozygosity (0.193 ± 0.042) was lower than that observed for the same loci in other African populations and the F ST value among ethnic groups for all loci was also notably low (0.0456). Multidimensional scaling analysis clearly separated Ivorians from other African samples, while in the neighbor-joining tree this population represented a basal branch of the tree, close to the hypothetical ancestral lineage. The picture emerging from our analyses reveals a conspicuous genetic homogeneity among Dioulà, Sénoufos, Boulè, and Bètè despite their sociocultural subdivision. Moreover, this northern Ivory Coast population, as a whole, turns out to be relatively isolated from the other African populations, possibly as a consequence of local patterns of population history, limited migration rates, and random genetic drift.

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Sequence diversity and chromosomal distribution of “young” Alu repeats

Cited by 42 publications

References 21 publications

Biased Distribution of Inverted and Direct Alus in the Human Genome: Implications for Insertion, Exclusion, and Genome Stability

Biased Distribution of Inverted and Direct Alus in the Human Genome: Implications for Insertion, Exclusion, and Genome Stability

Alu fossil relics--distribution and insertion polymorphism.

<i>Alu</i> insertion polymorphisms in four ethnic groups from northern Ivory Coast

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